Starting phenix.real_space_refine on Tue Feb 20 21:04:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/02_2024/7sbb_24976.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/02_2024/7sbb_24976.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/02_2024/7sbb_24976.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/02_2024/7sbb_24976.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/02_2024/7sbb_24976.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbb_24976/02_2024/7sbb_24976.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 113 5.16 5 C 18016 2.51 5 N 4970 2.21 5 O 5764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 66": "NH1" <-> "NH2" Residue "A ARG 73": "NH1" <-> "NH2" Residue "A GLU 78": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 66": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 190": "OE1" <-> "OE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "E ARG 66": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F ARG 73": "NH1" <-> "NH2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ARG 185": "NH1" <-> "NH2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F GLU 288": "OE1" <-> "OE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G GLU 97": "OE1" <-> "OE2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 152": "OE1" <-> "OE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G ARG 185": "NH1" <-> "NH2" Residue "G GLU 209": "OE1" <-> "OE2" Residue "G ARG 211": "NH1" <-> "NH2" Residue "G ARG 272": "NH1" <-> "NH2" Residue "H ARG 20": "NH1" <-> "NH2" Residue "H GLU 21": "OE1" <-> "OE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 195": "OE1" <-> "OE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I ARG 496": "NH1" <-> "NH2" Residue "I GLU 513": "OE1" <-> "OE2" Residue "I GLU 515": "OE1" <-> "OE2" Residue "I GLU 613": "OE1" <-> "OE2" Residue "I ARG 616": "NH1" <-> "NH2" Residue "I ARG 631": "NH1" <-> "NH2" Residue "I GLU 667": "OE1" <-> "OE2" Residue "I ARG 680": "NH1" <-> "NH2" Residue "I ARG 710": "NH1" <-> "NH2" Residue "I ARG 717": "NH1" <-> "NH2" Residue "I ARG 774": "NH1" <-> "NH2" Residue "I ARG 801": "NH1" <-> "NH2" Residue "I GLU 803": "OE1" <-> "OE2" Residue "I ARG 805": "NH1" <-> "NH2" Residue "I ARG 807": "NH1" <-> "NH2" Residue "I GLU 870": "OE1" <-> "OE2" Residue "I GLU 882": "OE1" <-> "OE2" Residue "I GLU 883": "OE1" <-> "OE2" Residue "I ARG 898": "NH1" <-> "NH2" Residue "I GLU 900": "OE1" <-> "OE2" Residue "I GLU 921": "OE1" <-> "OE2" Residue "I GLU 939": "OE1" <-> "OE2" Residue "I ARG 952": "NH1" <-> "NH2" Residue "I GLU 960": "OE1" <-> "OE2" Residue "I GLU 969": "OE1" <-> "OE2" Residue "J GLU 53": "OE1" <-> "OE2" Residue "J GLU 86": "OE1" <-> "OE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "J GLU 131": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K ARG 123": "NH1" <-> "NH2" Residue "K GLU 140": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28938 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "B" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "C" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "E" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "F" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "G" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2503 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 10, 'TRANS': 309} Chain: "H" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 209} Chain breaks: 1 Chain: "I" Number of atoms: 5593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5593 Classifications: {'peptide': 680} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 28, 'TRANS': 651} Chain breaks: 6 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "K" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1194 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "X" Number of atoms: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 713 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 18, 'rna3p_pyr': 10} Link IDs: {'rna2p': 5, 'rna3p': 27} Chain: "Z" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 904 Classifications: {'RNA': 43} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 9, 'rna3p_pyr': 14} Link IDs: {'rna2p': 20, 'rna3p': 22} Time building chain proxies: 15.52, per 1000 atoms: 0.54 Number of scatterers: 28938 At special positions: 0 Unit cell: (114.95, 123.31, 229.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 113 16.00 P 75 15.00 O 5764 8.00 N 4970 7.00 C 18016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.42 Conformation dependent library (CDL) restraints added in 4.8 seconds 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6424 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 34 sheets defined 46.5% alpha, 15.9% beta 15 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 10.17 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 64 through 83 Proline residue: A 71 - end of helix removed outlier: 3.724A pdb=" N LEU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 231 through 244 Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.656A pdb=" N THR A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.538A pdb=" N ILE A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 317 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 231 through 244 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.515A pdb=" N THR B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 294 removed outlier: 3.732A pdb=" N GLN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 317 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'C' and resid 7 through 9 No H-bonds generated for 'chain 'C' and resid 7 through 9' Processing helix chain 'C' and resid 64 through 68 removed outlier: 3.887A pdb=" N GLN C 68 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.891A pdb=" N ASP C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 Processing helix chain 'C' and resid 295 through 317 removed outlier: 3.516A pdb=" N GLY C 304 " --> pdb=" O THR C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 7 through 9 No H-bonds generated for 'chain 'D' and resid 7 through 9' Processing helix chain 'D' and resid 64 through 68 removed outlier: 3.976A pdb=" N GLN D 68 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 83 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 137 through 140 Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 231 through 243 Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.578A pdb=" N ASN D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 295 Processing helix chain 'D' and resid 295 through 317 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 64 through 83 removed outlier: 3.926A pdb=" N GLN E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Proline residue: E 71 - end of helix removed outlier: 3.651A pdb=" N ALA E 75 " --> pdb=" O PRO E 71 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 76 " --> pdb=" O GLU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 231 through 244 Processing helix chain 'E' and resid 250 through 267 Processing helix chain 'E' and resid 279 through 294 removed outlier: 3.771A pdb=" N GLN E 287 " --> pdb=" O ASP E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 317 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 7 through 9 No H-bonds generated for 'chain 'F' and resid 7 through 9' Processing helix chain 'F' and resid 69 through 83 Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 137 through 140 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 231 through 242 Processing helix chain 'F' and resid 250 through 267 Processing helix chain 'F' and resid 279 through 290 removed outlier: 3.938A pdb=" N THR F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 317 removed outlier: 3.599A pdb=" N LEU F 299 " --> pdb=" O ASN F 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.514A pdb=" N LYS G 6 " --> pdb=" O LEU G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 7 through 9 No H-bonds generated for 'chain 'G' and resid 7 through 9' Processing helix chain 'G' and resid 69 through 83 removed outlier: 3.602A pdb=" N LEU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.631A pdb=" N THR G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 231 through 244 removed outlier: 3.935A pdb=" N THR G 236 " --> pdb=" O ASN G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 266 removed outlier: 3.518A pdb=" N LEU G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA G 259 " --> pdb=" O CYS G 255 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 260 " --> pdb=" O GLU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 293 removed outlier: 3.940A pdb=" N THR G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 288 " --> pdb=" O THR G 284 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 317 removed outlier: 4.513A pdb=" N LYS G 301 " --> pdb=" O ALA G 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 43 Processing helix chain 'H' and resid 54 through 59 removed outlier: 4.068A pdb=" N ASN H 57 " --> pdb=" O VAL H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 79 removed outlier: 3.617A pdb=" N ASN H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.182A pdb=" N ARG I 11 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU I 13 " --> pdb=" O LEU I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 27 through 36 removed outlier: 4.258A pdb=" N ALA I 31 " --> pdb=" O THR I 27 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLU I 34 " --> pdb=" O PRO I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 96 removed outlier: 3.632A pdb=" N GLU I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.748A pdb=" N ARG I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU I 107 " --> pdb=" O ILE I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 148 removed outlier: 3.715A pdb=" N ASN I 139 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ILE I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG I 147 " --> pdb=" O GLU I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 154 removed outlier: 3.649A pdb=" N PHE I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 159 removed outlier: 4.030A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 removed outlier: 3.525A pdb=" N ALA I 168 " --> pdb=" O ILE I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 213 removed outlier: 4.021A pdb=" N ASP I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 201 - end of helix removed outlier: 3.569A pdb=" N HIS I 204 " --> pdb=" O HIS I 200 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY I 209 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP I 210 " --> pdb=" O LEU I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 222 removed outlier: 3.804A pdb=" N LEU I 221 " --> pdb=" O PRO I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 238 removed outlier: 6.364A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 269 removed outlier: 3.712A pdb=" N ASN I 257 " --> pdb=" O GLY I 253 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 316 removed outlier: 3.877A pdb=" N GLN I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 497 removed outlier: 3.807A pdb=" N ASP I 492 " --> pdb=" O GLN I 488 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 518 removed outlier: 3.705A pdb=" N ILE I 511 " --> pdb=" O HIS I 507 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN I 512 " --> pdb=" O GLN I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 571 through 584 Processing helix chain 'I' and resid 590 through 595 Processing helix chain 'I' and resid 608 through 620 removed outlier: 3.638A pdb=" N GLU I 613 " --> pdb=" O PRO I 609 " (cutoff:3.500A) Processing helix chain 'I' and resid 626 through 636 removed outlier: 3.569A pdb=" N VAL I 630 " --> pdb=" O ASN I 626 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS I 632 " --> pdb=" O TRP I 628 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP I 634 " --> pdb=" O VAL I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 647 removed outlier: 3.568A pdb=" N LEU I 647 " --> pdb=" O LEU I 644 " (cutoff:3.500A) Processing helix chain 'I' and resid 683 through 703 removed outlier: 4.815A pdb=" N LYS I 690 " --> pdb=" O ASP I 686 " (cutoff:3.500A) Proline residue: I 691 - end of helix Proline residue: I 699 - end of helix Processing helix chain 'I' and resid 720 through 724 removed outlier: 3.924A pdb=" N GLU I 724 " --> pdb=" O ASP I 721 " (cutoff:3.500A) Processing helix chain 'I' and resid 732 through 739 removed outlier: 4.249A pdb=" N SER I 736 " --> pdb=" O ALA I 732 " (cutoff:3.500A) Processing helix chain 'I' and resid 745 through 747 No H-bonds generated for 'chain 'I' and resid 745 through 747' Processing helix chain 'I' and resid 748 through 764 Processing helix chain 'I' and resid 774 through 776 No H-bonds generated for 'chain 'I' and resid 774 through 776' Processing helix chain 'I' and resid 777 through 788 Processing helix chain 'I' and resid 790 through 803 Processing helix chain 'I' and resid 809 through 824 removed outlier: 3.942A pdb=" N THR I 814 " --> pdb=" O GLU I 810 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TRP I 817 " --> pdb=" O VAL I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 827 through 845 removed outlier: 3.643A pdb=" N VAL I 841 " --> pdb=" O THR I 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 851 through 855 Processing helix chain 'I' and resid 857 through 862 Processing helix chain 'I' and resid 862 through 875 Processing helix chain 'I' and resid 880 through 897 removed outlier: 4.368A pdb=" N LEU I 886 " --> pdb=" O GLU I 882 " (cutoff:3.500A) Processing helix chain 'I' and resid 898 through 899 No H-bonds generated for 'chain 'I' and resid 898 through 899' Processing helix chain 'I' and resid 900 through 903 Processing helix chain 'I' and resid 904 through 909 removed outlier: 4.318A pdb=" N ASP I 909 " --> pdb=" O PRO I 905 " (cutoff:3.500A) Processing helix chain 'I' and resid 913 through 935 Processing helix chain 'I' and resid 944 through 974 removed outlier: 5.007A pdb=" N ASN I 953 " --> pdb=" O GLN I 949 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG I 954 " --> pdb=" O GLU I 950 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 removed outlier: 4.443A pdb=" N LYS J 4 " --> pdb=" O MET J 1 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 17 removed outlier: 3.648A pdb=" N TYR J 15 " --> pdb=" O LEU J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 Processing helix chain 'J' and resid 28 through 33 Processing helix chain 'J' and resid 33 through 46 Processing helix chain 'J' and resid 51 through 68 removed outlier: 3.907A pdb=" N LEU J 55 " --> pdb=" O ASP J 51 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 56 " --> pdb=" O GLU J 52 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU J 57 " --> pdb=" O GLU J 53 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA J 66 " --> pdb=" O GLN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 84 through 105 Processing helix chain 'J' and resid 115 through 122 removed outlier: 3.504A pdb=" N GLN J 122 " --> pdb=" O ILE J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 145 removed outlier: 3.704A pdb=" N GLN J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 17 removed outlier: 5.257A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL K 12 " --> pdb=" O THR K 8 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 26 Processing helix chain 'K' and resid 28 through 33 Processing helix chain 'K' and resid 33 through 45 Processing helix chain 'K' and resid 51 through 68 Processing helix chain 'K' and resid 71 through 74 Processing helix chain 'K' and resid 75 through 80 Processing helix chain 'K' and resid 84 through 106 Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 122 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.243A pdb=" N LEU A 27 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 219 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N HIS A 29 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 217 " --> pdb=" O HIS A 29 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN A 31 " --> pdb=" O MET A 215 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET A 215 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU A 275 " --> pdb=" O PHE A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 removed outlier: 3.665A pdb=" N THR A 38 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.011A pdb=" N GLY A 121 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 142 through 148 Processing sheet with id=AA6, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 128 removed outlier: 6.915A pdb=" N TYR B 21 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N PHE B 224 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS B 23 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 222 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU B 25 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR B 214 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 275 " --> pdb=" O PHE B 224 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.837A pdb=" N THR B 38 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 48 Processing sheet with id=AB1, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 148 Processing sheet with id=AB3, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.939A pdb=" N TYR C 21 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 224 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS C 23 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE C 222 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 25 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 214 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU C 275 " --> pdb=" O PHE C 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 37 through 38 removed outlier: 3.818A pdb=" N THR C 38 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 44 through 48 Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 148 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.937A pdb=" N TYR D 21 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE D 224 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS D 23 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE D 222 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 25 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 275 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 44 through 48 Processing sheet with id=AB9, first strand: chain 'D' and resid 142 through 148 Processing sheet with id=AC1, first strand: chain 'E' and resid 127 through 128 removed outlier: 6.489A pdb=" N LEU E 27 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU E 219 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N HIS E 29 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ASN E 217 " --> pdb=" O HIS E 29 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 44 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 142 through 148 Processing sheet with id=AC4, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.492A pdb=" N LEU F 27 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N LEU F 219 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N HIS F 29 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ASN F 217 " --> pdb=" O HIS F 29 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 275 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 44 through 48 Processing sheet with id=AC6, first strand: chain 'F' and resid 142 through 147 removed outlier: 4.456A pdb=" N ASN F 167 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 127 through 129 removed outlier: 6.534A pdb=" N LEU G 27 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LEU G 219 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N HIS G 29 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN G 217 " --> pdb=" O HIS G 29 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU G 275 " --> pdb=" O PHE G 224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 44 through 47 removed outlier: 6.549A pdb=" N SER G 59 " --> pdb=" O GLY G 136 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY G 136 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU G 61 " --> pdb=" O SER G 134 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 142 through 146 Processing sheet with id=AD1, first strand: chain 'H' and resid 80 through 82 removed outlier: 6.656A pdb=" N GLU H 135 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AD3, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AD4, first strand: chain 'H' and resid 174 through 182 removed outlier: 5.566A pdb=" N PHE H 211 " --> pdb=" O VAL H 203 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL H 203 " --> pdb=" O PHE H 211 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 213 " --> pdb=" O ASN H 201 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN H 217 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ILE H 197 " --> pdb=" O GLN H 217 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ASP H 219 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN H 195 " --> pdb=" O ASP H 219 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 174 through 182 removed outlier: 5.976A pdb=" N GLN H 222 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU H 229 " --> pdb=" O GLN H 222 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP H 224 " --> pdb=" O THR H 227 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 273 through 278 removed outlier: 6.863A pdb=" N ILE I 283 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE I 277 " --> pdb=" O GLY I 281 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLY I 281 " --> pdb=" O PHE I 277 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 673 through 677 removed outlier: 3.744A pdb=" N ALA I 673 " --> pdb=" O LEU I 601 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE I 597 " --> pdb=" O THR I 677 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 70 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 10.76 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 4705 1.28 - 1.42: 8082 1.42 - 1.55: 16491 1.55 - 1.69: 202 1.69 - 1.82: 180 Bond restraints: 29660 Sorted by residual: bond pdb=" C TYR E 313 " pdb=" O TYR E 313 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.17e-02 7.31e+03 6.39e+01 bond pdb=" C TYR F 313 " pdb=" O TYR F 313 " ideal model delta sigma weight residual 1.236 1.146 0.091 1.15e-02 7.56e+03 6.21e+01 bond pdb=" C TYR D 313 " pdb=" O TYR D 313 " ideal model delta sigma weight residual 1.237 1.145 0.091 1.16e-02 7.43e+03 6.21e+01 bond pdb=" C TYR C 313 " pdb=" O TYR C 313 " ideal model delta sigma weight residual 1.237 1.150 0.087 1.17e-02 7.31e+03 5.49e+01 bond pdb=" CA ASN H 71 " pdb=" C ASN H 71 " ideal model delta sigma weight residual 1.522 1.435 0.087 1.21e-02 6.83e+03 5.12e+01 ... (remaining 29655 not shown) Histogram of bond angle deviations from ideal: 91.34 - 100.17: 63 100.17 - 109.00: 4425 109.00 - 117.83: 16667 117.83 - 126.65: 18688 126.65 - 135.48: 624 Bond angle restraints: 40467 Sorted by residual: angle pdb=" N PHE I 285 " pdb=" CA PHE I 285 " pdb=" C PHE I 285 " ideal model delta sigma weight residual 110.32 91.34 18.98 1.59e+00 3.96e-01 1.42e+02 angle pdb=" CA ASP F 130 " pdb=" CB ASP F 130 " pdb=" CG ASP F 130 " ideal model delta sigma weight residual 112.60 122.48 -9.88 1.00e+00 1.00e+00 9.77e+01 angle pdb=" N GLY G 114 " pdb=" CA GLY G 114 " pdb=" C GLY G 114 " ideal model delta sigma weight residual 112.29 123.12 -10.83 1.12e+00 7.97e-01 9.36e+01 angle pdb=" CA ASP I 640 " pdb=" CB ASP I 640 " pdb=" CG ASP I 640 " ideal model delta sigma weight residual 112.60 122.23 -9.63 1.00e+00 1.00e+00 9.26e+01 angle pdb=" CA ASP A 130 " pdb=" CB ASP A 130 " pdb=" CG ASP A 130 " ideal model delta sigma weight residual 112.60 121.67 -9.07 1.00e+00 1.00e+00 8.22e+01 ... (remaining 40462 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 17274 35.55 - 71.11: 573 71.11 - 106.66: 95 106.66 - 142.22: 6 142.22 - 177.77: 3 Dihedral angle restraints: 17951 sinusoidal: 7972 harmonic: 9979 Sorted by residual: dihedral pdb=" O4' U Z 3 " pdb=" C1' U Z 3 " pdb=" N1 U Z 3 " pdb=" C2 U Z 3 " ideal model delta sinusoidal sigma weight residual -160.00 -0.90 -159.10 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U Z 34 " pdb=" C1' U Z 34 " pdb=" N1 U Z 34 " pdb=" C2 U Z 34 " ideal model delta sinusoidal sigma weight residual 200.00 62.15 137.85 1 1.50e+01 4.44e-03 7.43e+01 dihedral pdb=" O4' U Z 35 " pdb=" C1' U Z 35 " pdb=" N1 U Z 35 " pdb=" C2 U Z 35 " ideal model delta sinusoidal sigma weight residual 200.00 73.45 126.55 1 1.50e+01 4.44e-03 6.81e+01 ... (remaining 17948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 3643 0.157 - 0.313: 765 0.313 - 0.470: 117 0.470 - 0.627: 29 0.627 - 0.784: 11 Chirality restraints: 4565 Sorted by residual: chirality pdb=" CA GLU A 228 " pdb=" N GLU A 228 " pdb=" C GLU A 228 " pdb=" CB GLU A 228 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.54e+01 chirality pdb=" CA GLU A 288 " pdb=" N GLU A 288 " pdb=" C GLU A 288 " pdb=" CB GLU A 288 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CA GLU I 812 " pdb=" N GLU I 812 " pdb=" C GLU I 812 " pdb=" CB GLU I 812 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 4562 not shown) Planarity restraints: 4974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G Z 25 " -0.025 2.00e-02 2.50e+03 1.16e-01 4.01e+02 pdb=" N9 G Z 25 " -0.067 2.00e-02 2.50e+03 pdb=" C8 G Z 25 " 0.150 2.00e-02 2.50e+03 pdb=" N7 G Z 25 " 0.149 2.00e-02 2.50e+03 pdb=" C5 G Z 25 " -0.019 2.00e-02 2.50e+03 pdb=" C6 G Z 25 " -0.052 2.00e-02 2.50e+03 pdb=" O6 G Z 25 " -0.067 2.00e-02 2.50e+03 pdb=" N1 G Z 25 " -0.017 2.00e-02 2.50e+03 pdb=" C2 G Z 25 " -0.055 2.00e-02 2.50e+03 pdb=" N2 G Z 25 " 0.258 2.00e-02 2.50e+03 pdb=" N3 G Z 25 " -0.147 2.00e-02 2.50e+03 pdb=" C4 G Z 25 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U Z 34 " -0.263 2.00e-02 2.50e+03 1.28e-01 3.70e+02 pdb=" N1 U Z 34 " 0.058 2.00e-02 2.50e+03 pdb=" C2 U Z 34 " 0.047 2.00e-02 2.50e+03 pdb=" O2 U Z 34 " 0.102 2.00e-02 2.50e+03 pdb=" N3 U Z 34 " 0.004 2.00e-02 2.50e+03 pdb=" C4 U Z 34 " -0.015 2.00e-02 2.50e+03 pdb=" O4 U Z 34 " -0.179 2.00e-02 2.50e+03 pdb=" C5 U Z 34 " 0.114 2.00e-02 2.50e+03 pdb=" C6 U Z 34 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP I 584 " 0.189 2.00e-02 2.50e+03 1.18e-01 3.46e+02 pdb=" CG TRP I 584 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP I 584 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP I 584 " -0.074 2.00e-02 2.50e+03 pdb=" NE1 TRP I 584 " -0.115 2.00e-02 2.50e+03 pdb=" CE2 TRP I 584 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP I 584 " -0.166 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 584 " 0.143 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 584 " -0.090 2.00e-02 2.50e+03 pdb=" CH2 TRP I 584 " 0.153 2.00e-02 2.50e+03 ... (remaining 4971 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 148 2.60 - 3.18: 23739 3.18 - 3.75: 46863 3.75 - 4.33: 66230 4.33 - 4.90: 107426 Nonbonded interactions: 244406 Sorted by model distance: nonbonded pdb=" CB SER E 144 " pdb=" OD1 ASP E 170 " model vdw 2.030 3.440 nonbonded pdb=" CG MET D 162 " pdb=" O2' A X 10 " model vdw 2.161 3.440 nonbonded pdb=" NE2 GLN G 8 " pdb=" OE1 GLU G 275 " model vdw 2.188 2.520 nonbonded pdb=" O LEU E 302 " pdb=" OG SER E 305 " model vdw 2.213 2.440 nonbonded pdb=" N PHE I 285 " pdb=" O PHE I 285 " model vdw 2.226 2.496 ... (remaining 244401 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'J' selection = chain 'K' } 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: 3.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.090 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 82.350 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 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 : 0.013 0.094 29660 Z= 0.844 Angle : 2.086 18.976 40467 Z= 1.376 Chirality : 0.139 0.784 4565 Planarity : 0.021 0.251 4974 Dihedral : 18.010 177.772 11527 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.65 % Favored : 95.20 % Rotamer: Outliers : 3.53 % Allowed : 7.88 % Favored : 88.59 % Cbeta Deviations : 3.02 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.13), residues: 3399 helix: -1.94 (0.11), residues: 1445 sheet: -0.42 (0.23), residues: 377 loop : -0.94 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.189 0.031 TRP I 584 HIS 0.027 0.005 HIS E 171 PHE 0.084 0.013 PHE H 17 TYR 0.218 0.023 TYR I 497 ARG 0.020 0.002 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1148 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8227 (m110) cc_final: 0.7489 (m110) REVERT: A 48 GLN cc_start: 0.8016 (tt0) cc_final: 0.7499 (tt0) REVERT: A 60 ARG cc_start: 0.8630 (ptp-110) cc_final: 0.8302 (ptp90) REVERT: A 65 LYS cc_start: 0.8280 (ttpp) cc_final: 0.7905 (ttpp) REVERT: A 78 GLU cc_start: 0.7413 (tt0) cc_final: 0.7057 (tt0) REVERT: A 94 ASN cc_start: 0.8243 (p0) cc_final: 0.8019 (p0) REVERT: A 113 TYR cc_start: 0.8569 (m-80) cc_final: 0.8145 (m-80) REVERT: A 128 TYR cc_start: 0.7706 (m-10) cc_final: 0.7369 (m-10) REVERT: A 156 MET cc_start: 0.7853 (mmt) cc_final: 0.7568 (mmm) REVERT: A 170 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6815 (p0) REVERT: A 185 ARG cc_start: 0.8508 (mtp180) cc_final: 0.7888 (ttm170) REVERT: A 186 ASP cc_start: 0.7176 (m-30) cc_final: 0.6921 (m-30) REVERT: A 190 GLU cc_start: 0.7511 (mp0) cc_final: 0.6891 (mp0) REVERT: A 216 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7961 (ttpp) REVERT: A 253 GLU cc_start: 0.7104 (tp30) cc_final: 0.6829 (tp30) REVERT: A 254 LEU cc_start: 0.8633 (tp) cc_final: 0.8242 (tp) REVERT: A 313 TYR cc_start: 0.8805 (t80) cc_final: 0.8447 (t80) REVERT: B 1 MET cc_start: 0.8090 (mmm) cc_final: 0.7838 (mmt) REVERT: B 18 SER cc_start: 0.8597 (OUTLIER) cc_final: 0.8316 (p) REVERT: B 78 GLU cc_start: 0.7176 (tt0) cc_final: 0.6922 (tt0) REVERT: B 82 ASN cc_start: 0.8017 (t0) cc_final: 0.7794 (t0) REVERT: B 123 GLU cc_start: 0.7482 (tp30) cc_final: 0.7212 (tp30) REVERT: B 130 ASP cc_start: 0.7139 (t0) cc_final: 0.6934 (t0) REVERT: B 148 ASN cc_start: 0.7519 (m-40) cc_final: 0.7299 (m110) REVERT: B 151 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (t80) REVERT: B 176 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7966 (p) REVERT: B 190 GLU cc_start: 0.7759 (mp0) cc_final: 0.7224 (mp0) REVERT: B 198 ASN cc_start: 0.8430 (m-40) cc_final: 0.8110 (m-40) REVERT: B 212 THR cc_start: 0.8261 (m) cc_final: 0.7998 (t) REVERT: B 226 ASP cc_start: 0.6857 (p0) cc_final: 0.6375 (p0) REVERT: B 228 GLU cc_start: 0.7037 (pm20) cc_final: 0.6793 (pm20) REVERT: B 256 GLU cc_start: 0.7524 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 271 VAL cc_start: 0.8605 (m) cc_final: 0.7815 (t) REVERT: B 272 ARG cc_start: 0.8263 (mtm180) cc_final: 0.7763 (mtm180) REVERT: B 287 GLN cc_start: 0.7864 (tp-100) cc_final: 0.7560 (tp-100) REVERT: B 290 ASN cc_start: 0.8060 (m-40) cc_final: 0.7854 (m-40) REVERT: B 303 LEU cc_start: 0.8822 (mt) cc_final: 0.8615 (mp) REVERT: B 311 GLN cc_start: 0.8334 (tt0) cc_final: 0.8096 (tt0) REVERT: C 5 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8034 (mt) REVERT: C 18 SER cc_start: 0.8141 (m) cc_final: 0.7939 (p) REVERT: C 53 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6288 (pt0) REVERT: C 97 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7040 (mm-30) REVERT: C 140 GLN cc_start: 0.7656 (pm20) cc_final: 0.7375 (mp10) REVERT: C 190 GLU cc_start: 0.7529 (mp0) cc_final: 0.6777 (mp0) REVERT: C 241 ASP cc_start: 0.7490 (t0) cc_final: 0.7220 (t0) REVERT: C 264 ASP cc_start: 0.6948 (t70) cc_final: 0.6726 (t0) REVERT: C 268 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8151 (mtmm) REVERT: C 271 VAL cc_start: 0.8769 (t) cc_final: 0.8536 (m) REVERT: C 272 ARG cc_start: 0.7967 (mtm180) cc_final: 0.7493 (mtm180) REVERT: C 275 GLU cc_start: 0.6872 (tt0) cc_final: 0.6366 (tt0) REVERT: C 296 ASP cc_start: 0.7421 (t0) cc_final: 0.7209 (t0) REVERT: C 311 GLN cc_start: 0.8153 (tt0) cc_final: 0.7930 (tt0) REVERT: D 18 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.8085 (p) REVERT: D 43 ASN cc_start: 0.7906 (m110) cc_final: 0.7695 (m-40) REVERT: D 68 GLN cc_start: 0.7557 (pt0) cc_final: 0.6672 (pt0) REVERT: D 82 ASN cc_start: 0.8125 (t0) cc_final: 0.7733 (t0) REVERT: D 90 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7870 (mmtt) REVERT: D 93 LYS cc_start: 0.8047 (tppt) cc_final: 0.7783 (tppt) REVERT: D 101 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6616 (mm-30) REVERT: D 123 GLU cc_start: 0.7426 (tp30) cc_final: 0.7118 (tp30) REVERT: D 126 LYS cc_start: 0.8232 (mttp) cc_final: 0.7812 (mttp) REVERT: D 139 GLU cc_start: 0.7263 (mp0) cc_final: 0.6884 (mp0) REVERT: D 167 ASN cc_start: 0.8248 (t0) cc_final: 0.7976 (t0) REVERT: D 215 MET cc_start: 0.7819 (mtp) cc_final: 0.7499 (mtm) REVERT: D 241 ASP cc_start: 0.8116 (t0) cc_final: 0.7851 (t0) REVERT: D 246 GLU cc_start: 0.6994 (pt0) cc_final: 0.6588 (pt0) REVERT: D 249 LYS cc_start: 0.8164 (mttt) cc_final: 0.7900 (mttt) REVERT: D 253 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6697 (tm-30) REVERT: D 256 GLU cc_start: 0.7200 (tt0) cc_final: 0.6910 (tt0) REVERT: D 269 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7166 (mm-30) REVERT: E 21 TYR cc_start: 0.8109 (m-10) cc_final: 0.7870 (m-80) REVERT: E 31 GLN cc_start: 0.8301 (mm110) cc_final: 0.7875 (mm-40) REVERT: E 48 GLN cc_start: 0.7695 (tt0) cc_final: 0.7403 (tt0) REVERT: E 106 GLN cc_start: 0.8256 (mt0) cc_final: 0.7991 (mt0) REVERT: E 123 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6853 (mm-30) REVERT: E 146 THR cc_start: 0.7948 (p) cc_final: 0.7724 (t) REVERT: E 183 SER cc_start: 0.8009 (t) cc_final: 0.7771 (m) REVERT: E 190 GLU cc_start: 0.7510 (mp0) cc_final: 0.7160 (mp0) REVERT: E 200 LEU cc_start: 0.8477 (mt) cc_final: 0.8251 (mm) REVERT: E 226 ASP cc_start: 0.7019 (t0) cc_final: 0.5709 (t0) REVERT: E 231 SER cc_start: 0.8232 (t) cc_final: 0.7977 (p) REVERT: E 267 ASN cc_start: 0.8274 (m-40) cc_final: 0.8020 (m-40) REVERT: E 269 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6741 (mm-30) REVERT: E 283 ASP cc_start: 0.7562 (p0) cc_final: 0.7292 (p0) REVERT: E 286 LEU cc_start: 0.8443 (mp) cc_final: 0.8241 (mt) REVERT: E 287 GLN cc_start: 0.7542 (tp40) cc_final: 0.7188 (tp40) REVERT: E 288 GLU cc_start: 0.7062 (pt0) cc_final: 0.6804 (pt0) REVERT: E 290 ASN cc_start: 0.7906 (p0) cc_final: 0.7558 (p0) REVERT: E 291 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7206 (p0) REVERT: E 309 GLN cc_start: 0.8446 (mt0) cc_final: 0.7739 (mt0) REVERT: F 48 GLN cc_start: 0.7904 (tt0) cc_final: 0.7660 (tt0) REVERT: F 59 SER cc_start: 0.8484 (m) cc_final: 0.8057 (p) REVERT: F 66 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8059 (mtt90) REVERT: F 72 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: F 126 LYS cc_start: 0.8462 (mttp) cc_final: 0.8195 (mttp) REVERT: F 138 TYR cc_start: 0.8221 (t80) cc_final: 0.7946 (t80) REVERT: F 175 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6562 (mt-10) REVERT: F 180 THR cc_start: 0.7920 (m) cc_final: 0.7533 (p) REVERT: F 226 ASP cc_start: 0.7141 (p0) cc_final: 0.6934 (p0) REVERT: F 232 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7801 (m110) REVERT: F 249 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7754 (mmmt) REVERT: F 253 GLU cc_start: 0.7239 (tm-30) cc_final: 0.7020 (tm-30) REVERT: F 295 ASN cc_start: 0.7640 (m-40) cc_final: 0.7244 (t0) REVERT: F 298 GLU cc_start: 0.7346 (mp0) cc_final: 0.6622 (mp0) REVERT: F 301 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7979 (ttmm) REVERT: G 10 GLN cc_start: 0.7284 (mt0) cc_final: 0.7044 (mt0) REVERT: G 18 SER cc_start: 0.7665 (p) cc_final: 0.7407 (p) REVERT: G 24 PHE cc_start: 0.8152 (m-80) cc_final: 0.7942 (m-80) REVERT: G 25 LEU cc_start: 0.7986 (mp) cc_final: 0.7673 (mp) REVERT: G 77 ARG cc_start: 0.6687 (mtp85) cc_final: 0.5868 (mtp85) REVERT: G 119 ASP cc_start: 0.6797 (t0) cc_final: 0.6537 (t70) REVERT: G 124 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7363 (ttm110) REVERT: G 133 PHE cc_start: 0.7731 (m-80) cc_final: 0.7435 (m-80) REVERT: G 162 MET cc_start: -0.1396 (tpp) cc_final: -0.1651 (tpp) REVERT: G 182 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6608 (mt-10) REVERT: G 194 TYR cc_start: 0.7866 (t80) cc_final: 0.7373 (t80) REVERT: G 216 LYS cc_start: 0.8052 (tppt) cc_final: 0.7641 (tppt) REVERT: G 239 LEU cc_start: 0.8412 (tp) cc_final: 0.7848 (tp) REVERT: G 243 MET cc_start: 0.6935 (mtm) cc_final: 0.6369 (mtm) REVERT: G 251 ILE cc_start: 0.7371 (mm) cc_final: 0.7118 (mm) REVERT: G 288 GLU cc_start: 0.7513 (tp30) cc_final: 0.6955 (tp30) REVERT: H 136 PHE cc_start: 0.8528 (m-80) cc_final: 0.8255 (m-80) REVERT: H 180 TYR cc_start: 0.8473 (p90) cc_final: 0.8257 (p90) REVERT: H 195 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7229 (mm-40) REVERT: H 222 GLN cc_start: 0.7473 (tp40) cc_final: 0.6881 (tp40) REVERT: H 228 PHE cc_start: 0.8557 (m-80) cc_final: 0.7841 (m-80) REVERT: I 36 PHE cc_start: 0.7325 (m-10) cc_final: 0.6978 (m-10) REVERT: I 82 ILE cc_start: 0.9105 (mm) cc_final: 0.8755 (mt) REVERT: I 83 LEU cc_start: 0.8740 (tp) cc_final: 0.8532 (tp) REVERT: I 105 ARG cc_start: 0.7601 (mtt180) cc_final: 0.7393 (mtp85) REVERT: I 205 LEU cc_start: 0.7665 (mp) cc_final: 0.7434 (mm) REVERT: I 211 VAL cc_start: 0.8439 (p) cc_final: 0.7659 (m) REVERT: I 245 TYR cc_start: 0.7966 (p90) cc_final: 0.7692 (p90) REVERT: I 275 LEU cc_start: 0.8472 (tp) cc_final: 0.8214 (tp) REVERT: I 285 PHE cc_start: 0.7430 (m-80) cc_final: 0.7175 (m-80) REVERT: I 291 GLU cc_start: 0.7847 (pm20) cc_final: 0.7456 (pm20) REVERT: I 297 GLU cc_start: 0.7405 (pt0) cc_final: 0.6299 (pt0) REVERT: I 298 ILE cc_start: 0.8885 (mt) cc_final: 0.8431 (tp) REVERT: I 490 PHE cc_start: 0.8505 (t80) cc_final: 0.8289 (t80) REVERT: I 495 ASP cc_start: 0.7579 (m-30) cc_final: 0.7230 (m-30) REVERT: I 507 HIS cc_start: 0.7660 (p-80) cc_final: 0.7406 (p-80) REVERT: I 511 ILE cc_start: 0.8221 (mm) cc_final: 0.7709 (mt) REVERT: I 512 GLN cc_start: 0.7328 (tp40) cc_final: 0.6939 (tt0) REVERT: I 516 ASN cc_start: 0.7466 (m-40) cc_final: 0.7215 (m-40) REVERT: I 574 SER cc_start: 0.8614 (t) cc_final: 0.8041 (p) REVERT: I 612 VAL cc_start: 0.8837 (m) cc_final: 0.8605 (t) REVERT: I 635 VAL cc_start: 0.8866 (p) cc_final: 0.8646 (m) REVERT: I 638 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7995 (mmmt) REVERT: I 663 LYS cc_start: 0.7763 (pttt) cc_final: 0.7394 (pttt) REVERT: I 664 TYR cc_start: 0.7824 (m-80) cc_final: 0.7537 (m-80) REVERT: I 690 LYS cc_start: 0.8455 (mttt) cc_final: 0.8133 (mttt) REVERT: I 707 ILE cc_start: 0.8395 (tt) cc_final: 0.8112 (pt) REVERT: I 740 ILE cc_start: 0.8758 (tp) cc_final: 0.8508 (mt) REVERT: I 746 VAL cc_start: 0.8647 (p) cc_final: 0.8354 (p) REVERT: I 784 GLU cc_start: 0.7071 (pt0) cc_final: 0.6842 (pt0) REVERT: I 818 GLN cc_start: 0.7829 (mt0) cc_final: 0.7366 (mt0) REVERT: I 830 MET cc_start: 0.7031 (mtm) cc_final: 0.6595 (mtm) REVERT: I 832 GLU cc_start: 0.7553 (tp30) cc_final: 0.7344 (tp30) REVERT: I 848 TYR cc_start: 0.8721 (t80) cc_final: 0.8408 (t80) REVERT: I 871 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7668 (tm-30) REVERT: I 901 VAL cc_start: 0.8712 (t) cc_final: 0.8422 (p) REVERT: I 912 VAL cc_start: 0.8886 (t) cc_final: 0.8667 (p) REVERT: I 914 TYR cc_start: 0.7757 (t80) cc_final: 0.7279 (t80) REVERT: I 936 LEU cc_start: 0.8496 (tp) cc_final: 0.8125 (tp) REVERT: I 939 GLU cc_start: 0.7195 (tp30) cc_final: 0.6939 (tp30) REVERT: I 942 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8521 (mmmt) REVERT: I 954 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7510 (ptp90) REVERT: I 960 GLU cc_start: 0.7262 (tt0) cc_final: 0.7017 (tt0) REVERT: J 1 MET cc_start: -0.0989 (mmm) cc_final: -0.1190 (mmm) REVERT: J 53 GLU cc_start: 0.7189 (mp0) cc_final: 0.6689 (mp0) REVERT: J 63 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7568 (tp) REVERT: J 92 GLU cc_start: 0.8046 (tp30) cc_final: 0.7601 (tp30) REVERT: J 94 GLU cc_start: 0.7522 (pt0) cc_final: 0.7255 (pt0) REVERT: J 105 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.6819 (ptp90) REVERT: J 128 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8130 (p) REVERT: K 63 LEU cc_start: 0.8545 (tp) cc_final: 0.8319 (tp) REVERT: K 67 LEU cc_start: 0.7928 (mp) cc_final: 0.7597 (mp) REVERT: K 94 GLU cc_start: 0.7674 (tp30) cc_final: 0.6989 (tp30) REVERT: K 110 GLU cc_start: 0.7147 (tm-30) cc_final: 0.6845 (tm-30) outliers start: 105 outliers final: 28 residues processed: 1197 average time/residue: 0.4771 time to fit residues: 852.7797 Evaluate side-chains 1035 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 990 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 72 GLU Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 171 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 308 GLN Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain G residue 122 SER Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 685 THR Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 802 ARG Chi-restraints excluded: chain I residue 871 GLN Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 954 ARG Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 105 ARG Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 294 optimal weight: 0.8980 chunk 264 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 141 optimal weight: 0.5980 chunk 273 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 166 optimal weight: 0.6980 chunk 203 optimal weight: 0.6980 chunk 316 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 198 ASN A 218 HIS A 295 ASN B 10 GLN B 99 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 242 GLN B 309 GLN C 43 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 ASN C 281 HIS D 31 GLN D 68 GLN D 99 ASN D 208 GLN D 267 ASN D 308 GLN E 8 GLN E 48 GLN E 68 GLN E 82 ASN E 140 GLN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN E 232 ASN E 242 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 ASN F 106 GLN F 198 ASN ** F 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN G 20 HIS H 49 HIS H 70 GLN H 95 ASN H 143 GLN I 81 HIS I 84 ASN I 219 HIS I 235 ASN ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 308 GLN I 488 GLN I 636 ASN I 651 ASN I 754 ASN I 849 GLN ** I 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 891 GLN I 951 GLN J 62 GLN J 146 ASN K 89 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 29660 Z= 0.296 Angle : 0.782 10.520 40467 Z= 0.409 Chirality : 0.049 0.424 4565 Planarity : 0.005 0.086 4974 Dihedral : 16.142 177.586 5018 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 3.77 % Allowed : 13.73 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3399 helix: -0.09 (0.13), residues: 1499 sheet: 0.01 (0.24), residues: 399 loop : -0.91 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 50 HIS 0.013 0.001 HIS I 246 PHE 0.024 0.002 PHE E 151 TYR 0.029 0.002 TYR I 844 ARG 0.008 0.001 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1013 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 TYR cc_start: 0.8554 (m-80) cc_final: 0.8292 (m-80) REVERT: A 43 ASN cc_start: 0.8303 (m110) cc_final: 0.7849 (m-40) REVERT: A 45 THR cc_start: 0.8274 (t) cc_final: 0.8029 (p) REVERT: A 48 GLN cc_start: 0.7932 (tt0) cc_final: 0.7640 (tt0) REVERT: A 57 GLN cc_start: 0.8030 (mm-40) cc_final: 0.7781 (mm-40) REVERT: A 78 GLU cc_start: 0.7472 (tt0) cc_final: 0.7214 (tt0) REVERT: A 156 MET cc_start: 0.7794 (mmt) cc_final: 0.7543 (mmm) REVERT: A 166 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8481 (tp) REVERT: A 168 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6971 (mm-30) REVERT: A 170 ASP cc_start: 0.7216 (OUTLIER) cc_final: 0.6962 (p0) REVERT: A 241 ASP cc_start: 0.7814 (t70) cc_final: 0.7604 (t70) REVERT: A 253 GLU cc_start: 0.7180 (tp30) cc_final: 0.6976 (tp30) REVERT: A 254 LEU cc_start: 0.8417 (tp) cc_final: 0.8202 (tp) REVERT: A 313 TYR cc_start: 0.8598 (t80) cc_final: 0.8320 (t80) REVERT: B 53 GLU cc_start: 0.6787 (tp30) cc_final: 0.6424 (tp30) REVERT: B 87 SER cc_start: 0.8453 (t) cc_final: 0.8138 (t) REVERT: B 148 ASN cc_start: 0.6880 (m-40) cc_final: 0.6612 (m-40) REVERT: B 190 GLU cc_start: 0.7856 (mp0) cc_final: 0.7634 (mp0) REVERT: B 212 THR cc_start: 0.7938 (m) cc_final: 0.7710 (t) REVERT: B 226 ASP cc_start: 0.6683 (p0) cc_final: 0.6168 (p0) REVERT: B 253 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7016 (tm-30) REVERT: B 256 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6984 (tm-30) REVERT: B 287 GLN cc_start: 0.7716 (tp-100) cc_final: 0.7514 (tp40) REVERT: B 308 GLN cc_start: 0.8099 (tp40) cc_final: 0.7281 (tp-100) REVERT: B 312 ASP cc_start: 0.7726 (m-30) cc_final: 0.7114 (m-30) REVERT: C 1 MET cc_start: 0.7888 (tpt) cc_final: 0.7327 (tpt) REVERT: C 5 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8209 (mt) REVERT: C 53 GLU cc_start: 0.6728 (pt0) cc_final: 0.6444 (pt0) REVERT: C 89 ASP cc_start: 0.7056 (m-30) cc_final: 0.6818 (m-30) REVERT: C 95 LEU cc_start: 0.8661 (tp) cc_final: 0.8446 (tp) REVERT: C 117 ILE cc_start: 0.8649 (pt) cc_final: 0.8421 (pt) REVERT: C 161 VAL cc_start: 0.8399 (p) cc_final: 0.8174 (m) REVERT: C 215 MET cc_start: 0.7852 (mtp) cc_final: 0.7511 (mtt) REVERT: C 216 LYS cc_start: 0.8282 (ttpt) cc_final: 0.7740 (tttt) REVERT: C 226 ASP cc_start: 0.7008 (t0) cc_final: 0.6641 (t0) REVERT: C 241 ASP cc_start: 0.7516 (t0) cc_final: 0.7307 (t0) REVERT: C 246 GLU cc_start: 0.7184 (pt0) cc_final: 0.6865 (pt0) REVERT: C 264 ASP cc_start: 0.7137 (t70) cc_final: 0.6890 (t0) REVERT: C 268 LYS cc_start: 0.8728 (mtmm) cc_final: 0.8419 (mtmt) REVERT: C 271 VAL cc_start: 0.8840 (t) cc_final: 0.8630 (p) REVERT: C 275 GLU cc_start: 0.6871 (tt0) cc_final: 0.6471 (tt0) REVERT: C 288 GLU cc_start: 0.6857 (tt0) cc_final: 0.6125 (tt0) REVERT: C 303 LEU cc_start: 0.8787 (mt) cc_final: 0.8551 (mp) REVERT: C 316 GLU cc_start: 0.7391 (tp30) cc_final: 0.7068 (tp30) REVERT: D 78 GLU cc_start: 0.7234 (mt-10) cc_final: 0.6963 (mt-10) REVERT: D 127 VAL cc_start: 0.8483 (OUTLIER) cc_final: 0.8199 (t) REVERT: D 168 GLU cc_start: 0.7228 (pt0) cc_final: 0.7017 (pt0) REVERT: D 190 GLU cc_start: 0.7518 (mp0) cc_final: 0.7082 (mp0) REVERT: D 215 MET cc_start: 0.7797 (mtp) cc_final: 0.7479 (mtt) REVERT: D 243 MET cc_start: 0.7751 (ttm) cc_final: 0.7488 (mtp) REVERT: D 246 GLU cc_start: 0.7041 (pt0) cc_final: 0.6630 (pt0) REVERT: D 253 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6737 (tm-30) REVERT: D 256 GLU cc_start: 0.7239 (tt0) cc_final: 0.6950 (tt0) REVERT: D 269 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7223 (mm-30) REVERT: E 31 GLN cc_start: 0.8379 (mm110) cc_final: 0.8125 (mm110) REVERT: E 183 SER cc_start: 0.8113 (t) cc_final: 0.7873 (m) REVERT: E 190 GLU cc_start: 0.7495 (mp0) cc_final: 0.6944 (mp0) REVERT: E 205 TYR cc_start: 0.7586 (m-80) cc_final: 0.6786 (m-80) REVERT: E 226 ASP cc_start: 0.7035 (t0) cc_final: 0.6510 (t0) REVERT: E 249 LYS cc_start: 0.7850 (mmpt) cc_final: 0.7636 (mmpt) REVERT: E 254 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8041 (tt) REVERT: E 269 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6976 (mm-30) REVERT: E 273 LYS cc_start: 0.8387 (mtmm) cc_final: 0.8151 (mttm) REVERT: E 288 GLU cc_start: 0.6893 (pt0) cc_final: 0.6547 (pt0) REVERT: E 291 ASP cc_start: 0.6905 (p0) cc_final: 0.6530 (p0) REVERT: F 59 SER cc_start: 0.8543 (m) cc_final: 0.8003 (p) REVERT: F 66 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7967 (mtt90) REVERT: F 72 GLU cc_start: 0.7012 (mp0) cc_final: 0.6770 (mp0) REVERT: F 97 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6599 (mt-10) REVERT: F 123 GLU cc_start: 0.7385 (tp30) cc_final: 0.7164 (tp30) REVERT: F 180 THR cc_start: 0.7918 (m) cc_final: 0.7661 (p) REVERT: F 190 GLU cc_start: 0.7303 (mp0) cc_final: 0.6638 (mp0) REVERT: F 209 GLU cc_start: 0.7188 (tt0) cc_final: 0.6897 (tt0) REVERT: F 215 MET cc_start: 0.7971 (mtm) cc_final: 0.7649 (mtt) REVERT: F 249 LYS cc_start: 0.8245 (mmmt) cc_final: 0.7871 (mmmt) REVERT: F 283 ASP cc_start: 0.7596 (p0) cc_final: 0.7378 (p0) REVERT: F 286 LEU cc_start: 0.8247 (mt) cc_final: 0.7809 (mt) REVERT: F 290 ASN cc_start: 0.7644 (m-40) cc_final: 0.7309 (m-40) REVERT: F 295 ASN cc_start: 0.7703 (m-40) cc_final: 0.7023 (t0) REVERT: F 298 GLU cc_start: 0.7479 (mp0) cc_final: 0.6945 (mp0) REVERT: G 6 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8219 (ttpt) REVERT: G 25 LEU cc_start: 0.7870 (mp) cc_final: 0.7510 (mp) REVERT: G 72 GLU cc_start: 0.6875 (mp0) cc_final: 0.6462 (mp0) REVERT: G 77 ARG cc_start: 0.6755 (mtp85) cc_final: 0.5896 (mtp85) REVERT: G 106 GLN cc_start: 0.8070 (pt0) cc_final: 0.7732 (pt0) REVERT: G 123 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6775 (tm-30) REVERT: G 124 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7370 (ttm110) REVERT: G 162 MET cc_start: -0.1650 (tpp) cc_final: -0.2377 (tpp) REVERT: G 177 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7749 (p) REVERT: G 182 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6906 (mt-10) REVERT: G 194 TYR cc_start: 0.8180 (t80) cc_final: 0.7639 (t80) REVERT: G 216 LYS cc_start: 0.7989 (tppt) cc_final: 0.7650 (tppt) REVERT: G 239 LEU cc_start: 0.8523 (tp) cc_final: 0.7998 (tp) REVERT: G 268 LYS cc_start: 0.7655 (mtmt) cc_final: 0.7227 (mtmt) REVERT: G 288 GLU cc_start: 0.7789 (tp30) cc_final: 0.7138 (tp30) REVERT: H 19 SER cc_start: 0.8062 (p) cc_final: 0.7767 (p) REVERT: H 20 ARG cc_start: 0.7501 (ptp-110) cc_final: 0.7183 (ptp-110) REVERT: H 25 LEU cc_start: 0.8531 (tt) cc_final: 0.8249 (tp) REVERT: H 27 GLU cc_start: 0.6654 (pt0) cc_final: 0.6357 (pt0) REVERT: H 47 ILE cc_start: 0.8651 (mt) cc_final: 0.8407 (mt) REVERT: H 59 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7696 (mm110) REVERT: H 68 ARG cc_start: 0.8523 (mtp180) cc_final: 0.8197 (mtp180) REVERT: H 105 TYR cc_start: 0.7796 (t80) cc_final: 0.7580 (t80) REVERT: H 135 GLU cc_start: 0.7339 (pt0) cc_final: 0.7129 (pt0) REVERT: H 136 PHE cc_start: 0.8576 (m-80) cc_final: 0.8374 (m-80) REVERT: H 227 THR cc_start: 0.8481 (t) cc_final: 0.8274 (t) REVERT: H 228 PHE cc_start: 0.8571 (m-80) cc_final: 0.8369 (m-80) REVERT: I 34 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7234 (mm-30) REVERT: I 84 ASN cc_start: 0.7970 (m-40) cc_final: 0.7500 (m-40) REVERT: I 261 ASN cc_start: 0.8023 (m-40) cc_final: 0.7769 (m110) REVERT: I 284 TYR cc_start: 0.7688 (m-80) cc_final: 0.7101 (m-80) REVERT: I 297 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: I 298 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8458 (tp) REVERT: I 497 TYR cc_start: 0.7284 (m-80) cc_final: 0.7071 (m-80) REVERT: I 499 GLU cc_start: 0.7204 (tp30) cc_final: 0.6775 (tp30) REVERT: I 512 GLN cc_start: 0.7385 (tp40) cc_final: 0.6797 (tm-30) REVERT: I 574 SER cc_start: 0.8804 (t) cc_final: 0.8232 (p) REVERT: I 577 MET cc_start: 0.7056 (tpt) cc_final: 0.6827 (tpt) REVERT: I 581 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: I 620 TYR cc_start: 0.7971 (m-80) cc_final: 0.6821 (m-80) REVERT: I 638 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7884 (mmmt) REVERT: I 639 MET cc_start: 0.7048 (mmp) cc_final: 0.6779 (mmp) REVERT: I 667 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6969 (mm-30) REVERT: I 690 LYS cc_start: 0.8528 (mttt) cc_final: 0.8214 (mttt) REVERT: I 707 ILE cc_start: 0.8518 (tt) cc_final: 0.8154 (pt) REVERT: I 746 VAL cc_start: 0.8635 (p) cc_final: 0.8422 (p) REVERT: I 774 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7716 (ttm110) REVERT: I 776 GLN cc_start: 0.7770 (mp10) cc_final: 0.7406 (mp10) REVERT: I 783 GLN cc_start: 0.7678 (tm-30) cc_final: 0.7139 (tm-30) REVERT: I 818 GLN cc_start: 0.7901 (mt0) cc_final: 0.7382 (mt0) REVERT: I 832 GLU cc_start: 0.7605 (tp30) cc_final: 0.7316 (tp30) REVERT: I 833 LYS cc_start: 0.8461 (ttmt) cc_final: 0.8226 (ttmm) REVERT: I 859 HIS cc_start: 0.8296 (t70) cc_final: 0.7700 (t70) REVERT: I 870 GLU cc_start: 0.7059 (tp30) cc_final: 0.6647 (tp30) REVERT: I 900 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6472 (pm20) REVERT: I 901 VAL cc_start: 0.8725 (t) cc_final: 0.8465 (p) REVERT: I 909 ASP cc_start: 0.7515 (p0) cc_final: 0.7195 (p0) REVERT: I 914 TYR cc_start: 0.7831 (t80) cc_final: 0.7243 (t80) REVERT: I 917 ARG cc_start: 0.8317 (mtm-85) cc_final: 0.8102 (mtm180) REVERT: I 920 GLN cc_start: 0.8103 (mt0) cc_final: 0.7713 (mt0) REVERT: I 923 GLU cc_start: 0.7076 (pp20) cc_final: 0.6849 (pp20) REVERT: I 971 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: J 5 LEU cc_start: 0.4576 (pp) cc_final: 0.3939 (pt) REVERT: J 7 LEU cc_start: 0.8332 (tt) cc_final: 0.7990 (tp) REVERT: J 33 LEU cc_start: 0.7977 (pp) cc_final: 0.7731 (mt) REVERT: J 63 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7565 (tt) REVERT: J 90 LEU cc_start: 0.8202 (tt) cc_final: 0.7885 (tt) REVERT: J 92 GLU cc_start: 0.8079 (tp30) cc_final: 0.7627 (tp30) REVERT: J 94 GLU cc_start: 0.7666 (pt0) cc_final: 0.7367 (pt0) REVERT: J 101 THR cc_start: 0.8683 (t) cc_final: 0.8399 (p) REVERT: J 105 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7036 (mtp85) REVERT: J 110 GLU cc_start: 0.7475 (tp30) cc_final: 0.6874 (tp30) REVERT: J 120 GLN cc_start: 0.8287 (tp40) cc_final: 0.7782 (tt0) REVERT: J 128 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.8109 (p) REVERT: K 13 GLU cc_start: 0.7055 (tt0) cc_final: 0.6764 (tt0) REVERT: K 41 GLU cc_start: 0.7233 (tp30) cc_final: 0.6674 (tp30) REVERT: K 52 GLU cc_start: 0.7861 (pp20) cc_final: 0.7370 (pp20) REVERT: K 55 LEU cc_start: 0.7928 (tt) cc_final: 0.7675 (tp) REVERT: K 71 GLU cc_start: 0.7092 (pm20) cc_final: 0.6541 (pm20) REVERT: K 92 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7053 (pp20) REVERT: K 94 GLU cc_start: 0.7576 (tp30) cc_final: 0.6898 (tp30) REVERT: K 131 GLU cc_start: 0.7380 (tp30) cc_final: 0.7113 (tp30) outliers start: 112 outliers final: 47 residues processed: 1051 average time/residue: 0.4694 time to fit residues: 745.9663 Evaluate side-chains 1038 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 973 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 3 ASP Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 297 GLU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 308 GLN Chi-restraints excluded: chain I residue 581 GLN Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 685 THR Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 105 ARG Chi-restraints excluded: chain J residue 128 SER Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 176 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 317 optimal weight: 1.9990 chunk 342 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 314 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 295 ASN B 8 GLN B 43 ASN B 82 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 217 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 171 HIS D 267 ASN D 295 ASN E 48 GLN E 171 HIS E 208 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 GLN F 142 HIS F 167 ASN F 171 HIS F 198 ASN H 95 ASN I 81 HIS I 204 HIS ** I 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 29660 Z= 0.518 Angle : 0.781 10.707 40467 Z= 0.410 Chirality : 0.052 0.390 4565 Planarity : 0.005 0.065 4974 Dihedral : 15.746 179.786 4963 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.91 % Allowed : 16.12 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3399 helix: 0.36 (0.13), residues: 1505 sheet: -0.06 (0.23), residues: 406 loop : -1.01 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP I 154 HIS 0.014 0.001 HIS I 246 PHE 0.031 0.002 PHE H 17 TYR 0.029 0.002 TYR F 138 ARG 0.019 0.001 ARG I 802 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1141 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 995 time to evaluate : 3.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8341 (m110) cc_final: 0.7849 (m110) REVERT: A 72 GLU cc_start: 0.7039 (mp0) cc_final: 0.6475 (mp0) REVERT: A 78 GLU cc_start: 0.7482 (tt0) cc_final: 0.7229 (tt0) REVERT: A 140 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7716 (mp10) REVERT: A 166 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 168 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7028 (mm-30) REVERT: A 253 GLU cc_start: 0.7234 (tp30) cc_final: 0.7011 (tp30) REVERT: A 290 ASN cc_start: 0.8247 (m-40) cc_final: 0.7854 (m-40) REVERT: A 313 TYR cc_start: 0.8555 (t80) cc_final: 0.8337 (t80) REVERT: B 1 MET cc_start: 0.7242 (mmt) cc_final: 0.6995 (tpt) REVERT: B 53 GLU cc_start: 0.6832 (tp30) cc_final: 0.6433 (tp30) REVERT: B 72 GLU cc_start: 0.6908 (mp0) cc_final: 0.6517 (mp0) REVERT: B 82 ASN cc_start: 0.8467 (t0) cc_final: 0.8106 (t0) REVERT: B 99 ASN cc_start: 0.8492 (m110) cc_final: 0.8149 (m-40) REVERT: B 123 GLU cc_start: 0.7087 (tp30) cc_final: 0.6595 (tp30) REVERT: B 148 ASN cc_start: 0.7180 (m-40) cc_final: 0.6967 (m-40) REVERT: B 190 GLU cc_start: 0.7956 (mp0) cc_final: 0.7589 (mp0) REVERT: B 256 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7064 (tm-30) REVERT: B 268 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8162 (mtmm) REVERT: B 287 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7512 (tp-100) REVERT: B 288 GLU cc_start: 0.7379 (tt0) cc_final: 0.7074 (tt0) REVERT: B 301 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8031 (ttpt) REVERT: B 308 GLN cc_start: 0.8136 (tp40) cc_final: 0.7818 (tp40) REVERT: B 312 ASP cc_start: 0.7762 (m-30) cc_final: 0.7524 (m-30) REVERT: C 1 MET cc_start: 0.7825 (tpt) cc_final: 0.7357 (tpt) REVERT: C 5 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8163 (mt) REVERT: C 6 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8329 (mtmt) REVERT: C 53 GLU cc_start: 0.6720 (pt0) cc_final: 0.6457 (pt0) REVERT: C 89 ASP cc_start: 0.7137 (m-30) cc_final: 0.6930 (m-30) REVERT: C 90 LYS cc_start: 0.8347 (mmmm) cc_final: 0.8118 (mmmm) REVERT: C 109 ASP cc_start: 0.8222 (t70) cc_final: 0.7917 (t0) REVERT: C 215 MET cc_start: 0.7964 (mtp) cc_final: 0.7584 (mtt) REVERT: C 226 ASP cc_start: 0.7216 (t0) cc_final: 0.6863 (t0) REVERT: C 241 ASP cc_start: 0.7613 (t0) cc_final: 0.7391 (t0) REVERT: C 264 ASP cc_start: 0.7205 (t70) cc_final: 0.6960 (t0) REVERT: C 268 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8432 (mtmm) REVERT: C 271 VAL cc_start: 0.8806 (t) cc_final: 0.8530 (p) REVERT: C 275 GLU cc_start: 0.6790 (tt0) cc_final: 0.6436 (tt0) REVERT: C 302 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8377 (mp) REVERT: C 303 LEU cc_start: 0.8808 (mt) cc_final: 0.8581 (mp) REVERT: C 316 GLU cc_start: 0.7449 (tp30) cc_final: 0.7217 (tp30) REVERT: D 126 LYS cc_start: 0.8464 (mttp) cc_final: 0.7968 (mttp) REVERT: D 127 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8194 (t) REVERT: D 190 GLU cc_start: 0.7719 (mp0) cc_final: 0.7473 (mp0) REVERT: D 215 MET cc_start: 0.7855 (mtp) cc_final: 0.7562 (mtt) REVERT: D 243 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7449 (mtp) REVERT: D 246 GLU cc_start: 0.7298 (pt0) cc_final: 0.6977 (pt0) REVERT: D 273 LYS cc_start: 0.8252 (mtmm) cc_final: 0.7899 (mtmm) REVERT: D 291 ASP cc_start: 0.7633 (m-30) cc_final: 0.7402 (m-30) REVERT: E 31 GLN cc_start: 0.8380 (mm110) cc_final: 0.8140 (mm110) REVERT: E 182 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6845 (tm-30) REVERT: E 183 SER cc_start: 0.8137 (t) cc_final: 0.7710 (m) REVERT: E 190 GLU cc_start: 0.7439 (mp0) cc_final: 0.6768 (mp0) REVERT: E 205 TYR cc_start: 0.7748 (m-80) cc_final: 0.6985 (m-80) REVERT: E 249 LYS cc_start: 0.7847 (mmpt) cc_final: 0.7461 (mmpt) REVERT: E 253 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6774 (tm-30) REVERT: E 287 GLN cc_start: 0.7341 (tp40) cc_final: 0.6567 (tp-100) REVERT: E 288 GLU cc_start: 0.7088 (pt0) cc_final: 0.6618 (pt0) REVERT: E 291 ASP cc_start: 0.7116 (p0) cc_final: 0.6564 (p0) REVERT: E 303 LEU cc_start: 0.8492 (mt) cc_final: 0.8128 (mm) REVERT: F 1 MET cc_start: 0.8156 (tpp) cc_final: 0.7910 (tpp) REVERT: F 59 SER cc_start: 0.8626 (m) cc_final: 0.7999 (p) REVERT: F 66 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7946 (mtt90) REVERT: F 72 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6694 (mp0) REVERT: F 97 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6657 (mt-10) REVERT: F 173 LEU cc_start: 0.8364 (tp) cc_final: 0.8135 (tt) REVERT: F 180 THR cc_start: 0.7959 (m) cc_final: 0.7688 (p) REVERT: F 190 GLU cc_start: 0.7295 (mp0) cc_final: 0.6556 (mp0) REVERT: F 253 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7100 (tm-30) REVERT: F 312 ASP cc_start: 0.7814 (t0) cc_final: 0.7611 (m-30) REVERT: G 6 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8225 (ttpt) REVERT: G 25 LEU cc_start: 0.7957 (mp) cc_final: 0.7603 (mp) REVERT: G 48 GLN cc_start: 0.7418 (pt0) cc_final: 0.7090 (pt0) REVERT: G 72 GLU cc_start: 0.7095 (mp0) cc_final: 0.6571 (mp0) REVERT: G 106 GLN cc_start: 0.8165 (pt0) cc_final: 0.7871 (pt0) REVERT: G 123 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6854 (tm-30) REVERT: G 128 TYR cc_start: 0.7859 (m-80) cc_final: 0.7313 (m-80) REVERT: G 177 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7702 (p) REVERT: G 182 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6920 (mt-10) REVERT: G 188 THR cc_start: 0.8128 (p) cc_final: 0.7360 (p) REVERT: G 194 TYR cc_start: 0.8233 (t80) cc_final: 0.7899 (t80) REVERT: G 216 LYS cc_start: 0.8008 (tppt) cc_final: 0.7601 (tppt) REVERT: G 240 TYR cc_start: 0.8288 (t80) cc_final: 0.7836 (t80) REVERT: G 268 LYS cc_start: 0.7734 (mtmt) cc_final: 0.7280 (mtmt) REVERT: G 288 GLU cc_start: 0.7784 (tp30) cc_final: 0.7129 (tp30) REVERT: G 301 LYS cc_start: 0.7135 (tppt) cc_final: 0.6927 (tppt) REVERT: H 19 SER cc_start: 0.8084 (p) cc_final: 0.7772 (p) REVERT: H 20 ARG cc_start: 0.7507 (ptp-110) cc_final: 0.7252 (ptp-110) REVERT: H 27 GLU cc_start: 0.6683 (pt0) cc_final: 0.6389 (pt0) REVERT: H 59 GLN cc_start: 0.8212 (mm-40) cc_final: 0.7711 (mm110) REVERT: H 227 THR cc_start: 0.8581 (t) cc_final: 0.8369 (t) REVERT: H 228 PHE cc_start: 0.8579 (m-80) cc_final: 0.8244 (m-80) REVERT: I 34 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7442 (mm-30) REVERT: I 83 LEU cc_start: 0.8849 (tp) cc_final: 0.8588 (tt) REVERT: I 84 ASN cc_start: 0.8038 (m-40) cc_final: 0.7635 (m-40) REVERT: I 154 TRP cc_start: 0.6680 (p-90) cc_final: 0.6469 (p-90) REVERT: I 156 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7782 (t0) REVERT: I 220 ASP cc_start: 0.7347 (m-30) cc_final: 0.7083 (m-30) REVERT: I 241 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7420 (mmmt) REVERT: I 265 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7880 (mtt90) REVERT: I 271 ASP cc_start: 0.7630 (m-30) cc_final: 0.7410 (t0) REVERT: I 284 TYR cc_start: 0.7633 (m-80) cc_final: 0.7060 (m-80) REVERT: I 298 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8613 (tp) REVERT: I 512 GLN cc_start: 0.7529 (tp40) cc_final: 0.7281 (tm-30) REVERT: I 574 SER cc_start: 0.8763 (t) cc_final: 0.8336 (p) REVERT: I 577 MET cc_start: 0.7118 (tpt) cc_final: 0.5921 (tpt) REVERT: I 581 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7630 (mt0) REVERT: I 583 PHE cc_start: 0.8325 (m-80) cc_final: 0.8112 (m-10) REVERT: I 605 TYR cc_start: 0.7039 (m-80) cc_final: 0.6578 (m-80) REVERT: I 620 TYR cc_start: 0.8019 (m-80) cc_final: 0.6598 (m-80) REVERT: I 638 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7995 (mmmt) REVERT: I 667 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6996 (mm-30) REVERT: I 668 ASP cc_start: 0.6965 (p0) cc_final: 0.6664 (p0) REVERT: I 707 ILE cc_start: 0.8599 (tt) cc_final: 0.8123 (pt) REVERT: I 731 VAL cc_start: 0.8834 (p) cc_final: 0.8629 (p) REVERT: I 746 VAL cc_start: 0.8736 (p) cc_final: 0.8502 (p) REVERT: I 749 ILE cc_start: 0.8551 (pt) cc_final: 0.8223 (mm) REVERT: I 783 GLN cc_start: 0.7682 (tm-30) cc_final: 0.7217 (tm-30) REVERT: I 825 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7305 (tp40) REVERT: I 830 MET cc_start: 0.7063 (mtm) cc_final: 0.6821 (mtm) REVERT: I 832 GLU cc_start: 0.7650 (tp30) cc_final: 0.7402 (tp30) REVERT: I 833 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8227 (ttmm) REVERT: I 870 GLU cc_start: 0.7409 (tp30) cc_final: 0.6926 (tp30) REVERT: I 880 ASP cc_start: 0.7463 (t70) cc_final: 0.7251 (t70) REVERT: I 902 TYR cc_start: 0.8411 (p90) cc_final: 0.8154 (p90) REVERT: I 909 ASP cc_start: 0.7480 (p0) cc_final: 0.7244 (p0) REVERT: I 920 GLN cc_start: 0.8184 (mt0) cc_final: 0.7984 (mt0) REVERT: I 923 GLU cc_start: 0.7137 (pp20) cc_final: 0.6932 (pp20) REVERT: I 940 MET cc_start: 0.7677 (tmm) cc_final: 0.6894 (tmm) REVERT: I 942 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8579 (mmmt) REVERT: I 963 TYR cc_start: 0.8845 (t80) cc_final: 0.8110 (t80) REVERT: J 5 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4275 (pt) REVERT: J 16 ARG cc_start: 0.8494 (mtp85) cc_final: 0.8267 (mtp85) REVERT: J 52 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6944 (mm-30) REVERT: J 63 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7798 (tt) REVERT: J 90 LEU cc_start: 0.8318 (tt) cc_final: 0.8037 (tt) REVERT: J 91 GLN cc_start: 0.8461 (mt0) cc_final: 0.8147 (mt0) REVERT: J 92 GLU cc_start: 0.8074 (tp30) cc_final: 0.7654 (tp30) REVERT: J 94 GLU cc_start: 0.7752 (pt0) cc_final: 0.7366 (pt0) REVERT: J 110 GLU cc_start: 0.7502 (tp30) cc_final: 0.6917 (tp30) REVERT: J 111 MET cc_start: 0.7831 (ttm) cc_final: 0.7579 (mtp) REVERT: J 120 GLN cc_start: 0.8251 (tp40) cc_final: 0.7754 (tt0) REVERT: K 13 GLU cc_start: 0.6993 (tt0) cc_final: 0.6704 (tt0) REVERT: K 41 GLU cc_start: 0.7242 (tp30) cc_final: 0.6680 (tp30) REVERT: K 52 GLU cc_start: 0.7960 (pp20) cc_final: 0.7427 (pp20) REVERT: K 71 GLU cc_start: 0.7024 (pm20) cc_final: 0.6388 (pm20) REVERT: K 94 GLU cc_start: 0.7606 (tp30) cc_final: 0.6829 (tp30) outliers start: 146 outliers final: 90 residues processed: 1048 average time/residue: 0.4696 time to fit residues: 739.7572 Evaluate side-chains 1058 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 953 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 103 SER Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 301 LYS Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 156 ASP Chi-restraints excluded: chain I residue 269 LYS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 491 GLU Chi-restraints excluded: chain I residue 581 GLN Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 834 LEU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 900 GLU Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 15 TYR Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 313 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 151 optimal weight: 0.8980 chunk 213 optimal weight: 3.9990 chunk 318 optimal weight: 0.9990 chunk 337 optimal weight: 4.9990 chunk 166 optimal weight: 0.1980 chunk 301 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 217 ASN C 10 GLN C 20 HIS ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN D 295 ASN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 198 ASN F 232 ASN F 263 GLN H 70 GLN H 95 ASN ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS I 204 HIS I 661 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29660 Z= 0.271 Angle : 0.665 9.594 40467 Z= 0.346 Chirality : 0.045 0.398 4565 Planarity : 0.004 0.048 4974 Dihedral : 15.631 179.857 4952 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.34 % Allowed : 17.94 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3399 helix: 0.89 (0.14), residues: 1466 sheet: -0.10 (0.23), residues: 412 loop : -0.95 (0.16), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 50 HIS 0.011 0.001 HIS I 246 PHE 0.028 0.002 PHE E 151 TYR 0.027 0.002 TYR F 138 ARG 0.005 0.001 ARG J 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 972 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 SER cc_start: 0.7574 (t) cc_final: 0.7283 (p) REVERT: A 43 ASN cc_start: 0.8216 (m110) cc_final: 0.7819 (m-40) REVERT: A 72 GLU cc_start: 0.7039 (mt-10) cc_final: 0.6493 (mp0) REVERT: A 78 GLU cc_start: 0.7451 (tt0) cc_final: 0.7184 (tt0) REVERT: A 155 THR cc_start: 0.8014 (m) cc_final: 0.7735 (t) REVERT: A 166 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8564 (tp) REVERT: A 228 GLU cc_start: 0.7061 (pt0) cc_final: 0.6819 (pt0) REVERT: A 253 GLU cc_start: 0.7187 (tp30) cc_final: 0.6985 (tp30) REVERT: A 290 ASN cc_start: 0.8233 (m-40) cc_final: 0.7831 (m-40) REVERT: B 1 MET cc_start: 0.7142 (mmt) cc_final: 0.6846 (tpt) REVERT: B 53 GLU cc_start: 0.6830 (tp30) cc_final: 0.6411 (tp30) REVERT: B 99 ASN cc_start: 0.8410 (m110) cc_final: 0.8171 (m-40) REVERT: B 109 ASP cc_start: 0.7593 (t0) cc_final: 0.7330 (t0) REVERT: B 123 GLU cc_start: 0.7090 (tp30) cc_final: 0.6856 (tp30) REVERT: B 253 GLU cc_start: 0.7444 (tm-30) cc_final: 0.6897 (tm-30) REVERT: B 256 GLU cc_start: 0.7389 (tm-30) cc_final: 0.7150 (tm-30) REVERT: B 268 LYS cc_start: 0.8475 (mtmm) cc_final: 0.8147 (mtmm) REVERT: B 288 GLU cc_start: 0.7316 (tt0) cc_final: 0.7042 (tt0) REVERT: B 301 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7969 (ttpt) REVERT: B 308 GLN cc_start: 0.8117 (tp40) cc_final: 0.7805 (tp40) REVERT: C 1 MET cc_start: 0.7697 (tpt) cc_final: 0.7062 (tpt) REVERT: C 5 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8132 (mt) REVERT: C 6 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8255 (mtmt) REVERT: C 53 GLU cc_start: 0.6650 (pt0) cc_final: 0.6405 (pt0) REVERT: C 90 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8139 (mmmm) REVERT: C 109 ASP cc_start: 0.8179 (t70) cc_final: 0.7900 (t0) REVERT: C 126 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8266 (mmtm) REVERT: C 241 ASP cc_start: 0.7604 (t0) cc_final: 0.7375 (t0) REVERT: C 264 ASP cc_start: 0.7209 (t70) cc_final: 0.6925 (t0) REVERT: C 268 LYS cc_start: 0.8735 (mtmm) cc_final: 0.8386 (mtmm) REVERT: C 271 VAL cc_start: 0.8877 (t) cc_final: 0.8616 (p) REVERT: C 275 GLU cc_start: 0.6874 (tt0) cc_final: 0.6650 (tt0) REVERT: C 302 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8262 (mp) REVERT: C 303 LEU cc_start: 0.8804 (mt) cc_final: 0.8592 (mp) REVERT: C 316 GLU cc_start: 0.7420 (tp30) cc_final: 0.7191 (tp30) REVERT: D 126 LYS cc_start: 0.8412 (mttp) cc_final: 0.7931 (mttp) REVERT: D 127 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8128 (t) REVERT: D 215 MET cc_start: 0.7784 (mtp) cc_final: 0.7583 (mtt) REVERT: D 243 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7445 (mtp) REVERT: D 291 ASP cc_start: 0.7608 (m-30) cc_final: 0.7391 (m-30) REVERT: E 31 GLN cc_start: 0.8324 (mm110) cc_final: 0.8035 (mm110) REVERT: E 46 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7739 (mtp85) REVERT: E 173 LEU cc_start: 0.8419 (mp) cc_final: 0.8098 (mp) REVERT: E 182 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6804 (tm-30) REVERT: E 183 SER cc_start: 0.8106 (t) cc_final: 0.7672 (m) REVERT: E 190 GLU cc_start: 0.7391 (mp0) cc_final: 0.6860 (mp0) REVERT: E 205 TYR cc_start: 0.7562 (m-80) cc_final: 0.6824 (m-80) REVERT: E 228 GLU cc_start: 0.7057 (pm20) cc_final: 0.6831 (pm20) REVERT: E 249 LYS cc_start: 0.7921 (mmpt) cc_final: 0.7351 (mmpt) REVERT: E 253 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6771 (tm-30) REVERT: E 287 GLN cc_start: 0.7203 (tp40) cc_final: 0.6580 (tp40) REVERT: E 288 GLU cc_start: 0.7006 (pt0) cc_final: 0.6579 (pt0) REVERT: E 291 ASP cc_start: 0.6916 (p0) cc_final: 0.6469 (p0) REVERT: E 303 LEU cc_start: 0.8448 (mt) cc_final: 0.8083 (mm) REVERT: F 1 MET cc_start: 0.8135 (tpp) cc_final: 0.7833 (tpp) REVERT: F 6 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7285 (mtpp) REVERT: F 59 SER cc_start: 0.8707 (m) cc_final: 0.7843 (p) REVERT: F 66 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7645 (mtt90) REVERT: F 97 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6593 (mt-10) REVERT: F 139 GLU cc_start: 0.7343 (mp0) cc_final: 0.6889 (mp0) REVERT: F 173 LEU cc_start: 0.8327 (tp) cc_final: 0.8024 (tp) REVERT: F 180 THR cc_start: 0.7971 (m) cc_final: 0.7689 (p) REVERT: F 190 GLU cc_start: 0.7252 (mp0) cc_final: 0.6499 (mp0) REVERT: F 209 GLU cc_start: 0.7170 (tt0) cc_final: 0.6932 (tt0) REVERT: F 215 MET cc_start: 0.7934 (mtm) cc_final: 0.7647 (mtm) REVERT: F 249 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7911 (mmmt) REVERT: F 295 ASN cc_start: 0.7958 (t0) cc_final: 0.7684 (t0) REVERT: F 312 ASP cc_start: 0.7785 (t0) cc_final: 0.7544 (m-30) REVERT: G 6 LYS cc_start: 0.8461 (ttpt) cc_final: 0.8214 (ttpt) REVERT: G 25 LEU cc_start: 0.7911 (mp) cc_final: 0.7539 (mp) REVERT: G 48 GLN cc_start: 0.7112 (pt0) cc_final: 0.6777 (pt0) REVERT: G 54 LYS cc_start: 0.6678 (pttm) cc_final: 0.6397 (pttm) REVERT: G 72 GLU cc_start: 0.6996 (mp0) cc_final: 0.6492 (mp0) REVERT: G 123 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6713 (tm-30) REVERT: G 128 TYR cc_start: 0.7729 (m-80) cc_final: 0.7336 (m-80) REVERT: G 177 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7600 (p) REVERT: G 182 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6851 (mt-10) REVERT: G 183 SER cc_start: 0.7816 (OUTLIER) cc_final: 0.7541 (p) REVERT: G 194 TYR cc_start: 0.8238 (t80) cc_final: 0.7844 (t80) REVERT: G 216 LYS cc_start: 0.7988 (tppt) cc_final: 0.7566 (tppt) REVERT: G 240 TYR cc_start: 0.8287 (t80) cc_final: 0.7847 (t80) REVERT: G 256 GLU cc_start: 0.7105 (pp20) cc_final: 0.6849 (pp20) REVERT: G 268 LYS cc_start: 0.7746 (mtmt) cc_final: 0.7317 (mtmt) REVERT: G 288 GLU cc_start: 0.7758 (tp30) cc_final: 0.7110 (tp30) REVERT: G 307 TYR cc_start: 0.7729 (t80) cc_final: 0.7281 (t80) REVERT: H 19 SER cc_start: 0.8082 (p) cc_final: 0.7777 (p) REVERT: H 59 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7722 (mm110) REVERT: H 66 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7647 (mtp85) REVERT: H 227 THR cc_start: 0.8554 (t) cc_final: 0.8316 (t) REVERT: H 228 PHE cc_start: 0.8570 (m-80) cc_final: 0.8275 (m-80) REVERT: I 33 GLU cc_start: 0.7658 (pp20) cc_final: 0.7152 (pp20) REVERT: I 34 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7196 (mm-30) REVERT: I 83 LEU cc_start: 0.8835 (tp) cc_final: 0.8558 (tt) REVERT: I 84 ASN cc_start: 0.8001 (m-40) cc_final: 0.7567 (m-40) REVERT: I 220 ASP cc_start: 0.7465 (m-30) cc_final: 0.7001 (m-30) REVERT: I 235 ASN cc_start: 0.8390 (t0) cc_final: 0.8184 (t0) REVERT: I 241 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7478 (mmmt) REVERT: I 245 TYR cc_start: 0.7803 (p90) cc_final: 0.7556 (p90) REVERT: I 271 ASP cc_start: 0.7601 (m-30) cc_final: 0.7343 (t0) REVERT: I 284 TYR cc_start: 0.7507 (m-80) cc_final: 0.6829 (m-80) REVERT: I 291 GLU cc_start: 0.7666 (pm20) cc_final: 0.7422 (pm20) REVERT: I 496 ARG cc_start: 0.7200 (ttm170) cc_final: 0.6782 (ttm110) REVERT: I 501 GLN cc_start: 0.7447 (tt0) cc_final: 0.7115 (tt0) REVERT: I 512 GLN cc_start: 0.7459 (tp40) cc_final: 0.7201 (tm-30) REVERT: I 513 GLU cc_start: 0.7411 (tt0) cc_final: 0.7046 (tp30) REVERT: I 574 SER cc_start: 0.8699 (t) cc_final: 0.8153 (p) REVERT: I 577 MET cc_start: 0.7042 (tpt) cc_final: 0.6686 (tpt) REVERT: I 620 TYR cc_start: 0.7870 (m-80) cc_final: 0.7144 (m-80) REVERT: I 668 ASP cc_start: 0.7000 (p0) cc_final: 0.6784 (p0) REVERT: I 690 LYS cc_start: 0.8518 (mttt) cc_final: 0.8300 (mttt) REVERT: I 696 LEU cc_start: 0.8440 (mt) cc_final: 0.8177 (mm) REVERT: I 707 ILE cc_start: 0.8589 (tt) cc_final: 0.8107 (pt) REVERT: I 712 MET cc_start: 0.8331 (mtp) cc_final: 0.8052 (mtm) REVERT: I 746 VAL cc_start: 0.8686 (p) cc_final: 0.8476 (p) REVERT: I 749 ILE cc_start: 0.8535 (pt) cc_final: 0.8259 (mm) REVERT: I 755 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8199 (mttm) REVERT: I 772 LYS cc_start: 0.7253 (mptp) cc_final: 0.7031 (mptp) REVERT: I 776 GLN cc_start: 0.7678 (mp10) cc_final: 0.7441 (mp10) REVERT: I 783 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7217 (tm-30) REVERT: I 825 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7215 (tp40) REVERT: I 832 GLU cc_start: 0.7565 (tp30) cc_final: 0.7221 (tp30) REVERT: I 833 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8174 (ttmm) REVERT: I 859 HIS cc_start: 0.8304 (t70) cc_final: 0.7782 (t70) REVERT: I 870 GLU cc_start: 0.7218 (tp30) cc_final: 0.6721 (tp30) REVERT: I 902 TYR cc_start: 0.8418 (p90) cc_final: 0.8157 (p90) REVERT: I 940 MET cc_start: 0.7591 (tmm) cc_final: 0.7007 (tmm) REVERT: I 942 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8575 (mmmt) REVERT: I 963 TYR cc_start: 0.8850 (t80) cc_final: 0.8021 (t80) REVERT: I 971 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: J 5 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4174 (pt) REVERT: J 22 GLU cc_start: 0.7135 (pt0) cc_final: 0.6702 (pt0) REVERT: J 52 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6830 (mm-30) REVERT: J 62 GLN cc_start: 0.8176 (mm110) cc_final: 0.7910 (mm110) REVERT: J 63 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7937 (tt) REVERT: J 64 GLN cc_start: 0.7983 (tm-30) cc_final: 0.7451 (tm-30) REVERT: J 89 GLN cc_start: 0.8094 (mm110) cc_final: 0.7770 (mm110) REVERT: J 90 LEU cc_start: 0.8334 (tt) cc_final: 0.8033 (tt) REVERT: J 91 GLN cc_start: 0.8464 (mt0) cc_final: 0.8137 (mt0) REVERT: J 92 GLU cc_start: 0.8052 (tp30) cc_final: 0.7506 (tp30) REVERT: J 93 LEU cc_start: 0.8560 (tp) cc_final: 0.8329 (tt) REVERT: J 94 GLU cc_start: 0.7698 (pt0) cc_final: 0.7331 (pt0) REVERT: J 110 GLU cc_start: 0.7448 (tp30) cc_final: 0.6814 (tp30) REVERT: J 111 MET cc_start: 0.7792 (ttm) cc_final: 0.7453 (mtp) REVERT: J 120 GLN cc_start: 0.8092 (tp40) cc_final: 0.7695 (tt0) REVERT: K 13 GLU cc_start: 0.6948 (tt0) cc_final: 0.6687 (tt0) REVERT: K 22 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5837 (pp20) REVERT: K 41 GLU cc_start: 0.7221 (tp30) cc_final: 0.6628 (tp30) REVERT: K 44 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8229 (mp) REVERT: K 52 GLU cc_start: 0.7947 (pp20) cc_final: 0.7404 (pp20) REVERT: K 94 GLU cc_start: 0.7543 (tp30) cc_final: 0.6827 (tp30) REVERT: K 121 GLU cc_start: 0.7032 (tp30) cc_final: 0.6387 (tp30) outliers start: 129 outliers final: 82 residues processed: 1023 average time/residue: 0.4740 time to fit residues: 731.9345 Evaluate side-chains 1040 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 944 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 10 GLN Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 516 ASN Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 674 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 815 GLU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 63 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 280 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 251 optimal weight: 0.0170 chunk 139 optimal weight: 0.8980 chunk 287 optimal weight: 1.9990 chunk 233 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 302 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN D 68 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 198 ASN F 232 ASN G 106 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN ** H 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29660 Z= 0.246 Angle : 0.643 9.520 40467 Z= 0.334 Chirality : 0.044 0.377 4565 Planarity : 0.004 0.079 4974 Dihedral : 15.513 179.785 4947 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.78 % Allowed : 18.71 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3399 helix: 1.08 (0.14), residues: 1470 sheet: -0.16 (0.22), residues: 454 loop : -0.97 (0.16), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 PHE 0.029 0.001 PHE E 151 TYR 0.025 0.002 TYR F 138 ARG 0.020 0.001 ARG I 802 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1099 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 957 time to evaluate : 3.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8227 (mm-40) REVERT: A 32 SER cc_start: 0.7632 (t) cc_final: 0.7343 (p) REVERT: A 43 ASN cc_start: 0.8210 (m110) cc_final: 0.7817 (m-40) REVERT: A 72 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6465 (mp0) REVERT: A 78 GLU cc_start: 0.7395 (tt0) cc_final: 0.7148 (tt0) REVERT: A 138 TYR cc_start: 0.8305 (t80) cc_final: 0.7724 (t80) REVERT: A 155 THR cc_start: 0.8036 (m) cc_final: 0.7804 (t) REVERT: A 209 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7138 (mt-10) REVERT: A 228 GLU cc_start: 0.6999 (pt0) cc_final: 0.6775 (pt0) REVERT: A 253 GLU cc_start: 0.7194 (tp30) cc_final: 0.6915 (tp30) REVERT: A 290 ASN cc_start: 0.8252 (m-40) cc_final: 0.7870 (m-40) REVERT: A 308 GLN cc_start: 0.7893 (tp40) cc_final: 0.7498 (tp-100) REVERT: B 1 MET cc_start: 0.7109 (mmt) cc_final: 0.6840 (tpt) REVERT: B 18 SER cc_start: 0.8207 (m) cc_final: 0.7928 (p) REVERT: B 87 SER cc_start: 0.8527 (t) cc_final: 0.8238 (t) REVERT: B 109 ASP cc_start: 0.7642 (t0) cc_final: 0.7420 (t0) REVERT: B 123 GLU cc_start: 0.7133 (tp30) cc_final: 0.6907 (tp30) REVERT: B 190 GLU cc_start: 0.7929 (mp0) cc_final: 0.7395 (mp0) REVERT: B 253 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6807 (tm-30) REVERT: B 256 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 268 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8151 (mtmm) REVERT: B 288 GLU cc_start: 0.7299 (tt0) cc_final: 0.7002 (tt0) REVERT: B 301 LYS cc_start: 0.8391 (ttpt) cc_final: 0.7946 (ttpt) REVERT: B 308 GLN cc_start: 0.8048 (tp40) cc_final: 0.7774 (tp40) REVERT: C 1 MET cc_start: 0.7680 (tpt) cc_final: 0.6937 (tpt) REVERT: C 5 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8103 (mt) REVERT: C 6 LYS cc_start: 0.8510 (mtmt) cc_final: 0.8211 (mtmt) REVERT: C 53 GLU cc_start: 0.6660 (pt0) cc_final: 0.6424 (pt0) REVERT: C 109 ASP cc_start: 0.8147 (t70) cc_final: 0.7880 (t0) REVERT: C 126 LYS cc_start: 0.8475 (mmtt) cc_final: 0.8269 (mmtm) REVERT: C 241 ASP cc_start: 0.7599 (t0) cc_final: 0.7393 (t0) REVERT: C 264 ASP cc_start: 0.7223 (t70) cc_final: 0.6905 (t0) REVERT: C 268 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8363 (mtmm) REVERT: C 271 VAL cc_start: 0.8880 (t) cc_final: 0.8639 (p) REVERT: C 275 GLU cc_start: 0.6922 (tt0) cc_final: 0.6582 (tt0) REVERT: C 288 GLU cc_start: 0.6923 (tt0) cc_final: 0.6642 (tt0) REVERT: C 302 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8243 (mp) REVERT: C 303 LEU cc_start: 0.8793 (mt) cc_final: 0.8590 (mp) REVERT: C 316 GLU cc_start: 0.7451 (tp30) cc_final: 0.7191 (tp30) REVERT: D 62 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8471 (p) REVERT: D 126 LYS cc_start: 0.8423 (mttp) cc_final: 0.7953 (mttp) REVERT: D 127 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8143 (t) REVERT: D 215 MET cc_start: 0.7802 (mtp) cc_final: 0.7564 (mtt) REVERT: D 226 ASP cc_start: 0.7239 (t0) cc_final: 0.6970 (t0) REVERT: D 243 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7421 (mtp) REVERT: D 291 ASP cc_start: 0.7590 (m-30) cc_final: 0.7363 (m-30) REVERT: E 3 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7540 (p0) REVERT: E 31 GLN cc_start: 0.8338 (mm110) cc_final: 0.7984 (mm110) REVERT: E 46 ARG cc_start: 0.8058 (mmm-85) cc_final: 0.7753 (mtp85) REVERT: E 138 TYR cc_start: 0.8282 (t80) cc_final: 0.7939 (t80) REVERT: E 173 LEU cc_start: 0.8403 (mp) cc_final: 0.8084 (mp) REVERT: E 182 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6812 (tm-30) REVERT: E 183 SER cc_start: 0.8095 (t) cc_final: 0.7679 (m) REVERT: E 190 GLU cc_start: 0.7340 (mp0) cc_final: 0.6869 (mp0) REVERT: E 201 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7174 (mtp85) REVERT: E 205 TYR cc_start: 0.7534 (m-80) cc_final: 0.6914 (m-80) REVERT: E 226 ASP cc_start: 0.6802 (t0) cc_final: 0.6566 (t0) REVERT: E 249 LYS cc_start: 0.7926 (mmpt) cc_final: 0.7379 (mmpt) REVERT: E 253 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6728 (tm-30) REVERT: E 256 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6805 (mt-10) REVERT: E 269 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7025 (mm-30) REVERT: E 272 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7662 (mtm-85) REVERT: E 287 GLN cc_start: 0.7186 (tp40) cc_final: 0.6745 (tp40) REVERT: E 288 GLU cc_start: 0.6976 (pt0) cc_final: 0.6548 (pt0) REVERT: E 291 ASP cc_start: 0.6851 (p0) cc_final: 0.6429 (p0) REVERT: E 303 LEU cc_start: 0.8463 (mt) cc_final: 0.8118 (mm) REVERT: F 1 MET cc_start: 0.8110 (tpp) cc_final: 0.7814 (tpp) REVERT: F 18 SER cc_start: 0.8519 (m) cc_final: 0.7943 (p) REVERT: F 59 SER cc_start: 0.8698 (m) cc_final: 0.8157 (t) REVERT: F 66 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7622 (mpt180) REVERT: F 74 LEU cc_start: 0.8391 (mt) cc_final: 0.8187 (mm) REVERT: F 97 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6614 (mt-10) REVERT: F 139 GLU cc_start: 0.7349 (mp0) cc_final: 0.7057 (mp0) REVERT: F 173 LEU cc_start: 0.8338 (tp) cc_final: 0.8050 (tp) REVERT: F 180 THR cc_start: 0.7932 (m) cc_final: 0.7607 (p) REVERT: F 190 GLU cc_start: 0.7226 (mp0) cc_final: 0.6502 (mp0) REVERT: F 209 GLU cc_start: 0.7217 (tt0) cc_final: 0.6840 (tt0) REVERT: F 249 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7366 (mmmt) REVERT: F 253 GLU cc_start: 0.7137 (tm-30) cc_final: 0.6796 (tm-30) REVERT: F 295 ASN cc_start: 0.7955 (t0) cc_final: 0.7680 (t0) REVERT: F 312 ASP cc_start: 0.7798 (t0) cc_final: 0.7563 (m-30) REVERT: G 6 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8210 (ttpt) REVERT: G 25 LEU cc_start: 0.7907 (mp) cc_final: 0.7549 (mp) REVERT: G 48 GLN cc_start: 0.7191 (pt0) cc_final: 0.6809 (pt0) REVERT: G 54 LYS cc_start: 0.6724 (pttm) cc_final: 0.6358 (pttm) REVERT: G 60 ARG cc_start: 0.7542 (ptm160) cc_final: 0.7340 (ptp-170) REVERT: G 123 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6691 (tm-30) REVERT: G 130 ASP cc_start: 0.6994 (m-30) cc_final: 0.6770 (m-30) REVERT: G 177 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7494 (p) REVERT: G 182 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6879 (mt-10) REVERT: G 183 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7541 (p) REVERT: G 193 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7772 (mt) REVERT: G 194 TYR cc_start: 0.8209 (t80) cc_final: 0.7831 (t80) REVERT: G 216 LYS cc_start: 0.7970 (tppt) cc_final: 0.7569 (tppt) REVERT: G 256 GLU cc_start: 0.7100 (pp20) cc_final: 0.6586 (pp20) REVERT: G 268 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7361 (mtmt) REVERT: G 288 GLU cc_start: 0.7702 (tp30) cc_final: 0.7060 (tp30) REVERT: H 13 ASP cc_start: 0.6693 (p0) cc_final: 0.6491 (p0) REVERT: H 19 SER cc_start: 0.8047 (p) cc_final: 0.7813 (p) REVERT: H 59 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7756 (mm-40) REVERT: H 66 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7683 (mtp85) REVERT: H 156 LYS cc_start: 0.7578 (mmtp) cc_final: 0.7378 (mmtm) REVERT: H 228 PHE cc_start: 0.8535 (m-80) cc_final: 0.8204 (m-80) REVERT: H 231 GLN cc_start: 0.7760 (tt0) cc_final: 0.7545 (tt0) REVERT: I 26 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7346 (mm-40) REVERT: I 33 GLU cc_start: 0.7686 (pp20) cc_final: 0.7141 (pp20) REVERT: I 34 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7157 (mm-30) REVERT: I 83 LEU cc_start: 0.8833 (tp) cc_final: 0.8543 (tt) REVERT: I 84 ASN cc_start: 0.7996 (m-40) cc_final: 0.7547 (m-40) REVERT: I 158 ARG cc_start: 0.7151 (ttp80) cc_final: 0.6733 (ttp80) REVERT: I 220 ASP cc_start: 0.7465 (m-30) cc_final: 0.7013 (m-30) REVERT: I 234 LEU cc_start: 0.8573 (tt) cc_final: 0.8339 (tt) REVERT: I 235 ASN cc_start: 0.8345 (t0) cc_final: 0.8113 (t0) REVERT: I 271 ASP cc_start: 0.7589 (m-30) cc_final: 0.7319 (t0) REVERT: I 284 TYR cc_start: 0.7488 (m-80) cc_final: 0.6721 (m-80) REVERT: I 291 GLU cc_start: 0.7636 (pm20) cc_final: 0.7399 (pm20) REVERT: I 491 GLU cc_start: 0.7607 (tp30) cc_final: 0.7343 (tp30) REVERT: I 512 GLN cc_start: 0.7458 (tp40) cc_final: 0.7194 (tm-30) REVERT: I 515 GLU cc_start: 0.7563 (tp30) cc_final: 0.7081 (tp30) REVERT: I 574 SER cc_start: 0.8660 (t) cc_final: 0.8081 (p) REVERT: I 577 MET cc_start: 0.7063 (tpt) cc_final: 0.6752 (tpt) REVERT: I 605 TYR cc_start: 0.7095 (m-80) cc_final: 0.6737 (m-80) REVERT: I 620 TYR cc_start: 0.8079 (m-80) cc_final: 0.6865 (m-80) REVERT: I 668 ASP cc_start: 0.6961 (p0) cc_final: 0.6595 (p0) REVERT: I 696 LEU cc_start: 0.8457 (mt) cc_final: 0.8202 (mm) REVERT: I 712 MET cc_start: 0.8457 (mtp) cc_final: 0.8003 (mtm) REVERT: I 746 VAL cc_start: 0.8710 (p) cc_final: 0.8486 (p) REVERT: I 748 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.7355 (m-30) REVERT: I 749 ILE cc_start: 0.8451 (pt) cc_final: 0.8248 (mm) REVERT: I 772 LYS cc_start: 0.7288 (mptp) cc_final: 0.7017 (mptp) REVERT: I 776 GLN cc_start: 0.7622 (mp10) cc_final: 0.7362 (mp10) REVERT: I 783 GLN cc_start: 0.7643 (tm-30) cc_final: 0.7216 (tm-30) REVERT: I 830 MET cc_start: 0.7069 (mtm) cc_final: 0.6852 (mmm) REVERT: I 832 GLU cc_start: 0.7544 (tp30) cc_final: 0.7210 (tp30) REVERT: I 833 LYS cc_start: 0.8419 (ttmt) cc_final: 0.8165 (ttmm) REVERT: I 870 GLU cc_start: 0.7174 (tp30) cc_final: 0.6645 (tp30) REVERT: I 900 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7022 (mm-30) REVERT: I 902 TYR cc_start: 0.8412 (p90) cc_final: 0.8188 (p90) REVERT: I 909 ASP cc_start: 0.7363 (p0) cc_final: 0.7092 (p0) REVERT: I 940 MET cc_start: 0.7556 (tmm) cc_final: 0.6959 (tmm) REVERT: I 942 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8594 (mmmt) REVERT: I 963 TYR cc_start: 0.8848 (t80) cc_final: 0.7969 (t80) REVERT: I 971 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: J 5 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4193 (pt) REVERT: J 22 GLU cc_start: 0.7144 (pt0) cc_final: 0.6694 (pt0) REVERT: J 52 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6863 (mm-30) REVERT: J 64 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7834 (tm-30) REVERT: J 89 GLN cc_start: 0.8109 (mm110) cc_final: 0.7770 (mm110) REVERT: J 90 LEU cc_start: 0.8361 (tt) cc_final: 0.8083 (tt) REVERT: J 91 GLN cc_start: 0.8460 (mt0) cc_final: 0.8117 (mt0) REVERT: J 92 GLU cc_start: 0.8028 (tp30) cc_final: 0.7483 (tp30) REVERT: J 93 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8360 (tt) REVERT: J 94 GLU cc_start: 0.7695 (pt0) cc_final: 0.7309 (pt0) REVERT: J 110 GLU cc_start: 0.7428 (tp30) cc_final: 0.6885 (tp30) REVERT: J 120 GLN cc_start: 0.8060 (tp40) cc_final: 0.7730 (tt0) REVERT: J 140 GLU cc_start: 0.7345 (tm-30) cc_final: 0.6998 (tm-30) REVERT: K 13 GLU cc_start: 0.6940 (tt0) cc_final: 0.6665 (tt0) REVERT: K 22 GLU cc_start: 0.6717 (OUTLIER) cc_final: 0.5782 (pp20) REVERT: K 41 GLU cc_start: 0.7145 (tp30) cc_final: 0.6552 (tp30) REVERT: K 44 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8243 (mp) REVERT: K 52 GLU cc_start: 0.7972 (pp20) cc_final: 0.7350 (pp20) REVERT: K 90 LEU cc_start: 0.7710 (tp) cc_final: 0.7506 (tp) REVERT: K 94 GLU cc_start: 0.7545 (tp30) cc_final: 0.6873 (tp30) outliers start: 142 outliers final: 94 residues processed: 1017 average time/residue: 0.4731 time to fit residues: 724.6579 Evaluate side-chains 1043 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 932 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 228 GLU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 22 MET Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 507 HIS Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 815 GLU Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 113 optimal weight: 0.5980 chunk 303 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 198 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 337 optimal weight: 4.9990 chunk 280 optimal weight: 0.0370 chunk 156 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 198 ASN F 232 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN H 231 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS J 58 GLN K 30 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29660 Z= 0.230 Angle : 0.625 10.485 40467 Z= 0.323 Chirality : 0.044 0.364 4565 Planarity : 0.004 0.061 4974 Dihedral : 15.399 179.892 4943 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.54 % Allowed : 20.60 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3399 helix: 1.24 (0.14), residues: 1468 sheet: -0.15 (0.22), residues: 454 loop : -0.94 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 PHE 0.031 0.001 PHE E 151 TYR 0.025 0.002 TYR I 245 ARG 0.006 0.000 ARG J 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 934 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8244 (mt0) REVERT: A 32 SER cc_start: 0.7615 (t) cc_final: 0.7377 (p) REVERT: A 57 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7704 (mm-40) REVERT: A 72 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6454 (mp0) REVERT: A 78 GLU cc_start: 0.7378 (tt0) cc_final: 0.7151 (tt0) REVERT: A 138 TYR cc_start: 0.8334 (t80) cc_final: 0.7767 (t80) REVERT: A 155 THR cc_start: 0.8079 (m) cc_final: 0.7845 (t) REVERT: A 209 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 228 GLU cc_start: 0.7014 (pt0) cc_final: 0.6783 (pt0) REVERT: A 253 GLU cc_start: 0.7191 (tp30) cc_final: 0.6958 (tp30) REVERT: A 308 GLN cc_start: 0.7888 (tp40) cc_final: 0.7471 (tp-100) REVERT: B 1 MET cc_start: 0.7086 (mmt) cc_final: 0.6882 (tpt) REVERT: B 18 SER cc_start: 0.8170 (m) cc_final: 0.7890 (p) REVERT: B 109 ASP cc_start: 0.7649 (t0) cc_final: 0.7442 (t0) REVERT: B 162 MET cc_start: 0.7783 (mmt) cc_final: 0.7574 (mmt) REVERT: B 190 GLU cc_start: 0.7881 (mp0) cc_final: 0.7406 (mp0) REVERT: B 253 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6801 (tm-30) REVERT: B 288 GLU cc_start: 0.7288 (tt0) cc_final: 0.7013 (tt0) REVERT: B 301 LYS cc_start: 0.8386 (ttpt) cc_final: 0.7949 (ttpt) REVERT: B 308 GLN cc_start: 0.8031 (tp40) cc_final: 0.7739 (tp40) REVERT: C 1 MET cc_start: 0.7725 (tpt) cc_final: 0.7043 (tpt) REVERT: C 5 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8089 (mt) REVERT: C 6 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8147 (mtmt) REVERT: C 53 GLU cc_start: 0.6644 (pt0) cc_final: 0.6409 (pt0) REVERT: C 109 ASP cc_start: 0.8144 (t70) cc_final: 0.7880 (t0) REVERT: C 241 ASP cc_start: 0.7603 (t0) cc_final: 0.7399 (t0) REVERT: C 264 ASP cc_start: 0.7222 (t70) cc_final: 0.6925 (t0) REVERT: C 268 LYS cc_start: 0.8719 (mtmm) cc_final: 0.8400 (mtmm) REVERT: C 271 VAL cc_start: 0.8884 (t) cc_final: 0.8629 (p) REVERT: C 275 GLU cc_start: 0.6930 (tt0) cc_final: 0.6586 (tt0) REVERT: C 288 GLU cc_start: 0.6938 (tt0) cc_final: 0.6651 (tt0) REVERT: C 303 LEU cc_start: 0.8791 (mt) cc_final: 0.8565 (mp) REVERT: C 316 GLU cc_start: 0.7474 (tp30) cc_final: 0.7218 (tp30) REVERT: D 62 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8478 (p) REVERT: D 127 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.8120 (t) REVERT: D 215 MET cc_start: 0.7829 (mtp) cc_final: 0.7573 (mtt) REVERT: D 226 ASP cc_start: 0.7198 (t0) cc_final: 0.6970 (t0) REVERT: D 243 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7419 (mtp) REVERT: D 291 ASP cc_start: 0.7587 (m-30) cc_final: 0.7349 (m-30) REVERT: E 3 ASP cc_start: 0.7829 (p0) cc_final: 0.7525 (p0) REVERT: E 46 ARG cc_start: 0.8021 (mmm-85) cc_final: 0.7725 (mtp85) REVERT: E 72 GLU cc_start: 0.7118 (mp0) cc_final: 0.6324 (mp0) REVERT: E 140 GLN cc_start: 0.8039 (mp10) cc_final: 0.7741 (mp10) REVERT: E 173 LEU cc_start: 0.8423 (mp) cc_final: 0.8090 (mp) REVERT: E 182 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6795 (tm-30) REVERT: E 183 SER cc_start: 0.8049 (t) cc_final: 0.7664 (m) REVERT: E 190 GLU cc_start: 0.7319 (mp0) cc_final: 0.6879 (mp0) REVERT: E 201 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7194 (mtp85) REVERT: E 205 TYR cc_start: 0.7583 (m-80) cc_final: 0.7147 (m-80) REVERT: E 249 LYS cc_start: 0.7914 (mmpt) cc_final: 0.7386 (mmpt) REVERT: E 253 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6682 (tm-30) REVERT: E 269 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7044 (mm-30) REVERT: E 287 GLN cc_start: 0.7190 (tp40) cc_final: 0.6728 (tp40) REVERT: E 288 GLU cc_start: 0.6912 (pt0) cc_final: 0.6528 (pt0) REVERT: E 291 ASP cc_start: 0.6836 (p0) cc_final: 0.6414 (p0) REVERT: F 1 MET cc_start: 0.8154 (tpp) cc_final: 0.7924 (tpp) REVERT: F 6 LYS cc_start: 0.7565 (mtpp) cc_final: 0.7283 (mtpp) REVERT: F 18 SER cc_start: 0.8476 (m) cc_final: 0.7899 (p) REVERT: F 59 SER cc_start: 0.8701 (m) cc_final: 0.8241 (t) REVERT: F 66 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7552 (mpt180) REVERT: F 72 GLU cc_start: 0.7057 (mp0) cc_final: 0.6818 (mp0) REVERT: F 94 ASN cc_start: 0.8091 (p0) cc_final: 0.7795 (p0) REVERT: F 97 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6604 (mt-10) REVERT: F 173 LEU cc_start: 0.8339 (tp) cc_final: 0.8052 (tp) REVERT: F 180 THR cc_start: 0.7864 (m) cc_final: 0.7576 (p) REVERT: F 190 GLU cc_start: 0.7202 (mp0) cc_final: 0.6501 (mp0) REVERT: F 209 GLU cc_start: 0.7217 (tt0) cc_final: 0.6766 (tt0) REVERT: F 249 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7668 (mmmt) REVERT: F 295 ASN cc_start: 0.7933 (t0) cc_final: 0.7659 (t0) REVERT: F 312 ASP cc_start: 0.7795 (t0) cc_final: 0.7579 (m-30) REVERT: G 6 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8206 (ttpt) REVERT: G 25 LEU cc_start: 0.7906 (mp) cc_final: 0.7576 (mp) REVERT: G 48 GLN cc_start: 0.7200 (pt0) cc_final: 0.6921 (pt0) REVERT: G 54 LYS cc_start: 0.6751 (pttm) cc_final: 0.6325 (pttm) REVERT: G 69 THR cc_start: 0.7398 (p) cc_final: 0.7171 (p) REVERT: G 72 GLU cc_start: 0.6937 (mp0) cc_final: 0.6613 (mp0) REVERT: G 123 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6782 (mm-30) REVERT: G 130 ASP cc_start: 0.6968 (m-30) cc_final: 0.6712 (m-30) REVERT: G 177 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7397 (p) REVERT: G 182 GLU cc_start: 0.7210 (mt-10) cc_final: 0.6938 (mt-10) REVERT: G 183 SER cc_start: 0.7739 (OUTLIER) cc_final: 0.7520 (p) REVERT: G 193 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7741 (mt) REVERT: G 194 TYR cc_start: 0.8202 (t80) cc_final: 0.7845 (t80) REVERT: G 216 LYS cc_start: 0.7975 (tppt) cc_final: 0.7552 (tppt) REVERT: G 256 GLU cc_start: 0.7113 (pp20) cc_final: 0.6612 (pp20) REVERT: G 268 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7434 (mtmt) REVERT: G 272 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6877 (mtm180) REVERT: G 288 GLU cc_start: 0.7707 (tp30) cc_final: 0.7038 (tp30) REVERT: H 13 ASP cc_start: 0.6660 (p0) cc_final: 0.6444 (p0) REVERT: H 19 SER cc_start: 0.8090 (p) cc_final: 0.7833 (p) REVERT: H 59 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7711 (mm110) REVERT: H 180 TYR cc_start: 0.8422 (p90) cc_final: 0.8029 (p90) REVERT: H 228 PHE cc_start: 0.8528 (m-80) cc_final: 0.8241 (m-80) REVERT: I 26 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7339 (mm-40) REVERT: I 33 GLU cc_start: 0.7712 (pp20) cc_final: 0.7286 (pp20) REVERT: I 34 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7157 (mm-30) REVERT: I 83 LEU cc_start: 0.8835 (tp) cc_final: 0.8283 (tt) REVERT: I 84 ASN cc_start: 0.8002 (m-40) cc_final: 0.7560 (m-40) REVERT: I 158 ARG cc_start: 0.7164 (ttp80) cc_final: 0.6849 (ttp80) REVERT: I 220 ASP cc_start: 0.7446 (m-30) cc_final: 0.6974 (m-30) REVERT: I 235 ASN cc_start: 0.8364 (t0) cc_final: 0.8114 (t0) REVERT: I 241 LYS cc_start: 0.7974 (mmmt) cc_final: 0.7555 (mmmt) REVERT: I 271 ASP cc_start: 0.7569 (m-30) cc_final: 0.7302 (t0) REVERT: I 284 TYR cc_start: 0.7479 (m-80) cc_final: 0.6744 (m-80) REVERT: I 291 GLU cc_start: 0.7613 (pm20) cc_final: 0.7380 (pm20) REVERT: I 512 GLN cc_start: 0.7370 (tp40) cc_final: 0.7108 (tm-30) REVERT: I 574 SER cc_start: 0.8633 (t) cc_final: 0.8075 (p) REVERT: I 605 TYR cc_start: 0.7112 (m-80) cc_final: 0.6774 (m-80) REVERT: I 620 TYR cc_start: 0.8014 (m-80) cc_final: 0.6882 (m-80) REVERT: I 668 ASP cc_start: 0.6890 (p0) cc_final: 0.6544 (p0) REVERT: I 676 TYR cc_start: 0.7893 (p90) cc_final: 0.7689 (p90) REVERT: I 696 LEU cc_start: 0.8469 (mt) cc_final: 0.8215 (mm) REVERT: I 712 MET cc_start: 0.8492 (mtp) cc_final: 0.7948 (mtm) REVERT: I 746 VAL cc_start: 0.8666 (p) cc_final: 0.8445 (p) REVERT: I 747 GLU cc_start: 0.7145 (pp20) cc_final: 0.6864 (pp20) REVERT: I 750 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8476 (m) REVERT: I 772 LYS cc_start: 0.7341 (mptp) cc_final: 0.7083 (mptp) REVERT: I 776 GLN cc_start: 0.7536 (mp10) cc_final: 0.7256 (mp10) REVERT: I 783 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7210 (tm-30) REVERT: I 802 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7716 (ttp80) REVERT: I 830 MET cc_start: 0.7099 (mtm) cc_final: 0.6873 (mmm) REVERT: I 832 GLU cc_start: 0.7557 (tp30) cc_final: 0.7221 (tp30) REVERT: I 833 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8181 (ttmm) REVERT: I 870 GLU cc_start: 0.7134 (tp30) cc_final: 0.6597 (tp30) REVERT: I 900 GLU cc_start: 0.7247 (mm-30) cc_final: 0.7033 (mm-30) REVERT: I 909 ASP cc_start: 0.7445 (p0) cc_final: 0.7143 (p0) REVERT: I 940 MET cc_start: 0.7457 (tmm) cc_final: 0.6625 (tmm) REVERT: I 942 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8640 (mmmt) REVERT: I 963 TYR cc_start: 0.8858 (t80) cc_final: 0.7959 (t80) REVERT: J 5 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4065 (pt) REVERT: J 22 GLU cc_start: 0.7120 (pt0) cc_final: 0.6642 (pt0) REVERT: J 52 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6519 (mm-30) REVERT: J 89 GLN cc_start: 0.8081 (mm110) cc_final: 0.7738 (mm110) REVERT: J 90 LEU cc_start: 0.8341 (tt) cc_final: 0.8050 (tt) REVERT: J 91 GLN cc_start: 0.8459 (mt0) cc_final: 0.8114 (mt0) REVERT: J 93 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8324 (tt) REVERT: J 94 GLU cc_start: 0.7690 (pt0) cc_final: 0.7304 (pt0) REVERT: J 110 GLU cc_start: 0.7430 (tp30) cc_final: 0.6848 (tp30) REVERT: J 120 GLN cc_start: 0.8076 (tp40) cc_final: 0.7719 (tt0) REVERT: J 140 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7102 (tm-30) REVERT: J 143 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7225 (tp40) REVERT: K 13 GLU cc_start: 0.6941 (tt0) cc_final: 0.6672 (tt0) REVERT: K 22 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5759 (pp20) REVERT: K 41 GLU cc_start: 0.7144 (tp30) cc_final: 0.6576 (tp30) REVERT: K 52 GLU cc_start: 0.7944 (pp20) cc_final: 0.7336 (pp20) REVERT: K 63 LEU cc_start: 0.8398 (tp) cc_final: 0.8095 (tp) REVERT: K 71 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6150 (pm20) REVERT: K 90 LEU cc_start: 0.7686 (tp) cc_final: 0.7452 (tp) REVERT: K 94 GLU cc_start: 0.7550 (tp30) cc_final: 0.6889 (tp30) outliers start: 135 outliers final: 96 residues processed: 990 average time/residue: 0.4689 time to fit residues: 699.5843 Evaluate side-chains 1029 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 918 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 201 ARG Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 935 ASP Chi-restraints excluded: chain I residue 950 GLU Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 325 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 284 optimal weight: 2.9990 chunk 188 optimal weight: 0.5980 chunk 336 optimal weight: 0.8980 chunk 210 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 ASN E 31 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 ASN F 198 ASN F 232 ASN G 140 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** J 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29660 Z= 0.284 Angle : 0.641 12.368 40467 Z= 0.330 Chirality : 0.045 0.359 4565 Planarity : 0.004 0.049 4974 Dihedral : 15.347 179.588 4941 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.68 % Allowed : 21.14 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3399 helix: 1.29 (0.14), residues: 1465 sheet: -0.21 (0.22), residues: 456 loop : -0.93 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP I 154 HIS 0.010 0.001 HIS I 246 PHE 0.032 0.002 PHE E 151 TYR 0.024 0.002 TYR I 245 ARG 0.006 0.000 ARG J 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 928 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8247 (mt0) REVERT: A 32 SER cc_start: 0.7665 (t) cc_final: 0.7438 (p) REVERT: A 36 PHE cc_start: 0.8744 (m-80) cc_final: 0.8430 (m-80) REVERT: A 57 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7738 (mm-40) REVERT: A 72 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6439 (mp0) REVERT: A 78 GLU cc_start: 0.7342 (tt0) cc_final: 0.7118 (tt0) REVERT: A 155 THR cc_start: 0.8159 (m) cc_final: 0.7890 (t) REVERT: A 209 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7169 (mt-10) REVERT: A 228 GLU cc_start: 0.7065 (pt0) cc_final: 0.6840 (pt0) REVERT: A 253 GLU cc_start: 0.7200 (tp30) cc_final: 0.6965 (tp30) REVERT: A 308 GLN cc_start: 0.7896 (tp40) cc_final: 0.7456 (tp-100) REVERT: B 18 SER cc_start: 0.8190 (m) cc_final: 0.7863 (p) REVERT: B 109 ASP cc_start: 0.7678 (t0) cc_final: 0.7457 (t0) REVERT: B 162 MET cc_start: 0.7807 (mmt) cc_final: 0.7606 (mmt) REVERT: B 253 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6799 (tm-30) REVERT: B 268 LYS cc_start: 0.8501 (mtmm) cc_final: 0.8173 (mtmm) REVERT: B 288 GLU cc_start: 0.7299 (tt0) cc_final: 0.7014 (tt0) REVERT: B 301 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7954 (ttpt) REVERT: B 308 GLN cc_start: 0.8021 (tp40) cc_final: 0.7735 (tp40) REVERT: C 1 MET cc_start: 0.7741 (tpt) cc_final: 0.7078 (tpt) REVERT: C 5 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8100 (mt) REVERT: C 6 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8122 (mtmt) REVERT: C 53 GLU cc_start: 0.6632 (pt0) cc_final: 0.6399 (pt0) REVERT: C 109 ASP cc_start: 0.8157 (t70) cc_final: 0.7890 (t0) REVERT: C 203 LYS cc_start: 0.8735 (mmtm) cc_final: 0.8508 (mmmt) REVERT: C 241 ASP cc_start: 0.7618 (t0) cc_final: 0.7411 (t0) REVERT: C 264 ASP cc_start: 0.7223 (t70) cc_final: 0.6929 (t0) REVERT: C 268 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8395 (mtmm) REVERT: C 271 VAL cc_start: 0.8880 (t) cc_final: 0.8635 (p) REVERT: C 275 GLU cc_start: 0.6945 (tt0) cc_final: 0.6587 (tt0) REVERT: C 288 GLU cc_start: 0.6942 (tt0) cc_final: 0.6669 (tt0) REVERT: C 303 LEU cc_start: 0.8789 (mt) cc_final: 0.8582 (mp) REVERT: C 316 GLU cc_start: 0.7470 (tp30) cc_final: 0.7200 (tp30) REVERT: D 62 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8486 (p) REVERT: D 78 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6846 (mt-10) REVERT: D 127 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8116 (t) REVERT: D 215 MET cc_start: 0.7819 (mtp) cc_final: 0.7553 (mtt) REVERT: D 243 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7513 (mtp) REVERT: D 274 SER cc_start: 0.8508 (t) cc_final: 0.8305 (p) REVERT: D 291 ASP cc_start: 0.7596 (m-30) cc_final: 0.7353 (m-30) REVERT: E 3 ASP cc_start: 0.7847 (p0) cc_final: 0.7534 (p0) REVERT: E 46 ARG cc_start: 0.8051 (mmm-85) cc_final: 0.7776 (mtp85) REVERT: E 72 GLU cc_start: 0.7067 (mp0) cc_final: 0.6343 (mp0) REVERT: E 138 TYR cc_start: 0.8254 (t80) cc_final: 0.7988 (t80) REVERT: E 140 GLN cc_start: 0.8046 (mp10) cc_final: 0.7754 (mp10) REVERT: E 173 LEU cc_start: 0.8435 (mp) cc_final: 0.8084 (mp) REVERT: E 182 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6792 (tm-30) REVERT: E 183 SER cc_start: 0.8068 (t) cc_final: 0.7667 (m) REVERT: E 190 GLU cc_start: 0.7323 (mp0) cc_final: 0.6860 (mp0) REVERT: E 205 TYR cc_start: 0.7574 (m-80) cc_final: 0.7162 (m-80) REVERT: E 249 LYS cc_start: 0.7921 (mmpt) cc_final: 0.7397 (mmpt) REVERT: E 253 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6725 (tm-30) REVERT: E 269 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7039 (mm-30) REVERT: E 287 GLN cc_start: 0.7227 (tp40) cc_final: 0.6757 (tp40) REVERT: E 288 GLU cc_start: 0.6878 (pt0) cc_final: 0.6520 (pt0) REVERT: E 291 ASP cc_start: 0.6832 (p0) cc_final: 0.6436 (p0) REVERT: E 295 ASN cc_start: 0.8005 (t0) cc_final: 0.7797 (t0) REVERT: F 6 LYS cc_start: 0.7562 (mtpp) cc_final: 0.7230 (mtpp) REVERT: F 18 SER cc_start: 0.8450 (m) cc_final: 0.7870 (p) REVERT: F 45 THR cc_start: 0.8460 (m) cc_final: 0.8258 (p) REVERT: F 59 SER cc_start: 0.8710 (m) cc_final: 0.8242 (t) REVERT: F 66 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7547 (mpt180) REVERT: F 72 GLU cc_start: 0.7029 (mp0) cc_final: 0.6795 (mp0) REVERT: F 97 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6620 (mt-10) REVERT: F 173 LEU cc_start: 0.8338 (tp) cc_final: 0.8047 (tp) REVERT: F 180 THR cc_start: 0.7857 (m) cc_final: 0.7553 (p) REVERT: F 190 GLU cc_start: 0.7182 (mp0) cc_final: 0.6549 (mp0) REVERT: F 209 GLU cc_start: 0.7287 (tt0) cc_final: 0.6799 (tt0) REVERT: F 249 LYS cc_start: 0.8144 (mmmt) cc_final: 0.7818 (mmmt) REVERT: F 295 ASN cc_start: 0.7931 (t0) cc_final: 0.7570 (t0) REVERT: F 312 ASP cc_start: 0.7817 (t0) cc_final: 0.7575 (m-30) REVERT: G 6 LYS cc_start: 0.8444 (ttpt) cc_final: 0.8225 (ttpt) REVERT: G 25 LEU cc_start: 0.7898 (mp) cc_final: 0.7589 (mp) REVERT: G 48 GLN cc_start: 0.7224 (pt0) cc_final: 0.6777 (pt0) REVERT: G 54 LYS cc_start: 0.6822 (pttm) cc_final: 0.6566 (pttm) REVERT: G 69 THR cc_start: 0.7389 (p) cc_final: 0.7178 (p) REVERT: G 72 GLU cc_start: 0.6951 (mp0) cc_final: 0.6643 (mp0) REVERT: G 123 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6836 (mm-30) REVERT: G 177 THR cc_start: 0.7632 (OUTLIER) cc_final: 0.7377 (p) REVERT: G 183 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.7521 (p) REVERT: G 193 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7766 (mt) REVERT: G 194 TYR cc_start: 0.8222 (t80) cc_final: 0.7875 (t80) REVERT: G 216 LYS cc_start: 0.7979 (tppt) cc_final: 0.7547 (tppt) REVERT: G 256 GLU cc_start: 0.7120 (pp20) cc_final: 0.6641 (pp20) REVERT: G 268 LYS cc_start: 0.7891 (mtmt) cc_final: 0.7444 (mtmt) REVERT: G 288 GLU cc_start: 0.7681 (tp30) cc_final: 0.7231 (tp30) REVERT: H 13 ASP cc_start: 0.6653 (p0) cc_final: 0.6439 (p0) REVERT: H 59 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7701 (mm110) REVERT: H 66 ARG cc_start: 0.7851 (tpp80) cc_final: 0.7618 (mtp85) REVERT: H 156 LYS cc_start: 0.7600 (mmtp) cc_final: 0.7330 (mmtm) REVERT: H 228 PHE cc_start: 0.8553 (m-80) cc_final: 0.8243 (m-80) REVERT: I 26 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7373 (mm-40) REVERT: I 33 GLU cc_start: 0.7803 (pp20) cc_final: 0.7307 (pp20) REVERT: I 34 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7124 (mm-30) REVERT: I 83 LEU cc_start: 0.8741 (tp) cc_final: 0.8480 (tt) REVERT: I 84 ASN cc_start: 0.7996 (m-40) cc_final: 0.7534 (m-40) REVERT: I 158 ARG cc_start: 0.7116 (ttp80) cc_final: 0.6801 (ttp80) REVERT: I 220 ASP cc_start: 0.7426 (m-30) cc_final: 0.6969 (m-30) REVERT: I 235 ASN cc_start: 0.8365 (t0) cc_final: 0.8122 (t0) REVERT: I 241 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7297 (mmmt) REVERT: I 271 ASP cc_start: 0.7544 (m-30) cc_final: 0.7263 (t0) REVERT: I 284 TYR cc_start: 0.7491 (m-80) cc_final: 0.6805 (m-80) REVERT: I 496 ARG cc_start: 0.7366 (ttm170) cc_final: 0.7110 (ttt180) REVERT: I 512 GLN cc_start: 0.7450 (tp40) cc_final: 0.7109 (tm-30) REVERT: I 513 GLU cc_start: 0.7151 (tp30) cc_final: 0.6871 (tp30) REVERT: I 574 SER cc_start: 0.8610 (t) cc_final: 0.8042 (p) REVERT: I 605 TYR cc_start: 0.7107 (m-80) cc_final: 0.6818 (m-80) REVERT: I 620 TYR cc_start: 0.8041 (m-80) cc_final: 0.6922 (m-80) REVERT: I 667 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7733 (mm-30) REVERT: I 668 ASP cc_start: 0.6888 (p0) cc_final: 0.6555 (p0) REVERT: I 696 LEU cc_start: 0.8475 (mt) cc_final: 0.8225 (mm) REVERT: I 746 VAL cc_start: 0.8684 (p) cc_final: 0.8459 (p) REVERT: I 747 GLU cc_start: 0.7121 (pp20) cc_final: 0.6852 (pp20) REVERT: I 750 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8400 (m) REVERT: I 754 ASN cc_start: 0.8362 (m-40) cc_final: 0.7956 (m-40) REVERT: I 772 LYS cc_start: 0.7322 (mptp) cc_final: 0.7035 (mptp) REVERT: I 776 GLN cc_start: 0.7632 (mp10) cc_final: 0.7344 (mp10) REVERT: I 783 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7206 (tm-30) REVERT: I 802 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7644 (ttp80) REVERT: I 830 MET cc_start: 0.7090 (mtm) cc_final: 0.6856 (mmm) REVERT: I 832 GLU cc_start: 0.7596 (tp30) cc_final: 0.7258 (tp30) REVERT: I 833 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8206 (ttmm) REVERT: I 861 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8455 (mt) REVERT: I 870 GLU cc_start: 0.7136 (tp30) cc_final: 0.6602 (tp30) REVERT: I 909 ASP cc_start: 0.7450 (p0) cc_final: 0.7187 (p0) REVERT: I 940 MET cc_start: 0.7448 (tmm) cc_final: 0.6692 (tmm) REVERT: I 942 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8603 (mmmt) REVERT: J 5 LEU cc_start: 0.5081 (OUTLIER) cc_final: 0.4184 (pt) REVERT: J 22 GLU cc_start: 0.7155 (pt0) cc_final: 0.6662 (pt0) REVERT: J 52 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6591 (mm-30) REVERT: J 89 GLN cc_start: 0.8097 (mm110) cc_final: 0.7755 (mm110) REVERT: J 90 LEU cc_start: 0.8376 (tt) cc_final: 0.8084 (tt) REVERT: J 91 GLN cc_start: 0.8456 (mt0) cc_final: 0.8121 (mt0) REVERT: J 93 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8321 (tt) REVERT: J 94 GLU cc_start: 0.7677 (pt0) cc_final: 0.7334 (pt0) REVERT: J 120 GLN cc_start: 0.8118 (tp40) cc_final: 0.7766 (tt0) REVERT: J 140 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7096 (tm-30) REVERT: J 143 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7242 (tp40) REVERT: K 13 GLU cc_start: 0.6942 (tt0) cc_final: 0.6672 (tt0) REVERT: K 22 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5744 (pp20) REVERT: K 41 GLU cc_start: 0.7145 (tp30) cc_final: 0.6572 (tp30) REVERT: K 44 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8248 (mp) REVERT: K 52 GLU cc_start: 0.7878 (pp20) cc_final: 0.7278 (pp20) REVERT: K 71 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6258 (pm20) REVERT: K 90 LEU cc_start: 0.7697 (tp) cc_final: 0.7468 (tp) REVERT: K 94 GLU cc_start: 0.7545 (tp30) cc_final: 0.6952 (tp30) outliers start: 139 outliers final: 111 residues processed: 988 average time/residue: 0.4775 time to fit residues: 710.4651 Evaluate side-chains 1051 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 924 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 219 ASP Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 137 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 208 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 213 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 264 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 ASN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN D 68 GLN E 290 ASN E 294 GLN F 167 ASN F 198 ASN F 232 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 GLN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS J 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29660 Z= 0.345 Angle : 0.662 9.620 40467 Z= 0.343 Chirality : 0.046 0.354 4565 Planarity : 0.004 0.050 4974 Dihedral : 15.307 178.990 4941 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 5.18 % Allowed : 21.00 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3399 helix: 1.21 (0.14), residues: 1472 sheet: -0.11 (0.22), residues: 439 loop : -1.02 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 154 HIS 0.010 0.001 HIS I 246 PHE 0.033 0.002 PHE E 151 TYR 0.024 0.002 TYR I 245 ARG 0.005 0.001 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 941 time to evaluate : 3.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8233 (mt0) REVERT: A 32 SER cc_start: 0.7730 (t) cc_final: 0.7505 (p) REVERT: A 36 PHE cc_start: 0.8747 (m-80) cc_final: 0.8452 (m-80) REVERT: A 72 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6444 (mp0) REVERT: A 78 GLU cc_start: 0.7339 (tt0) cc_final: 0.7114 (tt0) REVERT: A 155 THR cc_start: 0.8206 (m) cc_final: 0.7951 (t) REVERT: A 156 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7429 (mmm) REVERT: A 253 GLU cc_start: 0.7221 (tp30) cc_final: 0.6971 (tp30) REVERT: B 18 SER cc_start: 0.8186 (m) cc_final: 0.7832 (p) REVERT: B 109 ASP cc_start: 0.7669 (t0) cc_final: 0.7458 (t0) REVERT: B 190 GLU cc_start: 0.7851 (mp0) cc_final: 0.7325 (mp0) REVERT: B 253 GLU cc_start: 0.7364 (tm-30) cc_final: 0.6816 (tm-30) REVERT: B 268 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8193 (mtmm) REVERT: B 288 GLU cc_start: 0.7316 (tt0) cc_final: 0.6979 (tt0) REVERT: B 301 LYS cc_start: 0.8393 (ttpt) cc_final: 0.7947 (ttpt) REVERT: B 308 GLN cc_start: 0.7990 (tp40) cc_final: 0.7738 (tp40) REVERT: C 1 MET cc_start: 0.7760 (tpt) cc_final: 0.7176 (tpt) REVERT: C 5 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8105 (mt) REVERT: C 6 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8134 (mtmt) REVERT: C 53 GLU cc_start: 0.6615 (pt0) cc_final: 0.6384 (pt0) REVERT: C 109 ASP cc_start: 0.8174 (t70) cc_final: 0.7879 (t0) REVERT: C 169 LEU cc_start: 0.8588 (tp) cc_final: 0.8310 (tp) REVERT: C 241 ASP cc_start: 0.7635 (t0) cc_final: 0.7425 (t0) REVERT: C 264 ASP cc_start: 0.7226 (t70) cc_final: 0.6928 (t0) REVERT: C 268 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8381 (mtmm) REVERT: C 271 VAL cc_start: 0.8876 (t) cc_final: 0.8619 (p) REVERT: C 275 GLU cc_start: 0.6960 (tt0) cc_final: 0.6590 (tt0) REVERT: C 288 GLU cc_start: 0.6971 (tt0) cc_final: 0.6701 (tt0) REVERT: C 303 LEU cc_start: 0.8792 (mt) cc_final: 0.8587 (mp) REVERT: C 316 GLU cc_start: 0.7480 (tp30) cc_final: 0.7222 (tp30) REVERT: D 62 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8499 (p) REVERT: D 126 LYS cc_start: 0.8475 (mttp) cc_final: 0.8002 (mttp) REVERT: D 127 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8174 (t) REVERT: D 215 MET cc_start: 0.7812 (mtp) cc_final: 0.7558 (mtt) REVERT: D 243 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7483 (mtp) REVERT: D 274 SER cc_start: 0.8543 (t) cc_final: 0.8302 (p) REVERT: D 291 ASP cc_start: 0.7606 (m-30) cc_final: 0.7375 (m-30) REVERT: D 303 LEU cc_start: 0.8685 (mt) cc_final: 0.8482 (mm) REVERT: E 3 ASP cc_start: 0.7875 (p0) cc_final: 0.7565 (p0) REVERT: E 46 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7855 (mtp85) REVERT: E 72 GLU cc_start: 0.7053 (mp0) cc_final: 0.6426 (mp0) REVERT: E 90 LYS cc_start: 0.7888 (tppt) cc_final: 0.7666 (tppt) REVERT: E 140 GLN cc_start: 0.8041 (mp10) cc_final: 0.7762 (mp10) REVERT: E 173 LEU cc_start: 0.8451 (mp) cc_final: 0.8115 (mp) REVERT: E 182 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6801 (tm-30) REVERT: E 183 SER cc_start: 0.8094 (t) cc_final: 0.7664 (m) REVERT: E 205 TYR cc_start: 0.7585 (m-80) cc_final: 0.7242 (m-80) REVERT: E 249 LYS cc_start: 0.7972 (mmpt) cc_final: 0.7768 (mmpt) REVERT: E 253 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6768 (tm-30) REVERT: E 269 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7078 (mm-30) REVERT: E 287 GLN cc_start: 0.7265 (tp40) cc_final: 0.6708 (tp40) REVERT: E 288 GLU cc_start: 0.6830 (pt0) cc_final: 0.6497 (pt0) REVERT: E 291 ASP cc_start: 0.6866 (p0) cc_final: 0.6490 (p0) REVERT: E 295 ASN cc_start: 0.8033 (t0) cc_final: 0.7825 (t0) REVERT: F 1 MET cc_start: 0.7910 (tpp) cc_final: 0.7569 (tpp) REVERT: F 18 SER cc_start: 0.8477 (m) cc_final: 0.7902 (p) REVERT: F 46 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7474 (mmm-85) REVERT: F 59 SER cc_start: 0.8716 (m) cc_final: 0.8259 (t) REVERT: F 66 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7624 (mpt180) REVERT: F 97 GLU cc_start: 0.6953 (mt-10) cc_final: 0.6608 (mt-10) REVERT: F 173 LEU cc_start: 0.8326 (tp) cc_final: 0.8053 (tp) REVERT: F 180 THR cc_start: 0.7825 (m) cc_final: 0.7534 (p) REVERT: F 190 GLU cc_start: 0.7183 (mp0) cc_final: 0.6545 (mp0) REVERT: F 209 GLU cc_start: 0.7329 (tt0) cc_final: 0.6772 (tt0) REVERT: F 211 ARG cc_start: 0.8416 (mmt180) cc_final: 0.8148 (mmt180) REVERT: F 249 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7858 (mmmt) REVERT: F 295 ASN cc_start: 0.7947 (t0) cc_final: 0.7587 (t0) REVERT: F 312 ASP cc_start: 0.7820 (t0) cc_final: 0.7578 (m-30) REVERT: G 6 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8262 (ttpt) REVERT: G 25 LEU cc_start: 0.7931 (mp) cc_final: 0.7621 (mp) REVERT: G 48 GLN cc_start: 0.7172 (pt0) cc_final: 0.6565 (pt0) REVERT: G 54 LYS cc_start: 0.6844 (pttm) cc_final: 0.6528 (pttm) REVERT: G 123 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6800 (mm-30) REVERT: G 177 THR cc_start: 0.7605 (OUTLIER) cc_final: 0.7364 (p) REVERT: G 182 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6951 (mt-10) REVERT: G 194 TYR cc_start: 0.8254 (t80) cc_final: 0.8020 (t80) REVERT: G 216 LYS cc_start: 0.7938 (tppt) cc_final: 0.7534 (tppt) REVERT: G 272 ARG cc_start: 0.7427 (mtm180) cc_final: 0.7046 (mtm180) REVERT: G 288 GLU cc_start: 0.7787 (tp30) cc_final: 0.7361 (tp30) REVERT: G 295 ASN cc_start: 0.7380 (t0) cc_final: 0.6986 (t0) REVERT: H 13 ASP cc_start: 0.6628 (p0) cc_final: 0.6419 (p0) REVERT: H 66 ARG cc_start: 0.7907 (tpp80) cc_final: 0.7641 (mtp85) REVERT: H 228 PHE cc_start: 0.8564 (m-80) cc_final: 0.8205 (m-80) REVERT: I 26 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7394 (mm-40) REVERT: I 33 GLU cc_start: 0.7762 (pp20) cc_final: 0.6943 (pp20) REVERT: I 34 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7018 (tp30) REVERT: I 83 LEU cc_start: 0.8799 (tp) cc_final: 0.8488 (tt) REVERT: I 84 ASN cc_start: 0.7989 (m-40) cc_final: 0.7535 (m-40) REVERT: I 158 ARG cc_start: 0.7125 (ttp80) cc_final: 0.6809 (ttp80) REVERT: I 220 ASP cc_start: 0.7458 (m-30) cc_final: 0.7003 (m-30) REVERT: I 235 ASN cc_start: 0.8368 (t0) cc_final: 0.8155 (t0) REVERT: I 241 LYS cc_start: 0.7746 (mmmt) cc_final: 0.7180 (mmmt) REVERT: I 271 ASP cc_start: 0.7532 (m-30) cc_final: 0.7175 (t0) REVERT: I 273 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7309 (mmpt) REVERT: I 284 TYR cc_start: 0.7494 (m-80) cc_final: 0.6867 (m-80) REVERT: I 496 ARG cc_start: 0.7407 (ttm170) cc_final: 0.7144 (ttt180) REVERT: I 512 GLN cc_start: 0.7550 (tp40) cc_final: 0.7210 (tm-30) REVERT: I 574 SER cc_start: 0.8602 (t) cc_final: 0.8073 (p) REVERT: I 577 MET cc_start: 0.7296 (tpt) cc_final: 0.6864 (tpt) REVERT: I 605 TYR cc_start: 0.7108 (m-80) cc_final: 0.6842 (m-80) REVERT: I 620 TYR cc_start: 0.8113 (m-80) cc_final: 0.6861 (m-80) REVERT: I 668 ASP cc_start: 0.6912 (p0) cc_final: 0.6569 (p0) REVERT: I 686 ASP cc_start: 0.7755 (t0) cc_final: 0.7508 (t0) REVERT: I 696 LEU cc_start: 0.8472 (mt) cc_final: 0.8220 (mm) REVERT: I 707 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8284 (mt) REVERT: I 712 MET cc_start: 0.8161 (mtp) cc_final: 0.7880 (mtt) REVERT: I 746 VAL cc_start: 0.8691 (p) cc_final: 0.8463 (p) REVERT: I 747 GLU cc_start: 0.7106 (pp20) cc_final: 0.6829 (pp20) REVERT: I 750 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8442 (m) REVERT: I 754 ASN cc_start: 0.8363 (m-40) cc_final: 0.7965 (m-40) REVERT: I 776 GLN cc_start: 0.7694 (mp10) cc_final: 0.7403 (mp10) REVERT: I 783 GLN cc_start: 0.7620 (tm-30) cc_final: 0.7211 (tm-30) REVERT: I 802 ARG cc_start: 0.8139 (ttm-80) cc_final: 0.7661 (ttp80) REVERT: I 827 ASN cc_start: 0.8049 (t0) cc_final: 0.7553 (p0) REVERT: I 830 MET cc_start: 0.7099 (mtm) cc_final: 0.6470 (mmm) REVERT: I 832 GLU cc_start: 0.7605 (tp30) cc_final: 0.7268 (tp30) REVERT: I 833 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8221 (ttmm) REVERT: I 870 GLU cc_start: 0.7286 (tp30) cc_final: 0.6744 (tp30) REVERT: I 878 ASP cc_start: 0.7815 (t0) cc_final: 0.7300 (t0) REVERT: I 909 ASP cc_start: 0.7462 (p0) cc_final: 0.7172 (p0) REVERT: I 917 ARG cc_start: 0.8461 (mtm180) cc_final: 0.8119 (mtm180) REVERT: I 921 GLU cc_start: 0.7708 (tt0) cc_final: 0.7407 (tt0) REVERT: I 940 MET cc_start: 0.7429 (tmm) cc_final: 0.6657 (tmm) REVERT: I 942 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8640 (mmmt) REVERT: I 963 TYR cc_start: 0.8857 (t80) cc_final: 0.7970 (t80) REVERT: J 52 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6692 (mm-30) REVERT: J 58 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7809 (mt0) REVERT: J 64 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7575 (tm-30) REVERT: J 89 GLN cc_start: 0.8110 (mm110) cc_final: 0.7768 (mm110) REVERT: J 91 GLN cc_start: 0.8435 (mt0) cc_final: 0.8218 (mt0) REVERT: J 93 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8339 (tt) REVERT: J 120 GLN cc_start: 0.8117 (tp40) cc_final: 0.7768 (tt0) REVERT: J 140 GLU cc_start: 0.7397 (tm-30) cc_final: 0.7121 (tm-30) REVERT: J 142 GLN cc_start: 0.7447 (pp30) cc_final: 0.7178 (pp30) REVERT: J 143 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.7385 (tp40) REVERT: K 13 GLU cc_start: 0.6952 (tt0) cc_final: 0.6683 (tt0) REVERT: K 22 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.5701 (pp20) REVERT: K 41 GLU cc_start: 0.7138 (tp30) cc_final: 0.6581 (tp30) REVERT: K 52 GLU cc_start: 0.7878 (pp20) cc_final: 0.7272 (pp20) REVERT: K 63 LEU cc_start: 0.8409 (tp) cc_final: 0.8103 (tp) REVERT: K 71 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6265 (pm20) REVERT: K 90 LEU cc_start: 0.7672 (tp) cc_final: 0.7441 (tp) REVERT: K 94 GLU cc_start: 0.7546 (tp30) cc_final: 0.6973 (tp30) outliers start: 154 outliers final: 122 residues processed: 1002 average time/residue: 0.4760 time to fit residues: 719.1589 Evaluate side-chains 1058 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 922 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 219 ASP Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 690 LYS Chi-restraints excluded: chain I residue 707 ILE Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 922 LEU Chi-restraints excluded: chain I residue 935 ASP Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 17 ARG Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 71 GLU Chi-restraints excluded: chain K residue 92 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 305 optimal weight: 0.5980 chunk 322 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 313 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 246 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 283 optimal weight: 0.9990 chunk 296 optimal weight: 0.7980 chunk 312 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN E 290 ASN F 198 ASN F 232 ASN G 43 ASN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 GLN I 81 HIS ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN J 97 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29660 Z= 0.281 Angle : 0.653 9.496 40467 Z= 0.337 Chirality : 0.045 0.348 4565 Planarity : 0.004 0.050 4974 Dihedral : 15.289 179.055 4941 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.88 % Allowed : 22.15 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3399 helix: 1.26 (0.14), residues: 1475 sheet: -0.14 (0.22), residues: 439 loop : -1.02 (0.16), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 154 HIS 0.010 0.001 HIS I 246 PHE 0.035 0.002 PHE E 151 TYR 0.024 0.002 TYR E 138 ARG 0.005 0.000 ARG J 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 926 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 PHE cc_start: 0.8741 (m-80) cc_final: 0.8431 (m-80) REVERT: A 72 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6440 (mp0) REVERT: A 78 GLU cc_start: 0.7319 (tt0) cc_final: 0.7094 (tt0) REVERT: A 155 THR cc_start: 0.8222 (m) cc_final: 0.7956 (t) REVERT: A 156 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7452 (mmm) REVERT: A 243 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7565 (mtp) REVERT: A 253 GLU cc_start: 0.7222 (tp30) cc_final: 0.6982 (tp30) REVERT: A 308 GLN cc_start: 0.7871 (tp40) cc_final: 0.7591 (tp-100) REVERT: B 18 SER cc_start: 0.8115 (m) cc_final: 0.7810 (p) REVERT: B 123 GLU cc_start: 0.7207 (tp30) cc_final: 0.6877 (tp30) REVERT: B 190 GLU cc_start: 0.7838 (mp0) cc_final: 0.7360 (mp0) REVERT: B 253 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6803 (tm-30) REVERT: B 268 LYS cc_start: 0.8521 (mtmm) cc_final: 0.8205 (mtmm) REVERT: B 288 GLU cc_start: 0.7284 (tt0) cc_final: 0.7074 (tt0) REVERT: B 301 LYS cc_start: 0.8392 (ttpt) cc_final: 0.7964 (ttpt) REVERT: B 308 GLN cc_start: 0.7976 (tp40) cc_final: 0.7715 (tp40) REVERT: C 1 MET cc_start: 0.7752 (tpt) cc_final: 0.7174 (tpt) REVERT: C 5 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8032 (mt) REVERT: C 6 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8114 (mtmt) REVERT: C 53 GLU cc_start: 0.6616 (pt0) cc_final: 0.6387 (pt0) REVERT: C 109 ASP cc_start: 0.8140 (t70) cc_final: 0.7869 (t0) REVERT: C 169 LEU cc_start: 0.8595 (tp) cc_final: 0.8331 (tp) REVERT: C 241 ASP cc_start: 0.7621 (t0) cc_final: 0.7408 (t0) REVERT: C 264 ASP cc_start: 0.7222 (t70) cc_final: 0.6921 (t0) REVERT: C 268 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8387 (mtmm) REVERT: C 271 VAL cc_start: 0.8886 (t) cc_final: 0.8633 (p) REVERT: C 275 GLU cc_start: 0.6954 (tt0) cc_final: 0.6595 (tt0) REVERT: C 288 GLU cc_start: 0.6969 (tt0) cc_final: 0.6704 (tt0) REVERT: C 316 GLU cc_start: 0.7478 (tp30) cc_final: 0.7168 (tp30) REVERT: C 317 PHE cc_start: 0.8961 (m-80) cc_final: 0.8681 (m-80) REVERT: D 62 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8488 (p) REVERT: D 78 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6849 (mt-10) REVERT: D 126 LYS cc_start: 0.8475 (mttp) cc_final: 0.8003 (mttp) REVERT: D 127 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8166 (t) REVERT: D 215 MET cc_start: 0.7804 (mtp) cc_final: 0.7572 (mtt) REVERT: D 243 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7523 (mtp) REVERT: D 274 SER cc_start: 0.8548 (t) cc_final: 0.8272 (p) REVERT: D 291 ASP cc_start: 0.7612 (m-30) cc_final: 0.7355 (m-30) REVERT: E 3 ASP cc_start: 0.7871 (p0) cc_final: 0.7558 (p0) REVERT: E 78 GLU cc_start: 0.7144 (tt0) cc_final: 0.6897 (tt0) REVERT: E 90 LYS cc_start: 0.7956 (tppt) cc_final: 0.7738 (tppt) REVERT: E 140 GLN cc_start: 0.8021 (mp10) cc_final: 0.7753 (mp10) REVERT: E 182 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6805 (tm-30) REVERT: E 183 SER cc_start: 0.8085 (t) cc_final: 0.7678 (m) REVERT: E 205 TYR cc_start: 0.7548 (m-80) cc_final: 0.7044 (m-80) REVERT: E 249 LYS cc_start: 0.7970 (mmpt) cc_final: 0.7768 (mmpt) REVERT: E 253 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6763 (tm-30) REVERT: E 269 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7115 (mm-30) REVERT: E 287 GLN cc_start: 0.7199 (tp40) cc_final: 0.6875 (tp40) REVERT: E 288 GLU cc_start: 0.6831 (pt0) cc_final: 0.6500 (pt0) REVERT: E 291 ASP cc_start: 0.6778 (p0) cc_final: 0.6463 (p0) REVERT: E 295 ASN cc_start: 0.8011 (t0) cc_final: 0.7806 (t0) REVERT: F 1 MET cc_start: 0.7972 (tpp) cc_final: 0.7739 (tpp) REVERT: F 6 LYS cc_start: 0.7555 (mtpp) cc_final: 0.7275 (mtpp) REVERT: F 18 SER cc_start: 0.8464 (m) cc_final: 0.7857 (p) REVERT: F 54 LYS cc_start: 0.7551 (mtmm) cc_final: 0.7349 (mtmm) REVERT: F 59 SER cc_start: 0.8709 (m) cc_final: 0.8260 (t) REVERT: F 66 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7570 (mpt180) REVERT: F 97 GLU cc_start: 0.6945 (mt-10) cc_final: 0.6608 (mt-10) REVERT: F 173 LEU cc_start: 0.8305 (tp) cc_final: 0.8048 (tp) REVERT: F 180 THR cc_start: 0.7813 (m) cc_final: 0.7521 (p) REVERT: F 190 GLU cc_start: 0.7166 (mp0) cc_final: 0.6528 (mp0) REVERT: F 209 GLU cc_start: 0.7315 (tt0) cc_final: 0.6788 (tt0) REVERT: F 249 LYS cc_start: 0.8207 (mmmt) cc_final: 0.7862 (mmmt) REVERT: F 295 ASN cc_start: 0.7938 (t0) cc_final: 0.7569 (t0) REVERT: F 312 ASP cc_start: 0.7811 (t0) cc_final: 0.7562 (m-30) REVERT: G 25 LEU cc_start: 0.7937 (mp) cc_final: 0.7617 (mp) REVERT: G 48 GLN cc_start: 0.7063 (pt0) cc_final: 0.6391 (pt0) REVERT: G 54 LYS cc_start: 0.6901 (pttm) cc_final: 0.6452 (pttm) REVERT: G 123 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6759 (mm-30) REVERT: G 177 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.7333 (p) REVERT: G 182 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6893 (mt-10) REVERT: G 216 LYS cc_start: 0.7939 (tppt) cc_final: 0.7519 (tppt) REVERT: G 268 LYS cc_start: 0.7993 (mtmt) cc_final: 0.7506 (mtmt) REVERT: G 272 ARG cc_start: 0.7438 (mtm180) cc_final: 0.6972 (mtm180) REVERT: G 288 GLU cc_start: 0.7792 (tp30) cc_final: 0.7449 (tp30) REVERT: G 295 ASN cc_start: 0.7382 (t0) cc_final: 0.6990 (t0) REVERT: H 13 ASP cc_start: 0.6576 (p0) cc_final: 0.6357 (p0) REVERT: H 228 PHE cc_start: 0.8554 (m-80) cc_final: 0.8238 (m-80) REVERT: I 26 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7394 (mm-40) REVERT: I 34 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7171 (tp30) REVERT: I 83 LEU cc_start: 0.8784 (tp) cc_final: 0.8475 (tt) REVERT: I 84 ASN cc_start: 0.7967 (m-40) cc_final: 0.7516 (m-40) REVERT: I 158 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6774 (ttp80) REVERT: I 220 ASP cc_start: 0.7435 (m-30) cc_final: 0.6976 (m-30) REVERT: I 241 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7425 (mmmt) REVERT: I 273 LYS cc_start: 0.7858 (mmpt) cc_final: 0.7311 (mmpt) REVERT: I 284 TYR cc_start: 0.7458 (m-80) cc_final: 0.6827 (m-80) REVERT: I 496 ARG cc_start: 0.7399 (ttm170) cc_final: 0.7068 (ttt180) REVERT: I 512 GLN cc_start: 0.7535 (tp40) cc_final: 0.7187 (tm-30) REVERT: I 513 GLU cc_start: 0.7229 (tp30) cc_final: 0.6872 (tp30) REVERT: I 574 SER cc_start: 0.8565 (t) cc_final: 0.8044 (p) REVERT: I 577 MET cc_start: 0.7292 (tpt) cc_final: 0.6886 (tpt) REVERT: I 605 TYR cc_start: 0.7093 (m-80) cc_final: 0.6836 (m-80) REVERT: I 620 TYR cc_start: 0.8085 (m-80) cc_final: 0.6904 (m-80) REVERT: I 639 MET cc_start: 0.6916 (mmp) cc_final: 0.6676 (mmp) REVERT: I 668 ASP cc_start: 0.6883 (p0) cc_final: 0.6541 (p0) REVERT: I 686 ASP cc_start: 0.7744 (t0) cc_final: 0.7498 (t0) REVERT: I 696 LEU cc_start: 0.8454 (mt) cc_final: 0.8208 (mm) REVERT: I 707 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8303 (mt) REVERT: I 712 MET cc_start: 0.8144 (mtp) cc_final: 0.7890 (mtt) REVERT: I 746 VAL cc_start: 0.8689 (p) cc_final: 0.8460 (p) REVERT: I 747 GLU cc_start: 0.7096 (pp20) cc_final: 0.6814 (pp20) REVERT: I 750 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8423 (m) REVERT: I 754 ASN cc_start: 0.8358 (m-40) cc_final: 0.7939 (m-40) REVERT: I 772 LYS cc_start: 0.7497 (mptp) cc_final: 0.7166 (mptp) REVERT: I 776 GLN cc_start: 0.7675 (mp10) cc_final: 0.7372 (mp10) REVERT: I 783 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7206 (tm-30) REVERT: I 802 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7743 (ttp80) REVERT: I 825 GLN cc_start: 0.7663 (tp40) cc_final: 0.7272 (tp40) REVERT: I 827 ASN cc_start: 0.8020 (t0) cc_final: 0.7502 (p0) REVERT: I 830 MET cc_start: 0.7100 (mtm) cc_final: 0.6445 (mmm) REVERT: I 832 GLU cc_start: 0.7596 (tp30) cc_final: 0.7257 (tp30) REVERT: I 833 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8220 (ttmm) REVERT: I 870 GLU cc_start: 0.7259 (tp30) cc_final: 0.6719 (tp30) REVERT: I 878 ASP cc_start: 0.7775 (t0) cc_final: 0.7334 (t0) REVERT: I 909 ASP cc_start: 0.7456 (p0) cc_final: 0.7186 (p0) REVERT: I 917 ARG cc_start: 0.8455 (mtm180) cc_final: 0.8111 (mtm180) REVERT: I 921 GLU cc_start: 0.7699 (tt0) cc_final: 0.7382 (tt0) REVERT: I 940 MET cc_start: 0.7406 (tmm) cc_final: 0.6650 (tmm) REVERT: I 942 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8624 (mmmt) REVERT: I 963 TYR cc_start: 0.8857 (t80) cc_final: 0.7947 (t80) REVERT: J 5 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4284 (pt) REVERT: J 52 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6656 (mm-30) REVERT: J 89 GLN cc_start: 0.8130 (mm110) cc_final: 0.7788 (mm110) REVERT: J 120 GLN cc_start: 0.8136 (tp40) cc_final: 0.7790 (tt0) REVERT: J 140 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7185 (tm-30) REVERT: J 142 GLN cc_start: 0.7489 (pp30) cc_final: 0.7205 (pp30) REVERT: J 143 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7404 (tp40) REVERT: K 13 GLU cc_start: 0.6943 (tt0) cc_final: 0.6673 (tt0) REVERT: K 22 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5637 (pp20) REVERT: K 41 GLU cc_start: 0.7149 (tp30) cc_final: 0.6543 (tp30) REVERT: K 44 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8242 (mp) REVERT: K 52 GLU cc_start: 0.7816 (pp20) cc_final: 0.7222 (pp20) REVERT: K 71 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6257 (pm20) REVERT: K 90 LEU cc_start: 0.7664 (tp) cc_final: 0.7434 (tp) REVERT: K 94 GLU cc_start: 0.7538 (tp30) cc_final: 0.6971 (tp30) outliers start: 145 outliers final: 116 residues processed: 981 average time/residue: 0.4798 time to fit residues: 712.2779 Evaluate side-chains 1056 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 925 time to evaluate : 2.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 707 ILE Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 749 ILE Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 922 LEU Chi-restraints excluded: chain I residue 935 ASP Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 17 ARG Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 205 optimal weight: 2.9990 chunk 331 optimal weight: 0.4980 chunk 202 optimal weight: 0.5980 chunk 157 optimal weight: 0.4980 chunk 230 optimal weight: 0.9990 chunk 347 optimal weight: 1.9990 chunk 320 optimal weight: 0.4980 chunk 276 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 213 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 68 GLN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN D 68 GLN E 290 ASN F 198 ASN F 232 ASN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN I 81 HIS ** I 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29660 Z= 0.235 Angle : 0.640 9.371 40467 Z= 0.330 Chirality : 0.044 0.339 4565 Planarity : 0.004 0.049 4974 Dihedral : 15.266 179.402 4938 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.54 % Allowed : 23.02 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3399 helix: 1.34 (0.14), residues: 1468 sheet: -0.14 (0.22), residues: 439 loop : -0.98 (0.16), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 PHE 0.035 0.001 PHE E 151 TYR 0.024 0.002 TYR H 124 ARG 0.006 0.000 ARG J 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6798 Ramachandran restraints generated. 3399 Oldfield, 0 Emsley, 3399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 933 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7080 (mtp) cc_final: 0.6869 (mtp) REVERT: A 36 PHE cc_start: 0.8730 (m-80) cc_final: 0.8419 (m-80) REVERT: A 72 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6420 (mp0) REVERT: A 78 GLU cc_start: 0.7303 (tt0) cc_final: 0.7068 (tt0) REVERT: A 155 THR cc_start: 0.8214 (m) cc_final: 0.7944 (t) REVERT: A 156 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7459 (mmm) REVERT: A 243 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7554 (mtp) REVERT: A 253 GLU cc_start: 0.7204 (tp30) cc_final: 0.6974 (tp30) REVERT: A 308 GLN cc_start: 0.7872 (tp40) cc_final: 0.7590 (tp-100) REVERT: B 18 SER cc_start: 0.8084 (m) cc_final: 0.7816 (p) REVERT: B 123 GLU cc_start: 0.7212 (tp30) cc_final: 0.6831 (tp30) REVERT: B 128 TYR cc_start: 0.8242 (m-10) cc_final: 0.7951 (m-80) REVERT: B 175 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6827 (mt-10) REVERT: B 190 GLU cc_start: 0.7818 (mp0) cc_final: 0.7365 (mp0) REVERT: B 253 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6793 (tm-30) REVERT: B 268 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8190 (mtmm) REVERT: B 272 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7803 (mtm180) REVERT: B 288 GLU cc_start: 0.7274 (tt0) cc_final: 0.7065 (tt0) REVERT: B 301 LYS cc_start: 0.8407 (ttpt) cc_final: 0.7965 (ttpt) REVERT: B 308 GLN cc_start: 0.7980 (tp40) cc_final: 0.7710 (tp40) REVERT: C 1 MET cc_start: 0.7740 (tpt) cc_final: 0.7119 (tpt) REVERT: C 5 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8021 (mt) REVERT: C 6 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8098 (mtmt) REVERT: C 53 GLU cc_start: 0.6605 (pt0) cc_final: 0.6374 (pt0) REVERT: C 109 ASP cc_start: 0.8120 (t70) cc_final: 0.7849 (t0) REVERT: C 169 LEU cc_start: 0.8580 (tp) cc_final: 0.8313 (tp) REVERT: C 241 ASP cc_start: 0.7617 (t0) cc_final: 0.7405 (t0) REVERT: C 264 ASP cc_start: 0.7221 (t70) cc_final: 0.6705 (t0) REVERT: C 268 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8117 (mttm) REVERT: C 271 VAL cc_start: 0.8887 (t) cc_final: 0.8660 (p) REVERT: C 275 GLU cc_start: 0.7025 (tt0) cc_final: 0.6672 (tt0) REVERT: C 288 GLU cc_start: 0.6953 (tt0) cc_final: 0.6693 (tt0) REVERT: C 316 GLU cc_start: 0.7474 (tp30) cc_final: 0.7169 (tp30) REVERT: C 317 PHE cc_start: 0.8949 (m-80) cc_final: 0.8690 (m-80) REVERT: D 62 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8447 (p) REVERT: D 126 LYS cc_start: 0.8446 (mttp) cc_final: 0.7989 (mttp) REVERT: D 127 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8115 (t) REVERT: D 215 MET cc_start: 0.7802 (mtp) cc_final: 0.7558 (mtt) REVERT: D 243 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7531 (mtp) REVERT: D 274 SER cc_start: 0.8555 (t) cc_final: 0.8270 (p) REVERT: D 291 ASP cc_start: 0.7593 (m-30) cc_final: 0.7360 (m-30) REVERT: E 46 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7509 (mtp85) REVERT: E 140 GLN cc_start: 0.8008 (mp10) cc_final: 0.7733 (mp10) REVERT: E 182 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6804 (tm-30) REVERT: E 183 SER cc_start: 0.8069 (t) cc_final: 0.7666 (m) REVERT: E 190 GLU cc_start: 0.7307 (mp0) cc_final: 0.6858 (mp0) REVERT: E 205 TYR cc_start: 0.7430 (m-80) cc_final: 0.6913 (m-80) REVERT: E 253 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6733 (tm-30) REVERT: E 269 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7116 (mm-30) REVERT: E 295 ASN cc_start: 0.7950 (t0) cc_final: 0.7749 (t0) REVERT: F 6 LYS cc_start: 0.7545 (mtpp) cc_final: 0.7271 (mtpp) REVERT: F 18 SER cc_start: 0.8450 (m) cc_final: 0.7829 (p) REVERT: F 54 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7336 (mtmm) REVERT: F 59 SER cc_start: 0.8712 (m) cc_final: 0.8263 (t) REVERT: F 97 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6574 (mt-10) REVERT: F 173 LEU cc_start: 0.8271 (tp) cc_final: 0.8041 (tt) REVERT: F 180 THR cc_start: 0.7793 (m) cc_final: 0.7501 (p) REVERT: F 190 GLU cc_start: 0.7126 (mp0) cc_final: 0.6579 (mp0) REVERT: F 209 GLU cc_start: 0.7372 (tt0) cc_final: 0.6790 (tt0) REVERT: F 249 LYS cc_start: 0.8208 (mmmt) cc_final: 0.7463 (mmmt) REVERT: F 253 GLU cc_start: 0.7106 (tm-30) cc_final: 0.6526 (tm-30) REVERT: F 295 ASN cc_start: 0.7920 (t0) cc_final: 0.7560 (t0) REVERT: F 312 ASP cc_start: 0.7813 (t0) cc_final: 0.7565 (m-30) REVERT: F 313 TYR cc_start: 0.8706 (t80) cc_final: 0.8496 (t80) REVERT: G 25 LEU cc_start: 0.7863 (mp) cc_final: 0.7582 (mp) REVERT: G 123 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6758 (mm-30) REVERT: G 177 THR cc_start: 0.7495 (OUTLIER) cc_final: 0.7268 (p) REVERT: G 216 LYS cc_start: 0.7934 (tppt) cc_final: 0.7513 (tppt) REVERT: G 268 LYS cc_start: 0.8005 (mtmt) cc_final: 0.7529 (mtmt) REVERT: G 272 ARG cc_start: 0.7457 (mtm180) cc_final: 0.6976 (mtm180) REVERT: G 288 GLU cc_start: 0.7782 (tp30) cc_final: 0.7494 (tp30) REVERT: G 295 ASN cc_start: 0.7332 (t0) cc_final: 0.6929 (t0) REVERT: H 13 ASP cc_start: 0.6593 (p0) cc_final: 0.6368 (p0) REVERT: H 59 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7726 (mm110) REVERT: H 228 PHE cc_start: 0.8489 (m-80) cc_final: 0.8164 (m-80) REVERT: I 26 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7390 (mm-40) REVERT: I 34 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7165 (tp30) REVERT: I 83 LEU cc_start: 0.8761 (tp) cc_final: 0.8449 (tt) REVERT: I 84 ASN cc_start: 0.7954 (m-40) cc_final: 0.7508 (m-40) REVERT: I 158 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6761 (ttp80) REVERT: I 220 ASP cc_start: 0.7385 (m-30) cc_final: 0.6926 (m-30) REVERT: I 241 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7426 (mmmt) REVERT: I 273 LYS cc_start: 0.7851 (mmpt) cc_final: 0.7304 (mmpt) REVERT: I 284 TYR cc_start: 0.7422 (m-80) cc_final: 0.6733 (m-80) REVERT: I 496 ARG cc_start: 0.7370 (ttm170) cc_final: 0.7033 (ttt180) REVERT: I 511 ILE cc_start: 0.8068 (mp) cc_final: 0.7864 (mt) REVERT: I 512 GLN cc_start: 0.7526 (tp40) cc_final: 0.7203 (tm-30) REVERT: I 574 SER cc_start: 0.8534 (t) cc_final: 0.8016 (p) REVERT: I 576 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7210 (tp30) REVERT: I 577 MET cc_start: 0.7256 (tpt) cc_final: 0.6771 (tpt) REVERT: I 580 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7961 (mtt90) REVERT: I 605 TYR cc_start: 0.7082 (m-80) cc_final: 0.6844 (m-80) REVERT: I 620 TYR cc_start: 0.8034 (m-80) cc_final: 0.6856 (m-80) REVERT: I 639 MET cc_start: 0.6912 (mmp) cc_final: 0.6651 (mmp) REVERT: I 668 ASP cc_start: 0.6851 (p0) cc_final: 0.6523 (p0) REVERT: I 686 ASP cc_start: 0.7749 (t0) cc_final: 0.7541 (t0) REVERT: I 696 LEU cc_start: 0.8430 (mt) cc_final: 0.8191 (mm) REVERT: I 707 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8290 (mt) REVERT: I 712 MET cc_start: 0.8172 (mtp) cc_final: 0.7909 (mtm) REVERT: I 746 VAL cc_start: 0.8683 (p) cc_final: 0.8416 (t) REVERT: I 747 GLU cc_start: 0.7077 (pp20) cc_final: 0.6789 (pp20) REVERT: I 750 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8421 (m) REVERT: I 754 ASN cc_start: 0.8395 (m-40) cc_final: 0.7981 (m-40) REVERT: I 772 LYS cc_start: 0.7520 (mptp) cc_final: 0.7244 (mptp) REVERT: I 776 GLN cc_start: 0.7658 (mp10) cc_final: 0.7339 (mp10) REVERT: I 783 GLN cc_start: 0.7612 (tm-30) cc_final: 0.7202 (tm-30) REVERT: I 802 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7867 (ttp80) REVERT: I 825 GLN cc_start: 0.7639 (tp40) cc_final: 0.7235 (tp40) REVERT: I 827 ASN cc_start: 0.7989 (t0) cc_final: 0.7493 (p0) REVERT: I 830 MET cc_start: 0.7097 (mtm) cc_final: 0.6416 (mmm) REVERT: I 832 GLU cc_start: 0.7583 (tp30) cc_final: 0.7246 (tp30) REVERT: I 833 LYS cc_start: 0.8424 (ttmt) cc_final: 0.8196 (ttmm) REVERT: I 870 GLU cc_start: 0.7232 (tp30) cc_final: 0.6678 (tp30) REVERT: I 878 ASP cc_start: 0.7763 (t0) cc_final: 0.7319 (t0) REVERT: I 909 ASP cc_start: 0.7445 (p0) cc_final: 0.7189 (p0) REVERT: I 917 ARG cc_start: 0.8447 (mtm180) cc_final: 0.8109 (mtm180) REVERT: I 921 GLU cc_start: 0.7664 (tt0) cc_final: 0.7356 (tt0) REVERT: I 940 MET cc_start: 0.7394 (tmm) cc_final: 0.6742 (tmm) REVERT: I 942 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8620 (mmmt) REVERT: I 963 TYR cc_start: 0.8853 (t80) cc_final: 0.8194 (t80) REVERT: J 5 LEU cc_start: 0.5240 (OUTLIER) cc_final: 0.4327 (pt) REVERT: J 52 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6638 (mm-30) REVERT: J 89 GLN cc_start: 0.8115 (mm110) cc_final: 0.7792 (mm110) REVERT: J 120 GLN cc_start: 0.8124 (tp40) cc_final: 0.7790 (tt0) REVERT: J 140 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7135 (tm-30) REVERT: J 142 GLN cc_start: 0.7500 (pp30) cc_final: 0.7215 (pp30) REVERT: J 143 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7379 (tp40) REVERT: K 13 GLU cc_start: 0.6904 (tt0) cc_final: 0.6651 (tt0) REVERT: K 22 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5697 (pp20) REVERT: K 41 GLU cc_start: 0.7127 (tp30) cc_final: 0.6497 (tp30) REVERT: K 52 GLU cc_start: 0.7797 (pp20) cc_final: 0.7210 (pp20) REVERT: K 63 LEU cc_start: 0.8391 (tp) cc_final: 0.8082 (tp) REVERT: K 71 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6254 (pm20) REVERT: K 90 LEU cc_start: 0.7674 (tp) cc_final: 0.7439 (tp) REVERT: K 94 GLU cc_start: 0.7531 (tp30) cc_final: 0.6959 (tp30) outliers start: 135 outliers final: 114 residues processed: 980 average time/residue: 0.5335 time to fit residues: 800.4700 Evaluate side-chains 1061 residues out of total 2975 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 934 time to evaluate : 3.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 228 GLU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 MET Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 218 HIS Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 26 MET Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLU Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 290 ASN Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 2 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 LYS Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 287 GLN Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 266 LEU Chi-restraints excluded: chain G residue 287 GLN Chi-restraints excluded: chain H residue 24 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 56 GLN Chi-restraints excluded: chain H residue 135 GLU Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 154 TRP Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 270 LEU Chi-restraints excluded: chain I residue 487 ARG Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 607 TYR Chi-restraints excluded: chain I residue 633 HIS Chi-restraints excluded: chain I residue 635 VAL Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 707 ILE Chi-restraints excluded: chain I residue 715 LEU Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 755 LYS Chi-restraints excluded: chain I residue 768 SER Chi-restraints excluded: chain I residue 780 LYS Chi-restraints excluded: chain I residue 835 LYS Chi-restraints excluded: chain I residue 844 TYR Chi-restraints excluded: chain I residue 874 SER Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 922 LEU Chi-restraints excluded: chain I residue 935 ASP Chi-restraints excluded: chain I residue 971 GLN Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain J residue 71 GLU Chi-restraints excluded: chain J residue 143 GLN Chi-restraints excluded: chain K residue 22 GLU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 71 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 349 random chunks: chunk 219 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 84 optimal weight: 0.0170 chunk 255 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 ASN D 68 GLN D 295 ASN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN F 232 ASN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 217 GLN I 81 HIS I 949 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.114476 restraints weight = 43803.348| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.92 r_work: 0.3356 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29660 Z= 0.251 Angle : 0.649 15.208 40467 Z= 0.333 Chirality : 0.044 0.336 4565 Planarity : 0.004 0.049 4974 Dihedral : 15.233 179.405 4934 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.58 % Allowed : 23.26 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3399 helix: 1.34 (0.14), residues: 1468 sheet: -0.16 (0.22), residues: 432 loop : -0.97 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP I 154 HIS 0.009 0.001 HIS I 246 PHE 0.035 0.001 PHE E 151 TYR 0.024 0.002 TYR H 124 ARG 0.006 0.000 ARG J 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11304.83 seconds wall clock time: 203 minutes 14.23 seconds (12194.23 seconds total)