Starting phenix.real_space_refine on Wed Feb 21 12:05:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sba_24974/02_2024/7sba_24974.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sba_24974/02_2024/7sba_24974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sba_24974/02_2024/7sba_24974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sba_24974/02_2024/7sba_24974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sba_24974/02_2024/7sba_24974.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sba_24974/02_2024/7sba_24974.pdb" } resolution = 2.9 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 69 5.49 5 S 117 5.16 5 C 19153 2.51 5 N 5247 2.21 5 O 6065 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 97": "OE1" <-> "OE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 139": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "C GLU 53": "OE1" <-> "OE2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 101": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "D GLU 53": "OE1" <-> "OE2" Residue "D ARG 66": "NH1" <-> "NH2" Residue "D ARG 73": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 246": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D GLU 298": "OE1" <-> "OE2" 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 TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E GLU 182": "OE1" <-> "OE2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E GLU 316": "OE1" <-> "OE2" Residue "F ARG 66": "NH1" <-> "NH2" Residue "F ARG 73": "NH1" <-> "NH2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F GLU 182": "OE1" <-> "OE2" Residue "F ARG 185": "NH1" <-> "NH2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 209": "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 GLU 27": "OE1" <-> "OE2" Residue "H ARG 66": "NH1" <-> "NH2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "I GLU 15": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I GLU 95": "OE1" <-> "OE2" Residue "I ARG 105": "NH1" <-> "NH2" Residue "I TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 195": "OE1" <-> "OE2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I ARG 249": "NH1" <-> "NH2" Residue "I GLU 294": "OE1" <-> "OE2" Residue "I GLU 309": "OE1" <-> "OE2" Residue "I GLU 368": "OE1" <-> "OE2" Residue "I GLU 371": "OE1" <-> "OE2" Residue "I GLU 426": "OE1" <-> "OE2" Residue "I GLU 427": "OE1" <-> "OE2" Residue "I GLU 456": "OE1" <-> "OE2" Residue "I GLU 474": "OE1" <-> "OE2" Residue "I GLU 475": "OE1" <-> "OE2" Residue "I GLU 476": "OE1" <-> "OE2" Residue "I ARG 496": "NH1" <-> "NH2" Residue "I GLU 513": "OE1" <-> "OE2" Residue "I GLU 515": "OE1" <-> "OE2" Residue "I GLU 536": "OE1" <-> "OE2" Residue "I GLU 576": "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 GLU 784": "OE1" <-> "OE2" Residue "I GLU 797": "OE1" <-> "OE2" Residue "I ARG 805": "NH1" <-> "NH2" Residue "I ARG 807": "NH1" <-> "NH2" Residue "I GLU 812": "OE1" <-> "OE2" Residue "I GLU 842": "OE1" <-> "OE2" Residue "I GLU 870": "OE1" <-> "OE2" Residue "I GLU 900": "OE1" <-> "OE2" Residue "I GLU 921": "OE1" <-> "OE2" Residue "I GLU 923": "OE1" <-> "OE2" Residue "I ARG 952": "NH1" <-> "NH2" Residue "I GLU 969": "OE1" <-> "OE2" Residue "J GLU 3": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J ARG 123": "NH1" <-> "NH2" Residue "K GLU 13": "OE1" <-> "OE2" Residue "K GLU 14": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K GLU 41": "OE1" <-> "OE2" Residue "K GLU 71": "OE1" <-> "OE2" Residue "K ARG 123": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30651 Number of models: 1 Model: "" Number of chains: 14 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: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1929 Classifications: {'peptide': 238} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 223} Chain: "I" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7323 Classifications: {'peptide': 899} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 39, 'TRANS': 859} Chain breaks: 4 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: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "Y" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 12} 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': 8, 'rna2p_pyr': 12, 'rna3p_pur': 10, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 23} Time building chain proxies: 14.40, per 1000 atoms: 0.47 Number of scatterers: 30651 At special positions: 0 Unit cell: (135.85, 127.49, 230.945, 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 117 16.00 P 69 15.00 O 6065 8.00 N 5247 7.00 C 19153 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: 10.80 Conformation dependent library (CDL) restraints added in 4.9 seconds 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6852 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 40 sheets defined 46.5% alpha, 15.1% beta 12 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 10.02 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: 3.590A pdb=" N ALA A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.766A 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 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.689A 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 7 through 9 No H-bonds generated for 'chain 'B' and resid 7 through 9' Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.595A pdb=" N GLN B 68 " --> pdb=" O LYS B 65 " (cutoff:3.500A) 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 243 Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.568A pdb=" N THR B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 294 removed outlier: 3.942A pdb=" N GLN B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 292 " --> pdb=" O GLU B 288 " (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 64 through 68 removed outlier: 4.087A 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 140 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: 3.703A pdb=" N ASP C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 294 removed outlier: 3.612A pdb=" N GLU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 317 removed outlier: 3.689A pdb=" N LYS C 301 " --> pdb=" O ALA C 297 " (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 65 through 83 removed outlier: 3.779A pdb=" N THR D 69 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Proline residue: D 71 - end of helix 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 Processing helix chain 'D' and resid 279 through 295 removed outlier: 3.567A pdb=" N ILE D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) 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: 4.091A pdb=" N GLN E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Proline residue: E 71 - end of helix 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: 3.952A 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 removed outlier: 3.511A pdb=" N ALA F 75 " --> pdb=" O PRO F 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) 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 Processing helix chain 'F' and resid 295 through 317 removed outlier: 3.638A pdb=" N LEU F 299 " --> pdb=" O ASN F 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.513A 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: 3.632A 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: 3.519A pdb=" N LEU G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.966A 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: 3.942A 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: 4.514A 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 55 through 59 Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.113A pdb=" N ARG I 11 " --> pdb=" O THR I 7 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU I 13 " --> pdb=" O LEU I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 17 removed outlier: 3.568A pdb=" N LYS I 17 " --> pdb=" O SER I 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 14 through 17' Processing helix chain 'I' and resid 18 through 36 removed outlier: 3.612A pdb=" N LEU I 22 " --> pdb=" O ASP I 18 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU I 29 " --> pdb=" O PHE I 25 " (cutoff:3.500A) Proline residue: I 30 - end of helix removed outlier: 3.789A pdb=" N GLU I 34 " --> pdb=" O PRO I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 94 Processing helix chain 'I' and resid 101 through 115 removed outlier: 3.829A pdb=" N ARG I 106 " --> pdb=" O ASP I 102 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR I 113 " --> pdb=" O CYS I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 148 removed outlier: 3.526A pdb=" N ASN I 139 " --> pdb=" O GLN I 135 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 154 removed outlier: 4.011A pdb=" N PHE I 153 " --> pdb=" O ASN I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 155 through 159 removed outlier: 4.193A pdb=" N ARG I 158 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 167 Processing helix chain 'I' and resid 195 through 213 removed outlier: 3.880A pdb=" N ASP I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 201 - end of helix removed outlier: 3.807A pdb=" N VAL I 211 " --> pdb=" O THR I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 222 removed outlier: 3.784A pdb=" N LEU I 221 " --> pdb=" O PRO I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 237 removed outlier: 3.850A pdb=" N GLY I 227 " --> pdb=" O SER I 223 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP I 228 " --> pdb=" O SER I 224 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 230 " --> pdb=" O MET I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 268 Processing helix chain 'I' and resid 269 through 271 No H-bonds generated for 'chain 'I' and resid 269 through 271' Processing helix chain 'I' and resid 294 through 317 removed outlier: 3.723A pdb=" N GLN I 300 " --> pdb=" O ASN I 296 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS I 313 " --> pdb=" O GLU I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 338 Processing helix chain 'I' and resid 339 through 355 removed outlier: 3.802A pdb=" N VAL I 344 " --> pdb=" O ALA I 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG I 345 " --> pdb=" O ALA I 341 " (cutoff:3.500A) Proline residue: I 348 - end of helix removed outlier: 3.605A pdb=" N SER I 352 " --> pdb=" O PRO I 348 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL I 353 " --> pdb=" O GLN I 349 " (cutoff:3.500A) Processing helix chain 'I' and resid 361 through 371 removed outlier: 4.683A pdb=" N LYS I 365 " --> pdb=" O PRO I 361 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS I 369 " --> pdb=" O LYS I 365 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU I 371 " --> pdb=" O LEU I 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 376 through 382 removed outlier: 3.659A pdb=" N LEU I 380 " --> pdb=" O GLU I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 402 removed outlier: 3.622A pdb=" N ASP I 389 " --> pdb=" O ASP I 385 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU I 391 " --> pdb=" O ARG I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 406 through 417 removed outlier: 4.069A pdb=" N TRP I 412 " --> pdb=" O PRO I 408 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS I 415 " --> pdb=" O GLU I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 Processing helix chain 'I' and resid 436 through 450 removed outlier: 4.393A pdb=" N TYR I 440 " --> pdb=" O ASN I 436 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG I 441 " --> pdb=" O TYR I 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 477 removed outlier: 3.688A pdb=" N GLY I 464 " --> pdb=" O GLU I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 484 through 497 removed outlier: 4.020A pdb=" N GLN I 488 " --> pdb=" O SER I 484 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 519 Processing helix chain 'I' and resid 571 through 585 Processing helix chain 'I' and resid 591 through 595 Processing helix chain 'I' and resid 608 through 620 Processing helix chain 'I' and resid 626 through 636 removed outlier: 3.819A pdb=" N VAL I 630 " --> pdb=" O ASN I 626 " (cutoff:3.500A) Processing helix chain 'I' and resid 640 through 647 Processing helix chain 'I' and resid 683 through 703 removed outlier: 5.399A 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: 3.720A pdb=" N GLU I 724 " --> pdb=" O ASP I 721 " (cutoff:3.500A) Processing helix chain 'I' and resid 733 through 738 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: 3.694A pdb=" N THR I 814 " --> pdb=" O GLU I 810 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP I 817 " --> pdb=" O VAL I 813 " (cutoff:3.500A) Processing helix chain 'I' and resid 827 through 845 removed outlier: 3.668A 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 removed outlier: 3.640A pdb=" N GLN I 871 " --> pdb=" O LYS I 867 " (cutoff:3.500A) Processing helix chain 'I' and resid 880 through 897 removed outlier: 4.063A 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 904 Processing helix chain 'I' and resid 913 through 935 Processing helix chain 'I' and resid 944 through 974 removed outlier: 3.582A pdb=" N GLN I 951 " --> pdb=" O ILE I 947 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ASN I 953 " --> pdb=" O GLN I 949 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ARG I 954 " --> pdb=" O GLU I 950 " (cutoff:3.500A) Processing helix chain 'J' and resid 1 through 5 removed outlier: 3.641A pdb=" N LEU J 5 " --> pdb=" O THR J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 17 removed outlier: 3.652A 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 removed outlier: 3.511A pdb=" N LEU J 33 " --> pdb=" O THR J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 46 Processing helix chain 'J' and resid 51 through 68 removed outlier: 3.527A pdb=" N GLN J 58 " --> pdb=" O GLU J 54 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA J 66 " --> pdb=" O GLN J 62 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP J 68 " --> pdb=" O GLN J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 70 No H-bonds generated for 'chain 'J' and resid 69 through 70' Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'J' and resid 84 through 106 removed outlier: 3.516A pdb=" N GLN J 89 " --> pdb=" O TYR J 85 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU J 94 " --> pdb=" O LEU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 145 removed outlier: 5.331A pdb=" N ASN J 124 " --> pdb=" O GLN J 120 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ARG J 125 " --> pdb=" O GLU J 121 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA J 130 " --> pdb=" O ILE J 126 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN J 142 " --> pdb=" O ALA J 138 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLN J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 17 removed outlier: 4.620A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL K 12 " --> pdb=" O THR K 8 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG K 17 " --> pdb=" O GLU K 13 " (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 67 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 removed outlier: 3.617A pdb=" N LEU K 90 " --> pdb=" O GLU K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 121 Processing helix chain 'K' and resid 122 through 144 removed outlier: 3.547A pdb=" N ARG K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU K 140 " --> pdb=" O LEU K 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 removed outlier: 6.808A pdb=" N TYR A 21 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A 224 " --> pdb=" O TYR A 21 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HIS A 23 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE A 222 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 25 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A 214 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.718A 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: 3.601A pdb=" N THR A 38 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 41 " --> pdb=" O THR A 38 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 6.224A 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: 6.918A pdb=" N TYR B 21 " --> pdb=" O PHE B 224 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N PHE B 224 " --> pdb=" O TYR B 21 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS B 23 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE B 222 " --> pdb=" O HIS B 23 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU B 25 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.000A 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: 3.970A pdb=" N THR B 38 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.795A 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: 6.867A pdb=" N TYR C 21 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N PHE C 224 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N HIS C 23 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE C 222 " --> pdb=" O HIS C 23 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU C 25 " --> pdb=" O VAL C 220 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR C 214 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.562A 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: 4.242A pdb=" N THR C 38 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.820A 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 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 127 through 128 removed outlier: 6.964A pdb=" N TYR D 21 " --> pdb=" O PHE D 224 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE D 224 " --> pdb=" O TYR D 21 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N HIS D 23 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE D 222 " --> pdb=" O HIS D 23 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU D 25 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 3.762A 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 115 through 116 Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 148 Processing sheet with id=AC2, first strand: chain 'E' and resid 127 through 128 removed outlier: 6.898A pdb=" N TYR E 21 " --> pdb=" O PHE E 224 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE E 224 " --> pdb=" O TYR E 21 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N HIS E 23 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE E 222 " --> pdb=" O HIS E 23 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU E 25 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 44 through 47 Processing sheet with id=AC4, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AC5, first strand: chain 'E' and resid 142 through 148 Processing sheet with id=AC6, first strand: chain 'F' and resid 127 through 128 removed outlier: 6.914A pdb=" N TYR F 21 " --> pdb=" O PHE F 224 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N PHE F 224 " --> pdb=" O TYR F 21 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N HIS F 23 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE F 222 " --> pdb=" O HIS F 23 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU F 25 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU F 275 " --> pdb=" O PHE F 224 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 44 through 48 Processing sheet with id=AC8, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.834A pdb=" N GLY F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 142 through 146 Processing sheet with id=AD1, 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: 5.459A pdb=" N ASN G 217 " --> pdb=" O HIS G 29 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU G 275 " --> pdb=" O PHE G 224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 44 through 47 removed outlier: 6.550A 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=AD3, first strand: chain 'G' and resid 115 through 116 Processing sheet with id=AD4, first strand: chain 'G' and resid 142 through 146 Processing sheet with id=AD5, first strand: chain 'H' and resid 80 through 82 removed outlier: 6.448A pdb=" N LEU H 137 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AD7, first strand: chain 'H' and resid 20 through 22 Processing sheet with id=AD8, first strand: chain 'H' and resid 174 through 181 removed outlier: 6.959A pdb=" N ASN H 201 " --> pdb=" O SER H 212 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N SER H 214 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU H 199 " --> pdb=" O SER H 214 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU H 216 " --> pdb=" O ILE H 197 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE H 197 " --> pdb=" O LEU H 216 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY H 218 " --> pdb=" O GLN H 195 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLN H 195 " --> pdb=" O GLY H 218 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 174 through 181 removed outlier: 6.985A pdb=" N THR H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 273 through 278 removed outlier: 6.779A pdb=" N ILE I 283 " --> pdb=" O LEU I 275 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N PHE I 277 " --> pdb=" O GLY I 281 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLY I 281 " --> pdb=" O PHE I 277 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 321 through 322 Processing sheet with id=AE3, first strand: chain 'I' and resid 539 through 541 Processing sheet with id=AE4, first strand: chain 'I' and resid 674 through 677 removed outlier: 3.688A pdb=" N ILE I 597 " --> pdb=" O THR I 677 " (cutoff:3.500A) 1366 hydrogen bonds defined for protein. 3897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 29 hydrogen bonds 58 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 10.54 Time building geometry restraints manager: 11.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 5032 1.27 - 1.41: 8333 1.41 - 1.55: 17627 1.55 - 1.69: 221 1.69 - 1.82: 186 Bond restraints: 31399 Sorted by residual: bond pdb=" C TYR E 313 " pdb=" O TYR E 313 " ideal model delta sigma weight residual 1.237 1.135 0.102 1.17e-02 7.31e+03 7.53e+01 bond pdb=" C TYR A 313 " pdb=" O TYR A 313 " ideal model delta sigma weight residual 1.237 1.143 0.094 1.19e-02 7.06e+03 6.21e+01 bond pdb=" C TYR C 313 " pdb=" O TYR C 313 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.17e-02 7.31e+03 5.92e+01 bond pdb=" C TYR B 313 " pdb=" O TYR B 313 " ideal model delta sigma weight residual 1.236 1.153 0.084 1.15e-02 7.56e+03 5.31e+01 bond pdb=" C PHE D 115 " pdb=" O PHE D 115 " ideal model delta sigma weight residual 1.234 1.150 0.084 1.20e-02 6.94e+03 4.93e+01 ... (remaining 31394 not shown) Histogram of bond angle deviations from ideal: 90.87 - 99.96: 61 99.96 - 109.06: 4326 109.06 - 118.15: 18643 118.15 - 127.25: 19304 127.25 - 136.34: 447 Bond angle restraints: 42781 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 109.24 90.87 18.37 1.63e+00 3.76e-01 1.27e+02 angle pdb=" O3' DT Y 13 " pdb=" C3' DT Y 13 " pdb=" C2' DT Y 13 " ideal model delta sigma weight residual 111.50 126.62 -15.12 1.50e+00 4.44e-01 1.02e+02 angle pdb=" C LYS J 26 " pdb=" CA LYS J 26 " pdb=" CB LYS J 26 " ideal model delta sigma weight residual 111.20 117.76 -6.56 7.10e-01 1.98e+00 8.55e+01 angle pdb=" CA ASP A 130 " pdb=" CB ASP A 130 " pdb=" CG ASP A 130 " ideal model delta sigma weight residual 112.60 121.75 -9.15 1.00e+00 1.00e+00 8.37e+01 angle pdb=" C5' A Z 37 " pdb=" C4' A Z 37 " pdb=" C3' A Z 37 " ideal model delta sigma weight residual 115.20 102.85 12.35 1.50e+00 4.44e-01 6.77e+01 ... (remaining 42776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 18190 33.25 - 66.50: 609 66.50 - 99.74: 113 99.74 - 132.99: 4 132.99 - 166.24: 3 Dihedral angle restraints: 18919 sinusoidal: 8268 harmonic: 10651 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 200.00 37.15 162.85 1 1.50e+01 4.44e-03 8.34e+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 69.86 130.14 1 1.50e+01 4.44e-03 7.02e+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 72.57 127.43 1 1.50e+01 4.44e-03 6.86e+01 ... (remaining 18916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.258: 4615 0.258 - 0.515: 167 0.515 - 0.773: 4 0.773 - 1.030: 0 1.030 - 1.288: 1 Chirality restraints: 4787 Sorted by residual: chirality pdb=" C3' DT Y 13 " pdb=" C4' DT Y 13 " pdb=" O3' DT Y 13 " pdb=" C2' DT Y 13 " both_signs ideal model delta sigma weight residual False -2.66 -1.37 -1.29 2.00e-01 2.50e+01 4.15e+01 chirality pdb=" CA ARG G 211 " pdb=" N ARG G 211 " pdb=" C ARG G 211 " pdb=" CB ARG G 211 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CA LYS J 6 " pdb=" N LYS J 6 " pdb=" C LYS J 6 " pdb=" CB LYS J 6 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.45e+00 ... (remaining 4784 not shown) Planarity restraints: 5308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA X 3 " 0.320 2.00e-02 2.50e+03 1.41e-01 5.48e+02 pdb=" N9 DA X 3 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA X 3 " -0.091 2.00e-02 2.50e+03 pdb=" N7 DA X 3 " -0.117 2.00e-02 2.50e+03 pdb=" C5 DA X 3 " -0.083 2.00e-02 2.50e+03 pdb=" C6 DA X 3 " 0.039 2.00e-02 2.50e+03 pdb=" N6 DA X 3 " 0.223 2.00e-02 2.50e+03 pdb=" N1 DA X 3 " 0.046 2.00e-02 2.50e+03 pdb=" C2 DA X 3 " -0.077 2.00e-02 2.50e+03 pdb=" N3 DA X 3 " -0.124 2.00e-02 2.50e+03 pdb=" C4 DA X 3 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G Z 13 " 0.299 2.00e-02 2.50e+03 1.23e-01 4.52e+02 pdb=" N9 G Z 13 " -0.047 2.00e-02 2.50e+03 pdb=" C8 G Z 13 " -0.149 2.00e-02 2.50e+03 pdb=" N7 G Z 13 " -0.112 2.00e-02 2.50e+03 pdb=" C5 G Z 13 " -0.029 2.00e-02 2.50e+03 pdb=" C6 G Z 13 " 0.063 2.00e-02 2.50e+03 pdb=" O6 G Z 13 " 0.150 2.00e-02 2.50e+03 pdb=" N1 G Z 13 " 0.082 2.00e-02 2.50e+03 pdb=" C2 G Z 13 " -0.022 2.00e-02 2.50e+03 pdb=" N2 G Z 13 " -0.108 2.00e-02 2.50e+03 pdb=" N3 G Z 13 " -0.065 2.00e-02 2.50e+03 pdb=" C4 G Z 13 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C Z 32 " -0.215 2.00e-02 2.50e+03 1.18e-01 3.15e+02 pdb=" N1 C Z 32 " -0.004 2.00e-02 2.50e+03 pdb=" C2 C Z 32 " 0.019 2.00e-02 2.50e+03 pdb=" O2 C Z 32 " 0.153 2.00e-02 2.50e+03 pdb=" N3 C Z 32 " -0.049 2.00e-02 2.50e+03 pdb=" C4 C Z 32 " -0.030 2.00e-02 2.50e+03 pdb=" N4 C Z 32 " -0.136 2.00e-02 2.50e+03 pdb=" C5 C Z 32 " 0.129 2.00e-02 2.50e+03 pdb=" C6 C Z 32 " 0.133 2.00e-02 2.50e+03 ... (remaining 5305 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 114 2.61 - 3.19: 25668 3.19 - 3.76: 48991 3.76 - 4.33: 69776 4.33 - 4.90: 113682 Nonbonded interactions: 258231 Sorted by model distance: nonbonded pdb=" O PRO I 770 " pdb=" C7 DT Y 13 " model vdw 2.044 3.460 nonbonded pdb=" ND1 HIS E 23 " pdb=" OG SER E 183 " model vdw 2.083 2.520 nonbonded pdb=" NH2 ARG D 28 " pdb=" OE2 GLU D 72 " model vdw 2.216 2.520 nonbonded pdb=" NE2 GLN B 10 " pdb=" OG SER B 18 " model vdw 2.252 2.520 nonbonded pdb=" NH2 ARG A 15 " pdb=" OE1 GLU H 69 " model vdw 2.276 2.520 ... (remaining 258226 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: 3.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.360 Check model and map are aligned: 0.440 Set scattering table: 0.250 Process input model: 80.630 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.210 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:10.590 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 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 0.102 31399 Z= 0.831 Angle : 2.006 18.369 42781 Z= 1.339 Chirality : 0.118 1.288 4787 Planarity : 0.018 0.182 5308 Dihedral : 17.448 166.238 12067 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.20 % Favored : 95.69 % Rotamer: Outliers : 2.75 % Allowed : 6.19 % Favored : 91.07 % Cbeta Deviations : 1.11 % Peptide Plane: Cis-proline : 0.76 % 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: -2.32 (0.12), residues: 3639 helix: -2.07 (0.10), residues: 1540 sheet: -0.23 (0.22), residues: 413 loop : -1.19 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.156 0.025 TRP I 472 HIS 0.023 0.004 HIS I 246 PHE 0.090 0.013 PHE I 722 TYR 0.179 0.022 TYR G 189 ARG 0.013 0.002 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1125 time to evaluate : 3.342 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 65 LYS cc_start: 0.8033 (mtmm) cc_final: 0.7823 (mtmm) REVERT: A 72 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6782 (mt-10) REVERT: A 101 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6080 (mt-10) REVERT: A 139 GLU cc_start: 0.7751 (mp0) cc_final: 0.7123 (mp0) REVERT: A 157 SER cc_start: 0.8389 (m) cc_final: 0.8131 (p) REVERT: A 247 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8584 (mm) REVERT: A 268 LYS cc_start: 0.8017 (mttp) cc_final: 0.7815 (mttp) REVERT: A 271 VAL cc_start: 0.8702 (m) cc_final: 0.8481 (p) REVERT: B 188 THR cc_start: 0.8364 (p) cc_final: 0.7970 (p) REVERT: B 190 GLU cc_start: 0.7917 (mp0) cc_final: 0.7040 (mp0) REVERT: B 290 ASN cc_start: 0.8058 (m-40) cc_final: 0.7857 (m110) REVERT: C 32 SER cc_start: 0.7967 (m) cc_final: 0.7471 (p) REVERT: C 54 LYS cc_start: 0.8039 (mptt) cc_final: 0.7820 (mmmm) REVERT: C 72 GLU cc_start: 0.6751 (mp0) cc_final: 0.6364 (mp0) REVERT: C 139 GLU cc_start: 0.7338 (mp0) cc_final: 0.6955 (mp0) REVERT: C 151 PHE cc_start: 0.8439 (m-80) cc_final: 0.8236 (m-80) REVERT: C 190 GLU cc_start: 0.7953 (mp0) cc_final: 0.7622 (mp0) REVERT: C 272 ARG cc_start: 0.8107 (mtm180) cc_final: 0.7741 (mtm180) REVERT: C 275 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7303 (mt-10) REVERT: C 298 GLU cc_start: 0.7161 (tp30) cc_final: 0.6944 (tp30) REVERT: D 38 THR cc_start: 0.8092 (p) cc_final: 0.7756 (p) REVERT: D 39 ASP cc_start: 0.7355 (m-30) cc_final: 0.7071 (m-30) REVERT: D 63 MET cc_start: 0.8072 (ttp) cc_final: 0.7777 (ttm) REVERT: D 65 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7458 (pmtt) REVERT: D 66 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (mtt90) REVERT: D 68 GLN cc_start: 0.7960 (pt0) cc_final: 0.7413 (pt0) REVERT: D 72 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6814 (mt-10) REVERT: D 78 GLU cc_start: 0.7099 (tt0) cc_final: 0.6665 (tt0) REVERT: D 90 LYS cc_start: 0.8313 (mttt) cc_final: 0.8051 (mttt) REVERT: D 147 PHE cc_start: 0.7973 (p90) cc_final: 0.7765 (p90) REVERT: D 156 MET cc_start: 0.7476 (mtp) cc_final: 0.7143 (mtp) REVERT: D 169 LEU cc_start: 0.8640 (tp) cc_final: 0.8431 (tp) REVERT: D 243 MET cc_start: 0.7598 (mmm) cc_final: 0.7278 (mmm) REVERT: D 264 ASP cc_start: 0.7148 (t70) cc_final: 0.6843 (t0) REVERT: D 283 ASP cc_start: 0.7267 (m-30) cc_final: 0.7064 (m-30) REVERT: E 45 THR cc_start: 0.8490 (t) cc_final: 0.8142 (m) REVERT: E 141 SER cc_start: 0.8344 (m) cc_final: 0.7844 (p) REVERT: E 156 MET cc_start: 0.6503 (mmt) cc_final: 0.6255 (mmt) REVERT: E 168 GLU cc_start: 0.6977 (tt0) cc_final: 0.6771 (tt0) REVERT: E 182 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7062 (mm-30) REVERT: E 199 LEU cc_start: 0.8520 (mp) cc_final: 0.8248 (mm) REVERT: E 249 LYS cc_start: 0.7889 (mmpt) cc_final: 0.7563 (mmpt) REVERT: E 273 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8647 (mttm) REVERT: E 286 LEU cc_start: 0.8551 (mp) cc_final: 0.8319 (mm) REVERT: E 288 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7067 (mt-10) REVERT: E 317 PHE cc_start: 0.8443 (m-80) cc_final: 0.8239 (m-10) REVERT: F 2 LEU cc_start: 0.7755 (mp) cc_final: 0.7329 (mt) REVERT: F 45 THR cc_start: 0.8135 (m) cc_final: 0.7924 (m) REVERT: F 72 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: F 141 SER cc_start: 0.8064 (m) cc_final: 0.7421 (p) REVERT: F 182 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6719 (mt-10) REVERT: F 212 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.7029 (p) REVERT: F 226 ASP cc_start: 0.6515 (p0) cc_final: 0.6106 (p0) REVERT: F 267 ASN cc_start: 0.7357 (m-40) cc_final: 0.7103 (m-40) REVERT: F 283 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7136 (p0) REVERT: F 295 ASN cc_start: 0.8347 (t0) cc_final: 0.7792 (t0) REVERT: F 298 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6588 (mp0) REVERT: F 303 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8315 (mt) REVERT: F 313 TYR cc_start: 0.8528 (t80) cc_final: 0.7859 (t80) REVERT: G 10 GLN cc_start: 0.7563 (mt0) cc_final: 0.7357 (mt0) REVERT: G 68 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.5815 (pp30) REVERT: G 72 GLU cc_start: 0.6969 (mp0) cc_final: 0.6625 (mp0) REVERT: G 83 LEU cc_start: 0.8026 (tp) cc_final: 0.7752 (tm) REVERT: G 122 SER cc_start: 0.8367 (p) cc_final: 0.8086 (t) REVERT: G 128 TYR cc_start: 0.8173 (m-80) cc_final: 0.7860 (m-80) REVERT: G 130 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: G 216 LYS cc_start: 0.7336 (tppt) cc_final: 0.7105 (tppt) REVERT: G 233 LEU cc_start: 0.8556 (tp) cc_final: 0.8168 (tm) REVERT: G 254 LEU cc_start: 0.7671 (mt) cc_final: 0.7340 (mm) REVERT: G 275 GLU cc_start: 0.5962 (OUTLIER) cc_final: 0.5697 (mt-10) REVERT: G 305 SER cc_start: 0.7357 (m) cc_final: 0.7152 (t) REVERT: H 95 ASN cc_start: 0.8268 (m-40) cc_final: 0.8021 (m110) REVERT: H 118 LYS cc_start: 0.8439 (mmtp) cc_final: 0.7969 (mttp) REVERT: H 168 ILE cc_start: 0.8163 (mt) cc_final: 0.7958 (mp) REVERT: H 174 LYS cc_start: 0.7740 (ptpt) cc_final: 0.7528 (ptpt) REVERT: H 181 VAL cc_start: 0.8464 (m) cc_final: 0.8201 (t) REVERT: H 201 ASN cc_start: 0.7351 (m-40) cc_final: 0.7005 (m-40) REVERT: I 22 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8264 (tp) REVERT: I 34 GLU cc_start: 0.7296 (tt0) cc_final: 0.7008 (tt0) REVERT: I 78 LEU cc_start: 0.8218 (mt) cc_final: 0.7937 (tp) REVERT: I 82 ILE cc_start: 0.8677 (mt) cc_final: 0.8433 (mt) REVERT: I 140 ILE cc_start: 0.8904 (pt) cc_final: 0.8639 (pp) REVERT: I 149 ASN cc_start: 0.7968 (m-40) cc_final: 0.7633 (m-40) REVERT: I 161 ILE cc_start: 0.8067 (tt) cc_final: 0.7838 (tp) REVERT: I 213 VAL cc_start: 0.8883 (m) cc_final: 0.8583 (p) REVERT: I 217 SER cc_start: 0.8464 (t) cc_final: 0.8002 (p) REVERT: I 229 ARG cc_start: 0.7474 (ptm160) cc_final: 0.7229 (ptm160) REVERT: I 233 LEU cc_start: 0.8193 (mt) cc_final: 0.7852 (mt) REVERT: I 235 ASN cc_start: 0.8163 (t0) cc_final: 0.7783 (t0) REVERT: I 240 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6425 (pm20) REVERT: I 294 GLU cc_start: 0.7123 (tp30) cc_final: 0.6591 (tm-30) REVERT: I 347 LEU cc_start: 0.8520 (mt) cc_final: 0.8089 (mm) REVERT: I 349 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7344 (tp40) REVERT: I 352 SER cc_start: 0.8257 (t) cc_final: 0.7933 (p) REVERT: I 386 LEU cc_start: 0.7896 (tp) cc_final: 0.7678 (tt) REVERT: I 400 LYS cc_start: 0.7964 (tttm) cc_final: 0.7298 (tppp) REVERT: I 407 GLU cc_start: 0.7188 (pm20) cc_final: 0.6807 (pm20) REVERT: I 460 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6964 (tm-30) REVERT: I 478 TYR cc_start: 0.7704 (m-80) cc_final: 0.7418 (m-80) REVERT: I 510 PHE cc_start: 0.7708 (m-80) cc_final: 0.7420 (m-80) REVERT: I 536 GLU cc_start: 0.6449 (pt0) cc_final: 0.6210 (pt0) REVERT: I 583 PHE cc_start: 0.8439 (m-80) cc_final: 0.8180 (m-10) REVERT: I 590 LYS cc_start: 0.8253 (tmtt) cc_final: 0.7837 (tmtt) REVERT: I 593 ASP cc_start: 0.7117 (t70) cc_final: 0.6509 (t70) REVERT: I 605 TYR cc_start: 0.7072 (m-80) cc_final: 0.6780 (m-80) REVERT: I 632 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7663 (ttpp) REVERT: I 635 VAL cc_start: 0.8531 (m) cc_final: 0.8024 (m) REVERT: I 663 LYS cc_start: 0.7943 (ptpt) cc_final: 0.7731 (ptpt) REVERT: I 721 ASP cc_start: 0.6972 (m-30) cc_final: 0.6717 (m-30) REVERT: I 743 ASP cc_start: 0.7455 (p0) cc_final: 0.7211 (p0) REVERT: I 745 ARG cc_start: 0.7133 (mtp180) cc_final: 0.5891 (mtp180) REVERT: I 746 VAL cc_start: 0.8467 (p) cc_final: 0.8208 (t) REVERT: I 747 GLU cc_start: 0.7149 (mp0) cc_final: 0.6030 (mp0) REVERT: I 777 ASP cc_start: 0.7498 (m-30) cc_final: 0.7269 (m-30) REVERT: I 797 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6510 (mt-10) REVERT: I 804 LYS cc_start: 0.8062 (mttp) cc_final: 0.7858 (mtmm) REVERT: I 807 ARG cc_start: 0.7361 (ptp90) cc_final: 0.6877 (ptp-110) REVERT: I 827 ASN cc_start: 0.7818 (t0) cc_final: 0.7520 (t0) REVERT: I 828 ILE cc_start: 0.8384 (mm) cc_final: 0.8017 (mm) REVERT: I 832 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6908 (mt-10) REVERT: I 835 LYS cc_start: 0.8340 (ttpp) cc_final: 0.8101 (ttmm) REVERT: I 897 ASP cc_start: 0.7329 (m-30) cc_final: 0.6887 (m-30) REVERT: I 922 LEU cc_start: 0.8359 (mt) cc_final: 0.7682 (mm) REVERT: I 927 ILE cc_start: 0.8459 (tt) cc_final: 0.8187 (pt) REVERT: I 969 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7128 (tm-30) REVERT: J 8 THR cc_start: 0.8307 (m) cc_final: 0.7952 (m) REVERT: J 11 LEU cc_start: 0.8286 (tp) cc_final: 0.7939 (tm) REVERT: J 14 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7156 (mm-30) REVERT: J 44 LEU cc_start: 0.8570 (mt) cc_final: 0.8263 (mm) REVERT: J 54 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6832 (tm-30) REVERT: J 57 LEU cc_start: 0.8310 (mp) cc_final: 0.8007 (mt) REVERT: K 100 MET cc_start: 0.7420 (mtm) cc_final: 0.7180 (mtm) outliers start: 87 outliers final: 25 residues processed: 1171 average time/residue: 1.6071 time to fit residues: 2190.5251 Evaluate side-chains 1009 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 971 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 182 GLU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain F residue 4 SER Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 275 GLU Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 285 PHE Chi-restraints excluded: chain I residue 324 ASP Chi-restraints excluded: chain I residue 349 GLN Chi-restraints excluded: chain I residue 416 ASP Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 312 optimal weight: 0.5980 chunk 280 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 336 optimal weight: 0.0170 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 20 HIS A 290 ASN A 308 GLN B 43 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 171 HIS B 217 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN C 10 GLN C 20 HIS C 43 ASN C 68 GLN C 242 GLN C 308 GLN D 31 GLN D 43 ASN D 218 HIS D 290 ASN D 295 ASN E 8 GLN E 10 GLN E 48 GLN F 10 GLN F 43 ASN F 94 ASN ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 ASN F 242 GLN G 20 HIS H 76 ASN H 184 HIS H 187 ASN H 195 GLN I 35 HIS I 200 HIS I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 651 ASN I 825 GLN I 899 GLN J 146 ASN K 62 GLN K 70 GLN K 146 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31399 Z= 0.260 Angle : 0.740 9.720 42781 Z= 0.390 Chirality : 0.046 0.244 4787 Planarity : 0.005 0.061 5308 Dihedral : 14.943 164.521 5082 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.45 % Allowed : 15.37 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: -0.87 (0.13), residues: 3639 helix: -0.30 (0.12), residues: 1604 sheet: 0.14 (0.24), residues: 401 loop : -0.92 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 628 HIS 0.013 0.001 HIS I 246 PHE 0.021 0.002 PHE I 479 TYR 0.031 0.002 TYR I 844 ARG 0.013 0.001 ARG I 774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1005 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8469 (p) cc_final: 0.8254 (m) REVERT: A 65 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7569 (mtmm) REVERT: A 122 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8285 (t) REVERT: A 139 GLU cc_start: 0.7840 (mp0) cc_final: 0.7453 (mp0) REVERT: A 148 ASN cc_start: 0.8521 (p0) cc_final: 0.8281 (p0) REVERT: A 210 SER cc_start: 0.8574 (m) cc_final: 0.8181 (p) REVERT: A 241 ASP cc_start: 0.7587 (t0) cc_final: 0.7229 (t0) REVERT: A 256 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6883 (mp0) REVERT: A 264 ASP cc_start: 0.7576 (t0) cc_final: 0.6842 (t70) REVERT: A 268 LYS cc_start: 0.8032 (mttp) cc_final: 0.7731 (mttp) REVERT: A 283 ASP cc_start: 0.7473 (m-30) cc_final: 0.7074 (m-30) REVERT: B 15 ARG cc_start: 0.7865 (ptm-80) cc_final: 0.7449 (ptm-80) REVERT: B 123 GLU cc_start: 0.7817 (tp30) cc_final: 0.7252 (tp30) REVERT: B 143 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7414 (ttp80) REVERT: B 290 ASN cc_start: 0.8061 (m-40) cc_final: 0.7844 (m-40) REVERT: C 32 SER cc_start: 0.8039 (m) cc_final: 0.7390 (p) REVERT: C 54 LYS cc_start: 0.8025 (mptt) cc_final: 0.7641 (mmmm) REVERT: C 97 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6477 (mm-30) REVERT: C 140 GLN cc_start: 0.7894 (mp10) cc_final: 0.7679 (mp10) REVERT: C 151 PHE cc_start: 0.8302 (m-80) cc_final: 0.8040 (m-80) REVERT: C 167 ASN cc_start: 0.7529 (t0) cc_final: 0.7297 (t0) REVERT: C 199 LEU cc_start: 0.8472 (mt) cc_final: 0.8214 (mt) REVERT: C 226 ASP cc_start: 0.6943 (t0) cc_final: 0.6708 (t0) REVERT: C 283 ASP cc_start: 0.7319 (m-30) cc_final: 0.7069 (m-30) REVERT: D 15 ARG cc_start: 0.7890 (ttp80) cc_final: 0.7348 (ttt-90) REVERT: D 38 THR cc_start: 0.8127 (p) cc_final: 0.7790 (p) REVERT: D 66 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8130 (mtt90) REVERT: D 68 GLN cc_start: 0.8029 (pt0) cc_final: 0.7613 (pt0) REVERT: D 78 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6842 (tt0) REVERT: D 120 SER cc_start: 0.7440 (OUTLIER) cc_final: 0.7118 (t) REVERT: D 127 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8359 (t) REVERT: D 130 ASP cc_start: 0.6666 (t0) cc_final: 0.5973 (t0) REVERT: D 156 MET cc_start: 0.7342 (mtp) cc_final: 0.7051 (mtp) REVERT: D 175 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7434 (mm-30) REVERT: D 243 MET cc_start: 0.7688 (mmm) cc_final: 0.7396 (mmm) REVERT: D 283 ASP cc_start: 0.7472 (m-30) cc_final: 0.7173 (m-30) REVERT: D 293 TYR cc_start: 0.8875 (m-80) cc_final: 0.8143 (m-80) REVERT: D 295 ASN cc_start: 0.7559 (t0) cc_final: 0.7261 (t0) REVERT: E 45 THR cc_start: 0.8480 (t) cc_final: 0.8202 (m) REVERT: E 46 ARG cc_start: 0.8090 (mtp-110) cc_final: 0.7795 (mmm160) REVERT: E 89 ASP cc_start: 0.8485 (p0) cc_final: 0.8253 (p0) REVERT: E 141 SER cc_start: 0.8410 (m) cc_final: 0.8077 (p) REVERT: E 144 SER cc_start: 0.7921 (p) cc_final: 0.7655 (t) REVERT: E 168 GLU cc_start: 0.6987 (tt0) cc_final: 0.6679 (tt0) REVERT: E 209 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6478 (mt-10) REVERT: E 212 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7622 (p) REVERT: E 256 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7079 (mm-30) REVERT: E 264 ASP cc_start: 0.7635 (t70) cc_final: 0.7351 (t0) REVERT: E 267 ASN cc_start: 0.8096 (m-40) cc_final: 0.7857 (m-40) REVERT: E 286 LEU cc_start: 0.8528 (mp) cc_final: 0.8301 (mm) REVERT: E 288 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6854 (mt-10) REVERT: E 308 GLN cc_start: 0.7502 (tp40) cc_final: 0.7107 (tp40) REVERT: E 309 GLN cc_start: 0.8390 (mt0) cc_final: 0.8126 (mt0) REVERT: E 312 ASP cc_start: 0.7747 (m-30) cc_final: 0.7503 (m-30) REVERT: F 15 ARG cc_start: 0.7821 (tpp80) cc_final: 0.7513 (ttp80) REVERT: F 26 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7405 (mtm) REVERT: F 56 ASP cc_start: 0.7129 (t0) cc_final: 0.6865 (t0) REVERT: F 61 LEU cc_start: 0.8579 (mt) cc_final: 0.8292 (tp) REVERT: F 72 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: F 74 LEU cc_start: 0.8403 (mt) cc_final: 0.8195 (mt) REVERT: F 117 ILE cc_start: 0.7985 (mm) cc_final: 0.7694 (mm) REVERT: F 128 TYR cc_start: 0.8349 (m-80) cc_final: 0.7742 (m-80) REVERT: F 130 ASP cc_start: 0.7100 (t0) cc_final: 0.6699 (t0) REVERT: F 139 GLU cc_start: 0.7264 (mp0) cc_final: 0.6968 (mp0) REVERT: F 176 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7600 (m) REVERT: F 190 GLU cc_start: 0.6568 (mp0) cc_final: 0.6305 (mp0) REVERT: F 203 LYS cc_start: 0.7760 (mttm) cc_final: 0.7522 (mtpt) REVERT: F 209 GLU cc_start: 0.6534 (tt0) cc_final: 0.5773 (tm-30) REVERT: F 249 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7738 (mmmt) REVERT: F 254 LEU cc_start: 0.8019 (tp) cc_final: 0.7631 (mp) REVERT: F 267 ASN cc_start: 0.7405 (m-40) cc_final: 0.7190 (m-40) REVERT: F 303 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (mt) REVERT: F 313 TYR cc_start: 0.8438 (t80) cc_final: 0.7834 (t80) REVERT: G 63 MET cc_start: 0.6815 (ttm) cc_final: 0.6603 (ptm) REVERT: G 72 GLU cc_start: 0.7046 (mp0) cc_final: 0.6578 (mp0) REVERT: G 74 LEU cc_start: 0.7034 (mm) cc_final: 0.6797 (mp) REVERT: G 83 LEU cc_start: 0.8245 (tp) cc_final: 0.7985 (tm) REVERT: G 106 GLN cc_start: 0.6966 (pm20) cc_final: 0.6669 (pm20) REVERT: G 122 SER cc_start: 0.8478 (p) cc_final: 0.8168 (t) REVERT: G 233 LEU cc_start: 0.8713 (tp) cc_final: 0.8448 (tm) REVERT: G 237 GLN cc_start: 0.7521 (mt0) cc_final: 0.7255 (mt0) REVERT: G 295 ASN cc_start: 0.7210 (t0) cc_final: 0.6898 (t0) REVERT: H 122 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7597 (pt) REVERT: H 168 ILE cc_start: 0.8134 (mt) cc_final: 0.7887 (mp) REVERT: H 173 ILE cc_start: 0.7878 (pt) cc_final: 0.7646 (pp) REVERT: I 19 TYR cc_start: 0.8614 (p90) cc_final: 0.8391 (p90) REVERT: I 20 ILE cc_start: 0.8741 (mt) cc_final: 0.8434 (mm) REVERT: I 23 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7262 (mt-10) REVERT: I 26 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7495 (mp10) REVERT: I 34 GLU cc_start: 0.7518 (tt0) cc_final: 0.7295 (tt0) REVERT: I 78 LEU cc_start: 0.8150 (mt) cc_final: 0.7883 (mt) REVERT: I 82 ILE cc_start: 0.8591 (mt) cc_final: 0.8359 (mt) REVERT: I 106 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.6577 (mtp180) REVERT: I 149 ASN cc_start: 0.7860 (m-40) cc_final: 0.7491 (m110) REVERT: I 152 GLU cc_start: 0.7582 (mp0) cc_final: 0.7312 (mp0) REVERT: I 206 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8060 (tp) REVERT: I 208 PHE cc_start: 0.7930 (t80) cc_final: 0.7702 (t80) REVERT: I 229 ARG cc_start: 0.7167 (ptm160) cc_final: 0.6850 (ptm160) REVERT: I 230 LEU cc_start: 0.8212 (mt) cc_final: 0.7995 (mp) REVERT: I 233 LEU cc_start: 0.8238 (mt) cc_final: 0.7861 (mt) REVERT: I 294 GLU cc_start: 0.6909 (tp30) cc_final: 0.6635 (mm-30) REVERT: I 295 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7399 (ttt90) REVERT: I 326 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8015 (mttm) REVERT: I 329 LYS cc_start: 0.8379 (mtmt) cc_final: 0.7889 (mtmm) REVERT: I 352 SER cc_start: 0.8325 (t) cc_final: 0.8078 (t) REVERT: I 407 GLU cc_start: 0.7579 (pm20) cc_final: 0.7310 (pm20) REVERT: I 460 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6966 (tm-30) REVERT: I 478 TYR cc_start: 0.7816 (m-80) cc_final: 0.7609 (m-80) REVERT: I 488 GLN cc_start: 0.7938 (tp40) cc_final: 0.7361 (tm-30) REVERT: I 489 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8283 (mt) REVERT: I 491 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6599 (mt-10) REVERT: I 495 ASP cc_start: 0.7224 (m-30) cc_final: 0.6869 (m-30) REVERT: I 576 GLU cc_start: 0.7389 (tp30) cc_final: 0.6907 (tp30) REVERT: I 590 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7878 (tmtt) REVERT: I 617 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7031 (mm-30) REVERT: I 632 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7637 (ttpp) REVERT: I 663 LYS cc_start: 0.7808 (ptpt) cc_final: 0.7603 (ptpt) REVERT: I 666 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7986 (mmmm) REVERT: I 681 GLU cc_start: 0.7569 (mp0) cc_final: 0.7355 (mp0) REVERT: I 745 ARG cc_start: 0.7206 (mtp180) cc_final: 0.6908 (mtp180) REVERT: I 780 LYS cc_start: 0.8367 (mptp) cc_final: 0.8063 (mttp) REVERT: I 797 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6698 (mt-10) REVERT: I 827 ASN cc_start: 0.7682 (t0) cc_final: 0.7348 (t0) REVERT: I 828 ILE cc_start: 0.8152 (mm) cc_final: 0.7937 (mm) REVERT: I 829 VAL cc_start: 0.8692 (m) cc_final: 0.8464 (p) REVERT: I 830 MET cc_start: 0.7387 (mmp) cc_final: 0.7174 (mmp) REVERT: I 832 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6870 (mt-10) REVERT: I 835 LYS cc_start: 0.8252 (ttpp) cc_final: 0.8021 (mtpt) REVERT: I 855 LYS cc_start: 0.8383 (mmtp) cc_final: 0.8096 (mmtp) REVERT: I 870 GLU cc_start: 0.6822 (pp20) cc_final: 0.6486 (pp20) REVERT: I 871 GLN cc_start: 0.7564 (tp-100) cc_final: 0.7232 (tp40) REVERT: I 893 GLN cc_start: 0.8069 (tt0) cc_final: 0.7468 (tt0) REVERT: I 897 ASP cc_start: 0.7493 (m-30) cc_final: 0.7151 (m-30) REVERT: I 927 ILE cc_start: 0.8534 (tt) cc_final: 0.8209 (pt) REVERT: J 14 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7245 (mm-30) REVERT: J 41 GLU cc_start: 0.7234 (tp30) cc_final: 0.6471 (tp30) REVERT: J 53 GLU cc_start: 0.7083 (tp30) cc_final: 0.6875 (mp0) REVERT: J 54 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6899 (tm-30) REVERT: J 57 LEU cc_start: 0.8267 (mp) cc_final: 0.8059 (mt) REVERT: J 94 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7700 (tm-30) REVERT: J 113 LYS cc_start: 0.8459 (mttp) cc_final: 0.8249 (mttp) REVERT: J 121 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6856 (tm-30) REVERT: J 131 GLU cc_start: 0.7641 (tp30) cc_final: 0.7085 (tp30) REVERT: K 100 MET cc_start: 0.7471 (mtm) cc_final: 0.7256 (mtm) outliers start: 141 outliers final: 43 residues processed: 1072 average time/residue: 1.5839 time to fit residues: 1963.8478 Evaluate side-chains 1005 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 944 time to evaluate : 3.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 303 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 216 SER Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 289 ASP Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 725 SER Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 843 GLU Chi-restraints excluded: chain I residue 916 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 121 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 186 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 279 optimal weight: 1.9990 chunk 228 optimal weight: 0.9980 chunk 92 optimal weight: 0.0870 chunk 336 optimal weight: 0.0670 chunk 363 optimal weight: 0.8980 chunk 299 optimal weight: 0.0980 chunk 333 optimal weight: 0.0060 chunk 114 optimal weight: 2.9990 chunk 270 optimal weight: 0.5980 overall best weight: 0.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 43 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 267 ASN B 295 ASN C 10 GLN C 43 ASN C 68 GLN C 232 ASN C 267 ASN C 290 ASN C 295 ASN D 68 GLN E 10 GLN E 295 ASN F 20 HIS F 43 ASN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 ASN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN H 71 ASN H 76 ASN H 93 GLN H 95 ASN H 119 ASN H 195 GLN I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 483 GLN I 519 ASN I 791 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31399 Z= 0.172 Angle : 0.629 12.808 42781 Z= 0.328 Chirality : 0.042 0.229 4787 Planarity : 0.004 0.053 5308 Dihedral : 14.390 164.788 5035 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.86 % Allowed : 18.09 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 3639 helix: 0.52 (0.13), residues: 1593 sheet: 0.03 (0.24), residues: 403 loop : -0.68 (0.16), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 453 HIS 0.011 0.001 HIS I 246 PHE 0.021 0.001 PHE E 147 TYR 0.026 0.001 TYR I 844 ARG 0.014 0.001 ARG I 846 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 974 time to evaluate : 3.382 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 65 LYS cc_start: 0.7851 (mtmm) cc_final: 0.7500 (mtmm) REVERT: A 72 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 101 GLU cc_start: 0.6433 (mt-10) cc_final: 0.5984 (mt-10) REVERT: A 126 LYS cc_start: 0.8408 (mttp) cc_final: 0.7990 (mmtm) REVERT: A 139 GLU cc_start: 0.7831 (mp0) cc_final: 0.7375 (mp0) REVERT: A 140 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8173 (mp-120) REVERT: A 210 SER cc_start: 0.8546 (m) cc_final: 0.8187 (p) REVERT: A 232 ASN cc_start: 0.8205 (m110) cc_final: 0.7985 (m110) REVERT: A 253 GLU cc_start: 0.7402 (tp30) cc_final: 0.7197 (tt0) REVERT: A 256 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6873 (mp0) REVERT: A 283 ASP cc_start: 0.7438 (m-30) cc_final: 0.7067 (m-30) REVERT: A 298 GLU cc_start: 0.7685 (tp30) cc_final: 0.7473 (tp30) REVERT: A 301 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7916 (ttpp) REVERT: B 54 LYS cc_start: 0.7802 (mptt) cc_final: 0.7552 (mmmm) REVERT: B 58 LEU cc_start: 0.8070 (tt) cc_final: 0.7865 (pt) REVERT: B 123 GLU cc_start: 0.7696 (tp30) cc_final: 0.7287 (tp30) REVERT: B 143 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: B 268 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8255 (mtpp) REVERT: B 271 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8075 (p) REVERT: C 32 SER cc_start: 0.7779 (m) cc_final: 0.6832 (p) REVERT: C 54 LYS cc_start: 0.8083 (mptt) cc_final: 0.7798 (mmmm) REVERT: C 97 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6355 (mm-30) REVERT: C 139 GLU cc_start: 0.7484 (mp0) cc_final: 0.7202 (mp0) REVERT: C 140 GLN cc_start: 0.7852 (mp10) cc_final: 0.7568 (mp10) REVERT: C 151 PHE cc_start: 0.8307 (m-80) cc_final: 0.8084 (m-80) REVERT: C 167 ASN cc_start: 0.7502 (t0) cc_final: 0.7269 (t0) REVERT: C 226 ASP cc_start: 0.6925 (t0) cc_final: 0.6698 (t0) REVERT: C 283 ASP cc_start: 0.7272 (m-30) cc_final: 0.7001 (m-30) REVERT: C 303 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8555 (mm) REVERT: D 15 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7350 (ttt-90) REVERT: D 65 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6867 (pttt) REVERT: D 66 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7844 (mtt90) REVERT: D 78 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6869 (tt0) REVERT: D 120 SER cc_start: 0.7010 (OUTLIER) cc_final: 0.6793 (t) REVERT: D 130 ASP cc_start: 0.6521 (t0) cc_final: 0.5753 (t0) REVERT: D 156 MET cc_start: 0.7217 (mtp) cc_final: 0.6919 (mtp) REVERT: D 175 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7439 (mm-30) REVERT: D 243 MET cc_start: 0.7648 (mmm) cc_final: 0.7429 (mmm) REVERT: D 253 GLU cc_start: 0.6923 (tp30) cc_final: 0.6509 (tp30) REVERT: D 283 ASP cc_start: 0.7412 (m-30) cc_final: 0.7094 (m-30) REVERT: E 9 PHE cc_start: 0.8526 (m-80) cc_final: 0.8266 (m-80) REVERT: E 45 THR cc_start: 0.8478 (t) cc_final: 0.8206 (m) REVERT: E 46 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7725 (mmm160) REVERT: E 89 ASP cc_start: 0.8479 (p0) cc_final: 0.8273 (p0) REVERT: E 141 SER cc_start: 0.8413 (m) cc_final: 0.8072 (p) REVERT: E 182 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7079 (mm-30) REVERT: E 209 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6473 (mt-10) REVERT: E 212 THR cc_start: 0.7757 (OUTLIER) cc_final: 0.7529 (p) REVERT: E 256 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7053 (mm-30) REVERT: E 264 ASP cc_start: 0.7602 (t70) cc_final: 0.7319 (t0) REVERT: E 275 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6800 (mt-10) REVERT: E 287 GLN cc_start: 0.7635 (tp40) cc_final: 0.7411 (tp40) REVERT: E 288 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7143 (mt-10) REVERT: E 295 ASN cc_start: 0.7841 (t0) cc_final: 0.7640 (t0) REVERT: E 308 GLN cc_start: 0.7561 (tp40) cc_final: 0.7146 (tp40) REVERT: E 309 GLN cc_start: 0.8359 (mt0) cc_final: 0.8135 (mt0) REVERT: E 312 ASP cc_start: 0.7701 (m-30) cc_final: 0.7439 (m-30) REVERT: F 15 ARG cc_start: 0.7816 (tpp80) cc_final: 0.7610 (ttp80) REVERT: F 56 ASP cc_start: 0.7243 (t0) cc_final: 0.6971 (t0) REVERT: F 61 LEU cc_start: 0.8538 (mt) cc_final: 0.8269 (tp) REVERT: F 117 ILE cc_start: 0.7901 (mm) cc_final: 0.7550 (mm) REVERT: F 123 GLU cc_start: 0.7335 (tp30) cc_final: 0.6854 (tm-30) REVERT: F 128 TYR cc_start: 0.8310 (m-80) cc_final: 0.7733 (m-80) REVERT: F 139 GLU cc_start: 0.7272 (mp0) cc_final: 0.6876 (mp0) REVERT: F 190 GLU cc_start: 0.6658 (mp0) cc_final: 0.6403 (mp0) REVERT: F 194 TYR cc_start: 0.8180 (t80) cc_final: 0.7906 (t80) REVERT: F 249 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7807 (mmmt) REVERT: F 267 ASN cc_start: 0.7387 (m-40) cc_final: 0.7168 (m-40) REVERT: F 313 TYR cc_start: 0.8427 (t80) cc_final: 0.7752 (t80) REVERT: G 72 GLU cc_start: 0.6915 (mp0) cc_final: 0.6519 (mp0) REVERT: G 74 LEU cc_start: 0.7016 (mm) cc_final: 0.6768 (mp) REVERT: G 83 LEU cc_start: 0.8122 (tp) cc_final: 0.7863 (tm) REVERT: G 106 GLN cc_start: 0.7042 (pm20) cc_final: 0.6714 (pm20) REVERT: G 133 PHE cc_start: 0.8402 (m-80) cc_final: 0.8181 (m-80) REVERT: G 230 PHE cc_start: 0.7583 (p90) cc_final: 0.7321 (p90) REVERT: G 233 LEU cc_start: 0.8664 (tp) cc_final: 0.8338 (tm) REVERT: G 253 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6758 (mm-30) REVERT: G 254 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7263 (mm) REVERT: G 305 SER cc_start: 0.7395 (m) cc_final: 0.7160 (p) REVERT: H 28 THR cc_start: 0.8482 (m) cc_final: 0.8207 (p) REVERT: H 86 GLN cc_start: 0.7866 (tt0) cc_final: 0.7479 (tt0) REVERT: H 95 ASN cc_start: 0.8320 (m-40) cc_final: 0.8082 (m-40) REVERT: H 118 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8045 (mttp) REVERT: H 168 ILE cc_start: 0.8182 (mt) cc_final: 0.7912 (mp) REVERT: H 201 ASN cc_start: 0.7473 (m-40) cc_final: 0.6996 (m-40) REVERT: H 217 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8025 (tp40) REVERT: I 19 TYR cc_start: 0.8581 (p90) cc_final: 0.8357 (p90) REVERT: I 20 ILE cc_start: 0.8718 (mt) cc_final: 0.8368 (mm) REVERT: I 22 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.6807 (tp) REVERT: I 23 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7517 (mt-10) REVERT: I 26 GLN cc_start: 0.8274 (mm-40) cc_final: 0.7495 (mp10) REVERT: I 78 LEU cc_start: 0.8118 (mt) cc_final: 0.7806 (mt) REVERT: I 82 ILE cc_start: 0.8556 (mt) cc_final: 0.8310 (mt) REVERT: I 105 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7544 (mtt180) REVERT: I 106 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.6912 (mtp180) REVERT: I 110 LEU cc_start: 0.8325 (mp) cc_final: 0.8069 (mt) REVERT: I 149 ASN cc_start: 0.7825 (m-40) cc_final: 0.7390 (m110) REVERT: I 152 GLU cc_start: 0.7584 (mp0) cc_final: 0.7122 (mp0) REVERT: I 163 GLU cc_start: 0.8091 (mp0) cc_final: 0.7660 (mp0) REVERT: I 208 PHE cc_start: 0.7880 (t80) cc_final: 0.7599 (t80) REVERT: I 213 VAL cc_start: 0.8928 (m) cc_final: 0.8704 (p) REVERT: I 229 ARG cc_start: 0.7087 (ptm160) cc_final: 0.6798 (ptm160) REVERT: I 230 LEU cc_start: 0.8126 (mt) cc_final: 0.7925 (mp) REVERT: I 233 LEU cc_start: 0.8072 (mt) cc_final: 0.7791 (mt) REVERT: I 294 GLU cc_start: 0.6789 (tp30) cc_final: 0.6472 (mm-30) REVERT: I 295 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7324 (ttt180) REVERT: I 300 GLN cc_start: 0.7639 (pp30) cc_final: 0.7402 (tm130) REVERT: I 326 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7925 (mmtt) REVERT: I 329 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7708 (mtpt) REVERT: I 400 LYS cc_start: 0.8256 (ttmm) cc_final: 0.7743 (mtpp) REVERT: I 401 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6743 (mm-30) REVERT: I 460 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7008 (tm-30) REVERT: I 472 TRP cc_start: 0.8388 (t60) cc_final: 0.8156 (t60) REVERT: I 474 GLU cc_start: 0.6614 (pt0) cc_final: 0.6408 (pt0) REVERT: I 483 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: I 488 GLN cc_start: 0.7805 (tp40) cc_final: 0.7122 (tm-30) REVERT: I 489 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8271 (mt) REVERT: I 491 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6449 (mt-10) REVERT: I 495 ASP cc_start: 0.7121 (m-30) cc_final: 0.6773 (m-30) REVERT: I 576 GLU cc_start: 0.7419 (tp30) cc_final: 0.6922 (tp30) REVERT: I 577 MET cc_start: 0.8442 (mmp) cc_final: 0.8140 (mmp) REVERT: I 590 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7683 (tmtt) REVERT: I 593 ASP cc_start: 0.7315 (t70) cc_final: 0.6958 (t0) REVERT: I 613 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7053 (mt-10) REVERT: I 617 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7007 (mm-30) REVERT: I 632 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7571 (ttpp) REVERT: I 642 THR cc_start: 0.8465 (m) cc_final: 0.8245 (p) REVERT: I 663 LYS cc_start: 0.7803 (ptpt) cc_final: 0.7589 (ptpt) REVERT: I 745 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7023 (mtp180) REVERT: I 780 LYS cc_start: 0.8345 (mttp) cc_final: 0.8025 (mttp) REVERT: I 807 ARG cc_start: 0.7581 (ptp-110) cc_final: 0.7136 (ptp-110) REVERT: I 827 ASN cc_start: 0.7622 (t0) cc_final: 0.7280 (t0) REVERT: I 829 VAL cc_start: 0.8660 (m) cc_final: 0.8411 (p) REVERT: I 830 MET cc_start: 0.7404 (mmp) cc_final: 0.7141 (mmp) REVERT: I 832 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6917 (mt-10) REVERT: I 855 LYS cc_start: 0.8313 (mmtp) cc_final: 0.8088 (mmtp) REVERT: I 870 GLU cc_start: 0.6761 (pp20) cc_final: 0.6384 (pp20) REVERT: I 927 ILE cc_start: 0.8528 (tt) cc_final: 0.8188 (pt) REVERT: I 972 GLN cc_start: 0.7549 (tm-30) cc_final: 0.7283 (pp30) REVERT: J 7 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8140 (tt) REVERT: J 14 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7307 (mm-30) REVERT: J 33 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6746 (pp) REVERT: J 41 GLU cc_start: 0.7124 (tp30) cc_final: 0.6341 (tp30) REVERT: J 53 GLU cc_start: 0.7047 (tp30) cc_final: 0.6832 (mp0) REVERT: J 54 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6755 (tm-30) REVERT: J 94 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7696 (tm-30) REVERT: J 119 LEU cc_start: 0.8474 (tp) cc_final: 0.8245 (tm) REVERT: J 121 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: J 135 ARG cc_start: 0.8016 (mtt-85) cc_final: 0.7804 (mtt-85) REVERT: K 100 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7138 (mtm) outliers start: 154 outliers final: 59 residues processed: 1038 average time/residue: 1.5450 time to fit residues: 1864.3867 Evaluate side-chains 986 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 905 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 140 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain D residue 3 ASP Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 483 GLN Chi-restraints excluded: chain I residue 489 ILE Chi-restraints excluded: chain I residue 533 SER Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 592 GLU Chi-restraints excluded: chain I residue 647 LEU Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 712 MET Chi-restraints excluded: chain I residue 721 ASP Chi-restraints excluded: chain I residue 724 GLU Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 332 optimal weight: 0.5980 chunk 253 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 160 optimal weight: 0.9990 chunk 226 optimal weight: 0.7980 chunk 337 optimal weight: 2.9990 chunk 357 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN B 43 ASN ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 232 ASN B 267 ASN B 295 ASN C 10 GLN C 43 ASN C 217 ASN C 232 ASN C 267 ASN C 290 ASN C 295 ASN D 8 GLN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 267 ASN D 290 ASN D 295 ASN E 10 GLN E 43 ASN E 198 ASN E 217 ASN F 20 HIS F 43 ASN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN H 76 ASN H 119 ASN H 195 GLN H 222 GLN I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31399 Z= 0.261 Angle : 0.634 9.304 42781 Z= 0.326 Chirality : 0.043 0.185 4787 Planarity : 0.004 0.050 5308 Dihedral : 14.333 171.742 5027 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.27 % Allowed : 20.90 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.06 (0.14), residues: 3639 helix: 0.81 (0.13), residues: 1588 sheet: 0.26 (0.23), residues: 445 loop : -0.74 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 453 HIS 0.011 0.001 HIS I 246 PHE 0.024 0.002 PHE I 409 TYR 0.028 0.002 TYR I 902 ARG 0.007 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 952 time to evaluate : 3.477 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 60 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8355 (ptm160) REVERT: A 65 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7547 (mtmm) REVERT: A 72 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7031 (mt-10) REVERT: A 87 SER cc_start: 0.8580 (t) cc_final: 0.8198 (p) REVERT: A 101 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6216 (mt-10) REVERT: A 139 GLU cc_start: 0.7858 (mp0) cc_final: 0.7396 (mp0) REVERT: A 201 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8052 (mtp85) REVERT: A 210 SER cc_start: 0.8553 (m) cc_final: 0.8195 (p) REVERT: A 232 ASN cc_start: 0.8300 (m-40) cc_final: 0.8052 (m110) REVERT: A 256 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6890 (mt-10) REVERT: A 264 ASP cc_start: 0.7496 (t0) cc_final: 0.6994 (t0) REVERT: A 283 ASP cc_start: 0.7409 (m-30) cc_final: 0.7046 (m-30) REVERT: A 298 GLU cc_start: 0.7698 (tp30) cc_final: 0.7486 (tp30) REVERT: A 301 LYS cc_start: 0.8231 (ttpp) cc_final: 0.7956 (ttpp) REVERT: B 54 LYS cc_start: 0.7836 (mptt) cc_final: 0.7634 (mmmm) REVERT: B 58 LEU cc_start: 0.8145 (tt) cc_final: 0.7899 (pt) REVERT: B 67 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7506 (mptp) REVERT: B 73 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8120 (mtp180) REVERT: B 109 ASP cc_start: 0.7533 (t0) cc_final: 0.7087 (t0) REVERT: B 123 GLU cc_start: 0.7712 (tp30) cc_final: 0.7322 (tp30) REVERT: B 143 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7053 (ttp80) REVERT: B 268 LYS cc_start: 0.8605 (ttmm) cc_final: 0.8320 (mtpp) REVERT: B 271 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8124 (p) REVERT: C 8 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8209 (mt0) REVERT: C 32 SER cc_start: 0.7807 (m) cc_final: 0.6848 (p) REVERT: C 54 LYS cc_start: 0.8077 (mptt) cc_final: 0.7837 (mmmm) REVERT: C 97 GLU cc_start: 0.6796 (mm-30) cc_final: 0.6368 (mm-30) REVERT: C 139 GLU cc_start: 0.7577 (mp0) cc_final: 0.7266 (mp0) REVERT: C 140 GLN cc_start: 0.7895 (mp10) cc_final: 0.7608 (mp10) REVERT: C 151 PHE cc_start: 0.8259 (m-80) cc_final: 0.8042 (m-80) REVERT: C 156 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7267 (mtm) REVERT: C 226 ASP cc_start: 0.7015 (t0) cc_final: 0.6801 (t0) REVERT: C 283 ASP cc_start: 0.7284 (m-30) cc_final: 0.7025 (m-30) REVERT: D 15 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7385 (ttt-90) REVERT: D 65 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.7079 (pttt) REVERT: D 72 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6951 (mt-10) REVERT: D 78 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: D 130 ASP cc_start: 0.6632 (t0) cc_final: 0.5886 (t0) REVERT: D 156 MET cc_start: 0.7424 (mtp) cc_final: 0.7082 (mtp) REVERT: D 175 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7368 (mm-30) REVERT: D 253 GLU cc_start: 0.6969 (tp30) cc_final: 0.6590 (tp30) REVERT: D 283 ASP cc_start: 0.7430 (m-30) cc_final: 0.7139 (m-30) REVERT: E 31 GLN cc_start: 0.8417 (mm110) cc_final: 0.8201 (mm110) REVERT: E 37 GLN cc_start: 0.8488 (pt0) cc_final: 0.8281 (pt0) REVERT: E 45 THR cc_start: 0.8486 (t) cc_final: 0.8205 (m) REVERT: E 46 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7739 (mmm160) REVERT: E 89 ASP cc_start: 0.8504 (p0) cc_final: 0.8297 (p0) REVERT: E 94 ASN cc_start: 0.8018 (p0) cc_final: 0.7752 (p0) REVERT: E 141 SER cc_start: 0.8451 (m) cc_final: 0.8072 (p) REVERT: E 209 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6483 (mt-10) REVERT: E 212 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7609 (p) REVERT: E 237 GLN cc_start: 0.8739 (mt0) cc_final: 0.8484 (mt0) REVERT: E 249 LYS cc_start: 0.7664 (mmpt) cc_final: 0.7356 (mmpt) REVERT: E 256 GLU cc_start: 0.7277 (mt-10) cc_final: 0.7059 (mm-30) REVERT: E 264 ASP cc_start: 0.7608 (t70) cc_final: 0.7324 (t0) REVERT: E 275 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6902 (mt-10) REVERT: E 286 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8451 (mm) REVERT: E 292 ILE cc_start: 0.8686 (tt) cc_final: 0.8470 (tt) REVERT: E 305 SER cc_start: 0.8748 (m) cc_final: 0.8081 (p) REVERT: E 308 GLN cc_start: 0.7581 (tp40) cc_final: 0.7159 (tp40) REVERT: E 309 GLN cc_start: 0.8342 (mt0) cc_final: 0.8057 (mt0) REVERT: E 312 ASP cc_start: 0.7692 (m-30) cc_final: 0.7432 (m-30) REVERT: F 56 ASP cc_start: 0.7235 (t0) cc_final: 0.6960 (t0) REVERT: F 61 LEU cc_start: 0.8622 (mt) cc_final: 0.8304 (tp) REVERT: F 94 ASN cc_start: 0.7173 (t0) cc_final: 0.6901 (t0) REVERT: F 117 ILE cc_start: 0.7927 (mm) cc_final: 0.7578 (mm) REVERT: F 123 GLU cc_start: 0.7387 (tp30) cc_final: 0.6928 (tm-30) REVERT: F 128 TYR cc_start: 0.8328 (m-80) cc_final: 0.7689 (m-80) REVERT: F 176 VAL cc_start: 0.7733 (OUTLIER) cc_final: 0.7509 (m) REVERT: F 190 GLU cc_start: 0.6648 (mp0) cc_final: 0.6407 (mp0) REVERT: F 194 TYR cc_start: 0.8251 (t80) cc_final: 0.8006 (t80) REVERT: F 273 LYS cc_start: 0.8469 (mttp) cc_final: 0.8248 (mttt) REVERT: F 313 TYR cc_start: 0.8469 (t80) cc_final: 0.7731 (t80) REVERT: G 68 GLN cc_start: 0.6899 (pp30) cc_final: 0.6644 (pp30) REVERT: G 72 GLU cc_start: 0.6876 (mp0) cc_final: 0.6526 (mp0) REVERT: G 74 LEU cc_start: 0.7046 (mm) cc_final: 0.6833 (mt) REVERT: G 83 LEU cc_start: 0.8268 (tp) cc_final: 0.7998 (tm) REVERT: G 106 GLN cc_start: 0.6995 (pm20) cc_final: 0.6651 (pm20) REVERT: G 185 ARG cc_start: 0.7341 (mtp85) cc_final: 0.7125 (ptp-110) REVERT: G 233 LEU cc_start: 0.8694 (tp) cc_final: 0.8345 (tm) REVERT: G 243 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7410 (ttm) REVERT: G 253 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6812 (mm-30) REVERT: G 254 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7285 (mm) REVERT: G 288 GLU cc_start: 0.7679 (tp30) cc_final: 0.7409 (tp30) REVERT: G 305 SER cc_start: 0.7442 (m) cc_final: 0.7181 (p) REVERT: H 95 ASN cc_start: 0.8402 (m-40) cc_final: 0.8163 (m-40) REVERT: H 110 GLN cc_start: 0.8380 (mt0) cc_final: 0.8156 (mt0) REVERT: H 118 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8129 (mttp) REVERT: H 122 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7600 (pt) REVERT: H 173 ILE cc_start: 0.7837 (pt) cc_final: 0.7580 (pp) REVERT: H 217 GLN cc_start: 0.8326 (tt0) cc_final: 0.8055 (tp40) REVERT: H 227 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7856 (p) REVERT: I 20 ILE cc_start: 0.8702 (mt) cc_final: 0.8422 (mm) REVERT: I 22 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.7835 (tp) REVERT: I 26 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7762 (mt0) REVERT: I 78 LEU cc_start: 0.8161 (mt) cc_final: 0.7849 (mt) REVERT: I 82 ILE cc_start: 0.8592 (mt) cc_final: 0.8354 (mt) REVERT: I 105 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7602 (mtt180) REVERT: I 106 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.6665 (mtp180) REVERT: I 110 LEU cc_start: 0.8315 (mp) cc_final: 0.8100 (mt) REVERT: I 149 ASN cc_start: 0.7875 (m-40) cc_final: 0.7394 (m-40) REVERT: I 152 GLU cc_start: 0.7606 (mp0) cc_final: 0.7147 (mp0) REVERT: I 206 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8121 (mm) REVERT: I 213 VAL cc_start: 0.8907 (m) cc_final: 0.8705 (p) REVERT: I 229 ARG cc_start: 0.7166 (ptm160) cc_final: 0.6924 (ptm160) REVERT: I 233 LEU cc_start: 0.8138 (mt) cc_final: 0.7893 (mt) REVERT: I 291 GLU cc_start: 0.7919 (pm20) cc_final: 0.7673 (pm20) REVERT: I 294 GLU cc_start: 0.6848 (tp30) cc_final: 0.6553 (mm-30) REVERT: I 295 ARG cc_start: 0.7791 (tpp80) cc_final: 0.7346 (ttt90) REVERT: I 300 GLN cc_start: 0.7691 (pp30) cc_final: 0.7452 (tm130) REVERT: I 329 LYS cc_start: 0.8249 (mtmt) cc_final: 0.8030 (mtmt) REVERT: I 346 ILE cc_start: 0.8517 (mp) cc_final: 0.8118 (pp) REVERT: I 349 GLN cc_start: 0.8158 (tp40) cc_final: 0.7436 (tp-100) REVERT: I 351 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8532 (mp) REVERT: I 400 LYS cc_start: 0.8277 (ttmm) cc_final: 0.7749 (mtpp) REVERT: I 401 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6784 (mm-30) REVERT: I 460 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7089 (tm-30) REVERT: I 472 TRP cc_start: 0.8448 (t60) cc_final: 0.7411 (t60) REVERT: I 474 GLU cc_start: 0.6766 (pt0) cc_final: 0.6536 (pt0) REVERT: I 476 GLU cc_start: 0.7512 (mp0) cc_final: 0.6858 (mp0) REVERT: I 488 GLN cc_start: 0.7788 (tp40) cc_final: 0.7183 (tp-100) REVERT: I 515 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7069 (tt0) REVERT: I 544 ASP cc_start: 0.7226 (t70) cc_final: 0.6999 (t0) REVERT: I 576 GLU cc_start: 0.7486 (tp30) cc_final: 0.6972 (tp30) REVERT: I 590 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7771 (tmtt) REVERT: I 606 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7809 (p) REVERT: I 617 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7001 (mm-30) REVERT: I 632 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7625 (ttpp) REVERT: I 642 THR cc_start: 0.8495 (m) cc_final: 0.8270 (p) REVERT: I 723 ARG cc_start: 0.6944 (mtp85) cc_final: 0.6734 (mtp85) REVERT: I 745 ARG cc_start: 0.7325 (mtp180) cc_final: 0.6990 (mtp180) REVERT: I 780 LYS cc_start: 0.8313 (mttp) cc_final: 0.8014 (mttp) REVERT: I 788 ASP cc_start: 0.6920 (t0) cc_final: 0.6529 (t70) REVERT: I 807 ARG cc_start: 0.7576 (ptp-110) cc_final: 0.7225 (ptp-110) REVERT: I 827 ASN cc_start: 0.7661 (t0) cc_final: 0.7279 (t0) REVERT: I 829 VAL cc_start: 0.8727 (m) cc_final: 0.8452 (p) REVERT: I 832 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6906 (mt-10) REVERT: I 870 GLU cc_start: 0.6841 (pp20) cc_final: 0.6503 (pp20) REVERT: I 907 ILE cc_start: 0.8639 (mp) cc_final: 0.7980 (mp) REVERT: I 927 ILE cc_start: 0.8571 (tt) cc_final: 0.8170 (pp) REVERT: I 972 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7292 (pp30) REVERT: J 5 LEU cc_start: 0.4909 (OUTLIER) cc_final: 0.4393 (pt) REVERT: J 14 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7314 (mm-30) REVERT: J 33 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6710 (pp) REVERT: J 41 GLU cc_start: 0.7195 (tp30) cc_final: 0.6333 (tp30) REVERT: J 52 GLU cc_start: 0.6596 (tt0) cc_final: 0.6062 (tm-30) REVERT: J 53 GLU cc_start: 0.7158 (tp30) cc_final: 0.6876 (mp0) REVERT: J 54 GLU cc_start: 0.7567 (mm-30) cc_final: 0.6794 (tm-30) REVERT: J 94 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7629 (tm-30) REVERT: J 121 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: J 135 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7738 (mtt-85) REVERT: K 100 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.7128 (mtm) outliers start: 167 outliers final: 73 residues processed: 1028 average time/residue: 1.6007 time to fit residues: 1898.0281 Evaluate side-chains 1017 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 918 time to evaluate : 3.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 8 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 144 SER Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 162 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 495 ASP Chi-restraints excluded: chain I residue 515 GLU Chi-restraints excluded: chain I residue 533 SER Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 712 MET Chi-restraints excluded: chain I residue 721 ASP Chi-restraints excluded: chain I residue 724 GLU Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 121 GLU Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 297 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 5 optimal weight: 0.0470 chunk 266 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 321 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 295 ASN C 10 GLN C 29 HIS C 232 ASN C 267 ASN C 290 ASN C 295 ASN ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 106 GLN E 171 HIS E 198 ASN E 232 ASN E 242 GLN E 295 ASN F 10 GLN F 43 ASN F 68 GLN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN H 14 ASN H 34 ASN H 71 ASN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 727 HIS ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31399 Z= 0.264 Angle : 0.624 8.796 42781 Z= 0.323 Chirality : 0.043 0.181 4787 Planarity : 0.004 0.068 5308 Dihedral : 14.298 178.908 5022 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.18 % Allowed : 22.00 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 3639 helix: 0.97 (0.13), residues: 1596 sheet: 0.15 (0.23), residues: 459 loop : -0.77 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 453 HIS 0.011 0.001 HIS I 246 PHE 0.023 0.002 PHE B 151 TYR 0.031 0.002 TYR I 902 ARG 0.013 0.001 ARG I 846 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 953 time to evaluate : 3.632 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 60 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8298 (ptm160) REVERT: A 72 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6995 (mt-10) REVERT: A 87 SER cc_start: 0.8563 (t) cc_final: 0.8150 (p) REVERT: A 101 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6355 (mt-10) REVERT: A 139 GLU cc_start: 0.7857 (mp0) cc_final: 0.7341 (mp0) REVERT: A 210 SER cc_start: 0.8564 (m) cc_final: 0.8195 (p) REVERT: A 232 ASN cc_start: 0.8278 (m-40) cc_final: 0.8039 (m110) REVERT: A 283 ASP cc_start: 0.7412 (m-30) cc_final: 0.7046 (m-30) REVERT: A 298 GLU cc_start: 0.7712 (tp30) cc_final: 0.7497 (tp30) REVERT: A 301 LYS cc_start: 0.8295 (ttpp) cc_final: 0.8018 (ttpp) REVERT: B 39 ASP cc_start: 0.5787 (t0) cc_final: 0.5576 (t0) REVERT: B 109 ASP cc_start: 0.7598 (t0) cc_final: 0.7100 (t0) REVERT: B 123 GLU cc_start: 0.7691 (tp30) cc_final: 0.7326 (tp30) REVERT: B 268 LYS cc_start: 0.8617 (ttmm) cc_final: 0.8337 (mtpp) REVERT: B 271 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8186 (p) REVERT: C 32 SER cc_start: 0.7733 (m) cc_final: 0.6891 (p) REVERT: C 54 LYS cc_start: 0.8106 (mptt) cc_final: 0.7860 (mmmm) REVERT: C 97 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6232 (mm-30) REVERT: C 139 GLU cc_start: 0.7536 (mp0) cc_final: 0.7164 (mp0) REVERT: C 140 GLN cc_start: 0.7899 (mp10) cc_final: 0.7601 (mp10) REVERT: C 151 PHE cc_start: 0.8288 (m-80) cc_final: 0.8061 (m-80) REVERT: C 156 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7216 (mtm) REVERT: C 199 LEU cc_start: 0.8587 (mt) cc_final: 0.8365 (mt) REVERT: C 283 ASP cc_start: 0.7288 (m-30) cc_final: 0.7025 (m-30) REVERT: D 15 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7206 (ttt-90) REVERT: D 47 THR cc_start: 0.8611 (m) cc_final: 0.8383 (p) REVERT: D 65 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7084 (pttt) REVERT: D 72 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6875 (mt-10) REVERT: D 78 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: D 127 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8442 (t) REVERT: D 130 ASP cc_start: 0.6685 (t0) cc_final: 0.6068 (t0) REVERT: D 175 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 242 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7743 (tm-30) REVERT: D 283 ASP cc_start: 0.7414 (m-30) cc_final: 0.7138 (m-30) REVERT: E 45 THR cc_start: 0.8455 (t) cc_final: 0.8194 (m) REVERT: E 46 ARG cc_start: 0.8007 (mtp-110) cc_final: 0.7529 (mmm160) REVERT: E 72 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6831 (mt-10) REVERT: E 89 ASP cc_start: 0.8543 (p0) cc_final: 0.8318 (p0) REVERT: E 141 SER cc_start: 0.8447 (m) cc_final: 0.8061 (p) REVERT: E 175 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7463 (mm-30) REVERT: E 199 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8229 (mm) REVERT: E 209 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6483 (mt-10) REVERT: E 231 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8184 (t) REVERT: E 249 LYS cc_start: 0.7689 (mmpt) cc_final: 0.7398 (mmpt) REVERT: E 256 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7055 (mm-30) REVERT: E 264 ASP cc_start: 0.7627 (t70) cc_final: 0.7360 (t0) REVERT: E 286 LEU cc_start: 0.8674 (mt) cc_final: 0.8469 (mm) REVERT: E 308 GLN cc_start: 0.7577 (tp40) cc_final: 0.7177 (tp40) REVERT: E 312 ASP cc_start: 0.7702 (m-30) cc_final: 0.7445 (m-30) REVERT: F 10 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: F 117 ILE cc_start: 0.7956 (mm) cc_final: 0.7613 (mm) REVERT: F 128 TYR cc_start: 0.8313 (m-80) cc_final: 0.7732 (m-80) REVERT: F 176 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7501 (m) REVERT: F 180 THR cc_start: 0.8272 (t) cc_final: 0.7928 (t) REVERT: F 205 TYR cc_start: 0.6889 (m-80) cc_final: 0.6607 (m-80) REVERT: F 242 GLN cc_start: 0.8438 (tp40) cc_final: 0.7905 (tm-30) REVERT: G 72 GLU cc_start: 0.6871 (mp0) cc_final: 0.6561 (mp0) REVERT: G 74 LEU cc_start: 0.7060 (mm) cc_final: 0.6836 (mt) REVERT: G 83 LEU cc_start: 0.8267 (tp) cc_final: 0.8018 (tm) REVERT: G 106 GLN cc_start: 0.6908 (pm20) cc_final: 0.6571 (pm20) REVERT: G 233 LEU cc_start: 0.8690 (tp) cc_final: 0.8330 (tm) REVERT: G 253 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6818 (mm-30) REVERT: G 254 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7329 (mm) REVERT: G 288 GLU cc_start: 0.7700 (tp30) cc_final: 0.7416 (tp30) REVERT: G 305 SER cc_start: 0.7429 (m) cc_final: 0.7190 (p) REVERT: H 118 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8132 (mttp) REVERT: H 122 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7661 (pt) REVERT: H 174 LYS cc_start: 0.7714 (ptpt) cc_final: 0.7485 (ptpt) REVERT: H 201 ASN cc_start: 0.7548 (m-40) cc_final: 0.6935 (m-40) REVERT: H 217 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8095 (tp40) REVERT: H 227 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.7882 (p) REVERT: I 11 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8347 (mtt180) REVERT: I 22 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7806 (tp) REVERT: I 26 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7800 (mt0) REVERT: I 78 LEU cc_start: 0.8238 (mt) cc_final: 0.7927 (mt) REVERT: I 82 ILE cc_start: 0.8616 (mt) cc_final: 0.8386 (mt) REVERT: I 93 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7791 (tmm) REVERT: I 105 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7578 (mtt180) REVERT: I 106 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.6910 (mtp180) REVERT: I 149 ASN cc_start: 0.7879 (m-40) cc_final: 0.7565 (m-40) REVERT: I 152 GLU cc_start: 0.7631 (mp0) cc_final: 0.6919 (mp0) REVERT: I 229 ARG cc_start: 0.7253 (ptm160) cc_final: 0.7030 (ptm160) REVERT: I 233 LEU cc_start: 0.8206 (mt) cc_final: 0.7941 (mt) REVERT: I 291 GLU cc_start: 0.8062 (pm20) cc_final: 0.7629 (pm20) REVERT: I 294 GLU cc_start: 0.6946 (tp30) cc_final: 0.6701 (mm-30) REVERT: I 295 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7316 (ttt90) REVERT: I 298 ILE cc_start: 0.8736 (pp) cc_final: 0.8423 (mt) REVERT: I 324 ASP cc_start: 0.7236 (p0) cc_final: 0.7027 (p0) REVERT: I 329 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7852 (mtmt) REVERT: I 346 ILE cc_start: 0.8544 (mp) cc_final: 0.8116 (pp) REVERT: I 349 GLN cc_start: 0.8201 (tp40) cc_final: 0.7440 (tp-100) REVERT: I 351 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8526 (mp) REVERT: I 400 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7781 (mtpp) REVERT: I 401 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6819 (mm-30) REVERT: I 460 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7110 (tm-30) REVERT: I 472 TRP cc_start: 0.8424 (t60) cc_final: 0.8168 (t60) REVERT: I 488 GLN cc_start: 0.7700 (tp40) cc_final: 0.6977 (tp-100) REVERT: I 544 ASP cc_start: 0.7330 (t70) cc_final: 0.7093 (t0) REVERT: I 576 GLU cc_start: 0.7500 (tp30) cc_final: 0.6975 (tp30) REVERT: I 590 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7770 (tmtt) REVERT: I 606 VAL cc_start: 0.8188 (OUTLIER) cc_final: 0.7843 (p) REVERT: I 620 TYR cc_start: 0.8086 (m-80) cc_final: 0.7547 (m-80) REVERT: I 632 LYS cc_start: 0.7994 (ttpt) cc_final: 0.7666 (ttpp) REVERT: I 642 THR cc_start: 0.8521 (m) cc_final: 0.8290 (p) REVERT: I 667 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6932 (mm-30) REVERT: I 668 ASP cc_start: 0.7096 (m-30) cc_final: 0.6890 (m-30) REVERT: I 723 ARG cc_start: 0.7024 (mtp85) cc_final: 0.6821 (mtp85) REVERT: I 745 ARG cc_start: 0.7296 (mtp180) cc_final: 0.7084 (mtp180) REVERT: I 780 LYS cc_start: 0.8311 (mttp) cc_final: 0.8007 (mttp) REVERT: I 788 ASP cc_start: 0.6885 (t0) cc_final: 0.6541 (t70) REVERT: I 822 LEU cc_start: 0.8722 (tp) cc_final: 0.8509 (tt) REVERT: I 827 ASN cc_start: 0.7684 (t0) cc_final: 0.7292 (t0) REVERT: I 829 VAL cc_start: 0.8730 (m) cc_final: 0.8466 (p) REVERT: I 832 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6929 (mt-10) REVERT: I 870 GLU cc_start: 0.6833 (pp20) cc_final: 0.6593 (pp20) REVERT: I 898 ARG cc_start: 0.7391 (mtp-110) cc_final: 0.7157 (mtp-110) REVERT: I 972 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7302 (pp30) REVERT: J 5 LEU cc_start: 0.4880 (OUTLIER) cc_final: 0.4345 (pt) REVERT: J 14 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7301 (mm-30) REVERT: J 33 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6743 (pp) REVERT: J 41 GLU cc_start: 0.7220 (tp30) cc_final: 0.6357 (tp30) REVERT: J 44 LEU cc_start: 0.8647 (mm) cc_final: 0.8447 (mm) REVERT: J 52 GLU cc_start: 0.6532 (tt0) cc_final: 0.6057 (tm-30) REVERT: J 53 GLU cc_start: 0.7202 (tp30) cc_final: 0.6929 (mp0) REVERT: J 54 GLU cc_start: 0.7555 (mm-30) cc_final: 0.6653 (tm-30) REVERT: J 121 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7036 (tm-30) REVERT: J 135 ARG cc_start: 0.8041 (mtt-85) cc_final: 0.7807 (mtm-85) REVERT: K 100 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7125 (mtm) outliers start: 164 outliers final: 82 residues processed: 1017 average time/residue: 1.6030 time to fit residues: 1884.9578 Evaluate side-chains 1038 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 931 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 10 GLN Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain G residue 2 LEU Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 162 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 257 THR Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 536 GLU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 712 MET Chi-restraints excluded: chain I residue 721 ASP Chi-restraints excluded: chain I residue 731 VAL Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 907 ILE Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 120 optimal weight: 0.2980 chunk 322 optimal weight: 0.0770 chunk 70 optimal weight: 0.7980 chunk 209 optimal weight: 3.9990 chunk 88 optimal weight: 0.0980 chunk 357 optimal weight: 5.9990 chunk 297 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 187 optimal weight: 0.4980 overall best weight: 0.3538 ------------------------------------------------------------------------------- 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** A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 295 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 10 GLN D 232 ASN D 290 ASN E 10 GLN E 48 GLN E 198 ASN E 232 ASN E 267 ASN E 295 ASN F 20 HIS F 43 ASN F 48 GLN F 68 GLN F 294 GLN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 95 ASN H 110 GLN H 119 ASN H 195 GLN I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 871 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 893 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31399 Z= 0.200 Angle : 0.621 9.324 42781 Z= 0.317 Chirality : 0.042 0.387 4787 Planarity : 0.004 0.051 5308 Dihedral : 14.231 178.714 5019 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.46 % Allowed : 22.76 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.31 (0.14), residues: 3639 helix: 1.23 (0.14), residues: 1568 sheet: 0.09 (0.22), residues: 469 loop : -0.74 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 303 HIS 0.010 0.001 HIS I 246 PHE 0.025 0.001 PHE I 150 TYR 0.034 0.001 TYR I 902 ARG 0.011 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 947 time to evaluate : 3.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 60 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: A 65 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7518 (mtmm) REVERT: A 72 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6969 (mt-10) REVERT: A 87 SER cc_start: 0.8507 (t) cc_final: 0.8109 (p) REVERT: A 101 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6283 (mt-10) REVERT: A 139 GLU cc_start: 0.7835 (mp0) cc_final: 0.7332 (mp0) REVERT: A 209 GLU cc_start: 0.7240 (pt0) cc_final: 0.6993 (pt0) REVERT: A 210 SER cc_start: 0.8535 (m) cc_final: 0.8179 (p) REVERT: A 232 ASN cc_start: 0.8272 (m-40) cc_final: 0.7975 (m110) REVERT: A 283 ASP cc_start: 0.7426 (m-30) cc_final: 0.7058 (m-30) REVERT: A 287 GLN cc_start: 0.7419 (tm-30) cc_final: 0.7130 (tm-30) REVERT: A 298 GLU cc_start: 0.7712 (tp30) cc_final: 0.7465 (tp30) REVERT: A 301 LYS cc_start: 0.8295 (ttpp) cc_final: 0.8010 (ttpp) REVERT: B 58 LEU cc_start: 0.8148 (tt) cc_final: 0.7909 (pt) REVERT: B 67 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7532 (mptp) REVERT: B 90 LYS cc_start: 0.8333 (mmtp) cc_final: 0.8111 (mmtp) REVERT: B 109 ASP cc_start: 0.7589 (t0) cc_final: 0.7126 (t0) REVERT: B 123 GLU cc_start: 0.7688 (tp30) cc_final: 0.7323 (tp30) REVERT: B 185 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8122 (mtp85) REVERT: B 226 ASP cc_start: 0.6850 (t0) cc_final: 0.6411 (t0) REVERT: B 268 LYS cc_start: 0.8644 (ttmm) cc_final: 0.8341 (mtpp) REVERT: B 271 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 283 ASP cc_start: 0.7355 (p0) cc_final: 0.6876 (p0) REVERT: C 32 SER cc_start: 0.7613 (m) cc_final: 0.7002 (p) REVERT: C 54 LYS cc_start: 0.8086 (mptt) cc_final: 0.7795 (mmmm) REVERT: C 97 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6435 (mm-30) REVERT: C 139 GLU cc_start: 0.7510 (mp0) cc_final: 0.7208 (mp0) REVERT: C 151 PHE cc_start: 0.8290 (m-80) cc_final: 0.8048 (m-80) REVERT: C 156 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7191 (mtm) REVERT: C 199 LEU cc_start: 0.8559 (mt) cc_final: 0.8342 (mt) REVERT: C 283 ASP cc_start: 0.7268 (m-30) cc_final: 0.6993 (m-30) REVERT: D 15 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7537 (ttt-90) REVERT: D 65 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6796 (pttt) REVERT: D 72 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6835 (mt-10) REVERT: D 78 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6799 (tt0) REVERT: D 127 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8362 (t) REVERT: D 130 ASP cc_start: 0.6601 (t0) cc_final: 0.5893 (t0) REVERT: D 175 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7321 (mm-30) REVERT: D 242 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: D 253 GLU cc_start: 0.6954 (tp30) cc_final: 0.6521 (tp30) REVERT: D 283 ASP cc_start: 0.7402 (m-30) cc_final: 0.7118 (m-30) REVERT: E 45 THR cc_start: 0.8465 (t) cc_final: 0.8177 (m) REVERT: E 46 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7490 (mmm160) REVERT: E 72 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6812 (mt-10) REVERT: E 89 ASP cc_start: 0.8547 (p0) cc_final: 0.8273 (p0) REVERT: E 141 SER cc_start: 0.8386 (m) cc_final: 0.8049 (p) REVERT: E 148 ASN cc_start: 0.7530 (p0) cc_final: 0.7265 (p0) REVERT: E 175 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7500 (mm-30) REVERT: E 199 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8201 (mm) REVERT: E 209 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6421 (mt-10) REVERT: E 231 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8169 (t) REVERT: E 249 LYS cc_start: 0.7642 (mmpt) cc_final: 0.7355 (mmpt) REVERT: E 256 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7056 (mm-30) REVERT: E 264 ASP cc_start: 0.7605 (t70) cc_final: 0.7341 (t0) REVERT: E 286 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8451 (mm) REVERT: E 305 SER cc_start: 0.8733 (m) cc_final: 0.8190 (p) REVERT: E 308 GLN cc_start: 0.7570 (tp40) cc_final: 0.7156 (tp40) REVERT: E 312 ASP cc_start: 0.7594 (m-30) cc_final: 0.7333 (m-30) REVERT: F 48 GLN cc_start: 0.8007 (tt0) cc_final: 0.7726 (tt0) REVERT: F 67 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7966 (mtpp) REVERT: F 68 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6981 (tp-100) REVERT: F 72 GLU cc_start: 0.7364 (mp0) cc_final: 0.7000 (mp0) REVERT: F 117 ILE cc_start: 0.7877 (mm) cc_final: 0.7545 (mm) REVERT: F 128 TYR cc_start: 0.8289 (m-80) cc_final: 0.7691 (m-80) REVERT: F 176 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7538 (m) REVERT: F 180 THR cc_start: 0.8328 (t) cc_final: 0.8029 (t) REVERT: F 208 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7153 (mt0) REVERT: F 242 GLN cc_start: 0.8427 (tp40) cc_final: 0.7916 (tm-30) REVERT: F 273 LYS cc_start: 0.8390 (mtmm) cc_final: 0.8131 (mptt) REVERT: G 70 THR cc_start: 0.7312 (OUTLIER) cc_final: 0.7042 (p) REVERT: G 72 GLU cc_start: 0.6814 (mp0) cc_final: 0.6566 (mp0) REVERT: G 74 LEU cc_start: 0.7088 (mm) cc_final: 0.6841 (mt) REVERT: G 83 LEU cc_start: 0.8226 (tp) cc_final: 0.7987 (tm) REVERT: G 106 GLN cc_start: 0.6858 (pm20) cc_final: 0.6633 (pm20) REVERT: G 233 LEU cc_start: 0.8659 (tp) cc_final: 0.8252 (tm) REVERT: G 253 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6824 (mm-30) REVERT: G 288 GLU cc_start: 0.7690 (tp30) cc_final: 0.7421 (tp30) REVERT: G 305 SER cc_start: 0.7421 (m) cc_final: 0.7194 (p) REVERT: H 26 TYR cc_start: 0.8169 (m-80) cc_final: 0.7828 (m-80) REVERT: H 95 ASN cc_start: 0.8433 (m-40) cc_final: 0.8158 (m-40) REVERT: H 118 LYS cc_start: 0.8524 (mmtp) cc_final: 0.8140 (mttp) REVERT: H 122 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7593 (pt) REVERT: H 201 ASN cc_start: 0.7410 (m-40) cc_final: 0.6932 (m-40) REVERT: H 202 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7754 (ptp-170) REVERT: H 217 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8093 (tp40) REVERT: H 227 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7860 (p) REVERT: H 231 GLN cc_start: 0.8376 (tt0) cc_final: 0.8157 (tt0) REVERT: I 20 ILE cc_start: 0.8658 (mt) cc_final: 0.8285 (mm) REVERT: I 22 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7813 (tp) REVERT: I 26 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7803 (mt0) REVERT: I 78 LEU cc_start: 0.8223 (mt) cc_final: 0.7908 (mt) REVERT: I 82 ILE cc_start: 0.8616 (mt) cc_final: 0.8389 (mt) REVERT: I 86 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8379 (tt) REVERT: I 93 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7834 (tmm) REVERT: I 105 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7527 (mtt180) REVERT: I 106 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.6795 (mtp180) REVERT: I 149 ASN cc_start: 0.7860 (m-40) cc_final: 0.7481 (m-40) REVERT: I 152 GLU cc_start: 0.7508 (mp0) cc_final: 0.7179 (mp0) REVERT: I 206 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (mm) REVERT: I 216 SER cc_start: 0.8204 (m) cc_final: 0.7978 (t) REVERT: I 229 ARG cc_start: 0.7256 (ptm160) cc_final: 0.7050 (ptm160) REVERT: I 233 LEU cc_start: 0.8216 (mt) cc_final: 0.7956 (mt) REVERT: I 294 GLU cc_start: 0.6893 (tp30) cc_final: 0.6647 (mm-30) REVERT: I 295 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7321 (ttt90) REVERT: I 298 ILE cc_start: 0.8696 (pp) cc_final: 0.8423 (mt) REVERT: I 329 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8017 (mtmm) REVERT: I 346 ILE cc_start: 0.8549 (mp) cc_final: 0.8106 (pp) REVERT: I 349 GLN cc_start: 0.8178 (tp40) cc_final: 0.7373 (tp-100) REVERT: I 351 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8493 (mm) REVERT: I 400 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7782 (mtpp) REVERT: I 401 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6841 (mm-30) REVERT: I 427 GLU cc_start: 0.7550 (pt0) cc_final: 0.7270 (pt0) REVERT: I 460 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7096 (tm-30) REVERT: I 472 TRP cc_start: 0.8416 (t60) cc_final: 0.8131 (t60) REVERT: I 474 GLU cc_start: 0.6636 (pt0) cc_final: 0.6278 (pt0) REVERT: I 488 GLN cc_start: 0.7681 (tp40) cc_final: 0.6839 (tm-30) REVERT: I 504 GLU cc_start: 0.6679 (tp30) cc_final: 0.6381 (tp30) REVERT: I 544 ASP cc_start: 0.7336 (t70) cc_final: 0.7111 (t0) REVERT: I 576 GLU cc_start: 0.7474 (tp30) cc_final: 0.7147 (mm-30) REVERT: I 590 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7743 (tmtt) REVERT: I 606 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7789 (p) REVERT: I 620 TYR cc_start: 0.8096 (m-80) cc_final: 0.7522 (m-80) REVERT: I 632 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7621 (ttpp) REVERT: I 642 THR cc_start: 0.8479 (m) cc_final: 0.8252 (p) REVERT: I 667 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6904 (mm-30) REVERT: I 668 ASP cc_start: 0.7082 (m-30) cc_final: 0.6874 (m-30) REVERT: I 723 ARG cc_start: 0.6939 (mtp85) cc_final: 0.6681 (mtp85) REVERT: I 780 LYS cc_start: 0.8253 (mttp) cc_final: 0.7968 (mttp) REVERT: I 788 ASP cc_start: 0.6781 (t0) cc_final: 0.6493 (t70) REVERT: I 822 LEU cc_start: 0.8707 (tp) cc_final: 0.8502 (tt) REVERT: I 827 ASN cc_start: 0.7651 (t0) cc_final: 0.7296 (t0) REVERT: I 829 VAL cc_start: 0.8709 (m) cc_final: 0.8444 (p) REVERT: I 830 MET cc_start: 0.7453 (mmp) cc_final: 0.7090 (mmp) REVERT: I 832 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6920 (mt-10) REVERT: I 835 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8113 (mtpp) REVERT: I 870 GLU cc_start: 0.6812 (pp20) cc_final: 0.6532 (pp20) REVERT: I 927 ILE cc_start: 0.8497 (tt) cc_final: 0.8196 (pt) REVERT: I 972 GLN cc_start: 0.7616 (tm-30) cc_final: 0.7370 (pp30) REVERT: J 5 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4409 (pt) REVERT: J 14 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7310 (mm-30) REVERT: J 33 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6662 (pp) REVERT: J 41 GLU cc_start: 0.7214 (tp30) cc_final: 0.6321 (tp30) REVERT: J 54 GLU cc_start: 0.7532 (mm-30) cc_final: 0.6617 (tm-30) REVERT: J 119 LEU cc_start: 0.8460 (tp) cc_final: 0.8206 (tm) REVERT: J 121 GLU cc_start: 0.7266 (tm-30) cc_final: 0.7056 (tm-30) REVERT: J 135 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7756 (mtm-85) REVERT: K 100 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7123 (mtm) outliers start: 173 outliers final: 82 residues processed: 1020 average time/residue: 1.5926 time to fit residues: 1879.0611 Evaluate side-chains 1031 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 917 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 242 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 286 LEU 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 41 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 162 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 309 GLU Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 705 LYS Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 843 GLU Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 907 ILE Chi-restraints excluded: chain I residue 923 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 345 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 202 optimal weight: 0.9990 chunk 301 optimal weight: 0.9990 chunk 199 optimal weight: 0.6980 chunk 356 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 217 optimal weight: 0.0370 chunk 164 optimal weight: 1.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 43 ASN D 267 ASN D 290 ASN E 10 GLN E 232 ASN E 267 ASN E 295 ASN F 20 HIS F 43 ASN F 68 GLN F 311 GLN G 68 GLN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 76 ASN H 110 GLN ** H 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 GLN I 35 HIS I 81 HIS I 399 GLN I 871 GLN I 893 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31399 Z= 0.290 Angle : 0.642 10.342 42781 Z= 0.328 Chirality : 0.043 0.174 4787 Planarity : 0.004 0.078 5308 Dihedral : 14.224 174.523 5019 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.27 % Allowed : 23.67 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.30 (0.14), residues: 3639 helix: 1.26 (0.13), residues: 1572 sheet: 0.05 (0.22), residues: 471 loop : -0.79 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 303 HIS 0.009 0.001 HIS I 246 PHE 0.022 0.002 PHE B 151 TYR 0.026 0.002 TYR I 446 ARG 0.019 0.001 ARG I 846 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 940 time to evaluate : 3.630 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 44 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8306 (m) REVERT: A 58 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7940 (tt) REVERT: A 60 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7968 (mtp85) REVERT: A 65 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7543 (mtmm) REVERT: A 87 SER cc_start: 0.8544 (t) cc_final: 0.8153 (p) REVERT: A 101 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6430 (mt-10) REVERT: A 126 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8059 (mttp) REVERT: A 139 GLU cc_start: 0.7859 (mp0) cc_final: 0.7339 (mp0) REVERT: A 194 TYR cc_start: 0.8498 (t80) cc_final: 0.8096 (t80) REVERT: A 209 GLU cc_start: 0.7390 (pt0) cc_final: 0.7141 (pt0) REVERT: A 210 SER cc_start: 0.8555 (m) cc_final: 0.8192 (p) REVERT: A 232 ASN cc_start: 0.8249 (m-40) cc_final: 0.7992 (m110) REVERT: A 283 ASP cc_start: 0.7433 (m-30) cc_final: 0.7085 (m-30) REVERT: A 287 GLN cc_start: 0.7442 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 298 GLU cc_start: 0.7716 (tp30) cc_final: 0.7467 (tp30) REVERT: A 301 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8012 (ttpp) REVERT: A 311 GLN cc_start: 0.8016 (tt0) cc_final: 0.7813 (tt0) REVERT: B 39 ASP cc_start: 0.5887 (t0) cc_final: 0.5654 (t0) REVERT: B 53 GLU cc_start: 0.6942 (tp30) cc_final: 0.6727 (tp30) REVERT: B 90 LYS cc_start: 0.8418 (mmtp) cc_final: 0.8192 (mmtp) REVERT: B 109 ASP cc_start: 0.7654 (t70) cc_final: 0.7189 (t0) REVERT: B 123 GLU cc_start: 0.7695 (tp30) cc_final: 0.7338 (tp30) REVERT: B 226 ASP cc_start: 0.6940 (t0) cc_final: 0.6587 (t0) REVERT: B 268 LYS cc_start: 0.8657 (ttmm) cc_final: 0.8365 (mtpp) REVERT: B 271 VAL cc_start: 0.8463 (OUTLIER) cc_final: 0.8243 (p) REVERT: B 283 ASP cc_start: 0.7341 (p0) cc_final: 0.6847 (p0) REVERT: C 1 MET cc_start: 0.7564 (tpp) cc_final: 0.7086 (tpt) REVERT: C 32 SER cc_start: 0.7644 (m) cc_final: 0.7075 (p) REVERT: C 54 LYS cc_start: 0.8048 (mptt) cc_final: 0.7780 (mmmm) REVERT: C 139 GLU cc_start: 0.7540 (mp0) cc_final: 0.7168 (mp0) REVERT: C 151 PHE cc_start: 0.8285 (m-80) cc_final: 0.8043 (m-80) REVERT: C 156 MET cc_start: 0.7587 (OUTLIER) cc_final: 0.7224 (mtm) REVERT: C 199 LEU cc_start: 0.8607 (mt) cc_final: 0.8400 (mt) REVERT: C 283 ASP cc_start: 0.7281 (m-30) cc_final: 0.7015 (m-30) REVERT: D 15 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7558 (ttt-90) REVERT: D 65 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6817 (pttt) REVERT: D 72 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6901 (mt-10) REVERT: D 78 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6835 (tt0) REVERT: D 130 ASP cc_start: 0.6612 (t0) cc_final: 0.6085 (t0) REVERT: D 182 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6692 (mt-10) REVERT: D 283 ASP cc_start: 0.7409 (m-30) cc_final: 0.7133 (m-30) REVERT: E 45 THR cc_start: 0.8468 (t) cc_final: 0.8182 (m) REVERT: E 46 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7603 (mmm160) REVERT: E 72 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6862 (mt-10) REVERT: E 89 ASP cc_start: 0.8552 (p0) cc_final: 0.8319 (p0) REVERT: E 141 SER cc_start: 0.8428 (m) cc_final: 0.8065 (p) REVERT: E 199 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8238 (mm) REVERT: E 209 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6460 (mt-10) REVERT: E 231 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8216 (t) REVERT: E 249 LYS cc_start: 0.7715 (mmpt) cc_final: 0.7440 (mmpt) REVERT: E 256 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7064 (mm-30) REVERT: E 264 ASP cc_start: 0.7609 (t70) cc_final: 0.7357 (t0) REVERT: E 286 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8465 (mm) REVERT: E 308 GLN cc_start: 0.7576 (tp40) cc_final: 0.7153 (tp40) REVERT: E 312 ASP cc_start: 0.7626 (m-30) cc_final: 0.7360 (m-30) REVERT: F 68 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6884 (tp-100) REVERT: F 72 GLU cc_start: 0.7641 (mp0) cc_final: 0.7023 (mp0) REVERT: F 128 TYR cc_start: 0.8316 (m-80) cc_final: 0.7719 (m-80) REVERT: F 139 GLU cc_start: 0.7192 (mp0) cc_final: 0.6730 (mp0) REVERT: F 180 THR cc_start: 0.8320 (t) cc_final: 0.8051 (t) REVERT: F 273 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8236 (mptt) REVERT: G 70 THR cc_start: 0.7346 (OUTLIER) cc_final: 0.7050 (p) REVERT: G 72 GLU cc_start: 0.7027 (mp0) cc_final: 0.6677 (mp0) REVERT: G 74 LEU cc_start: 0.7124 (mm) cc_final: 0.6866 (mt) REVERT: G 83 LEU cc_start: 0.8270 (tp) cc_final: 0.8021 (tm) REVERT: G 106 GLN cc_start: 0.6902 (pm20) cc_final: 0.6659 (pm20) REVERT: G 233 LEU cc_start: 0.8731 (tp) cc_final: 0.8271 (tm) REVERT: G 253 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6839 (mm-30) REVERT: G 254 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7299 (mm) REVERT: G 288 GLU cc_start: 0.7718 (tp30) cc_final: 0.7330 (tp30) REVERT: H 86 GLN cc_start: 0.7992 (tt0) cc_final: 0.7677 (tt0) REVERT: H 118 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8168 (mttp) REVERT: H 122 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (pt) REVERT: H 137 LEU cc_start: 0.8437 (tp) cc_final: 0.8169 (tt) REVERT: H 202 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7791 (ptp-170) REVERT: H 205 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7772 (ttm) REVERT: H 217 GLN cc_start: 0.8370 (tt0) cc_final: 0.8143 (tp40) REVERT: H 227 THR cc_start: 0.8232 (OUTLIER) cc_final: 0.7894 (p) REVERT: I 20 ILE cc_start: 0.8647 (mt) cc_final: 0.8272 (mm) REVERT: I 22 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7807 (tp) REVERT: I 26 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7780 (mt0) REVERT: I 78 LEU cc_start: 0.8245 (mt) cc_final: 0.7938 (mt) REVERT: I 82 ILE cc_start: 0.8623 (mt) cc_final: 0.8412 (mt) REVERT: I 86 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8371 (tt) REVERT: I 93 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7830 (tmm) REVERT: I 94 GLN cc_start: 0.8385 (mm110) cc_final: 0.8165 (mm-40) REVERT: I 105 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7582 (mtt180) REVERT: I 106 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.6854 (mtp180) REVERT: I 110 LEU cc_start: 0.8283 (mp) cc_final: 0.8081 (mm) REVERT: I 149 ASN cc_start: 0.7879 (m-40) cc_final: 0.7455 (m-40) REVERT: I 152 GLU cc_start: 0.7544 (mp0) cc_final: 0.7148 (mp0) REVERT: I 206 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8114 (mm) REVERT: I 216 SER cc_start: 0.8230 (m) cc_final: 0.8000 (t) REVERT: I 233 LEU cc_start: 0.8275 (mt) cc_final: 0.7964 (mt) REVERT: I 294 GLU cc_start: 0.6887 (tp30) cc_final: 0.6641 (mm-30) REVERT: I 295 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7368 (ttt90) REVERT: I 298 ILE cc_start: 0.8703 (pp) cc_final: 0.8410 (mt) REVERT: I 346 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8164 (pp) REVERT: I 349 GLN cc_start: 0.8186 (tp40) cc_final: 0.7379 (tp-100) REVERT: I 351 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8552 (mp) REVERT: I 400 LYS cc_start: 0.8324 (ttmm) cc_final: 0.7799 (mtpp) REVERT: I 401 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6863 (mm-30) REVERT: I 460 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7094 (tm-30) REVERT: I 472 TRP cc_start: 0.8413 (t60) cc_final: 0.8134 (t60) REVERT: I 474 GLU cc_start: 0.6690 (pt0) cc_final: 0.6295 (pt0) REVERT: I 488 GLN cc_start: 0.7718 (tp40) cc_final: 0.6934 (tm-30) REVERT: I 544 ASP cc_start: 0.7401 (t70) cc_final: 0.7171 (t0) REVERT: I 576 GLU cc_start: 0.7489 (tp30) cc_final: 0.6987 (tp30) REVERT: I 590 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7736 (tmtt) REVERT: I 606 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7951 (t) REVERT: I 620 TYR cc_start: 0.8173 (m-80) cc_final: 0.7510 (m-80) REVERT: I 632 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7594 (ttpp) REVERT: I 642 THR cc_start: 0.8482 (m) cc_final: 0.8244 (p) REVERT: I 667 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6834 (mm-30) REVERT: I 668 ASP cc_start: 0.7113 (m-30) cc_final: 0.6907 (m-30) REVERT: I 686 ASP cc_start: 0.7571 (m-30) cc_final: 0.7169 (t0) REVERT: I 723 ARG cc_start: 0.7038 (mtp85) cc_final: 0.6716 (mtp85) REVERT: I 746 VAL cc_start: 0.8567 (p) cc_final: 0.8324 (t) REVERT: I 774 ARG cc_start: 0.8028 (ttp-110) cc_final: 0.7651 (mtm110) REVERT: I 780 LYS cc_start: 0.8295 (mttp) cc_final: 0.8008 (mttp) REVERT: I 788 ASP cc_start: 0.6832 (t0) cc_final: 0.6590 (t70) REVERT: I 797 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6913 (mm-30) REVERT: I 822 LEU cc_start: 0.8726 (tp) cc_final: 0.8519 (tt) REVERT: I 829 VAL cc_start: 0.8734 (m) cc_final: 0.8506 (p) REVERT: I 830 MET cc_start: 0.7444 (mmp) cc_final: 0.7174 (mmp) REVERT: I 832 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6947 (mt-10) REVERT: I 835 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8098 (mtpp) REVERT: I 870 GLU cc_start: 0.6849 (pp20) cc_final: 0.6546 (pp20) REVERT: I 871 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: I 927 ILE cc_start: 0.8500 (tt) cc_final: 0.8209 (pt) REVERT: I 934 ARG cc_start: 0.7633 (tpp80) cc_final: 0.7271 (mtm-85) REVERT: I 972 GLN cc_start: 0.7631 (tm-30) cc_final: 0.7352 (pp30) REVERT: J 14 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7300 (mm-30) REVERT: J 33 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6655 (mp) REVERT: J 41 GLU cc_start: 0.7269 (tp30) cc_final: 0.6339 (tp30) REVERT: J 54 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6756 (tm-30) REVERT: J 121 GLU cc_start: 0.7258 (tm-30) cc_final: 0.7031 (tm-30) REVERT: J 135 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7768 (mtm-85) REVERT: K 100 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7118 (mtm) outliers start: 167 outliers final: 97 residues processed: 1018 average time/residue: 1.6126 time to fit residues: 1907.6339 Evaluate side-chains 1059 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 932 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 3 ASP Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 162 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 138 THR Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 195 GLN Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 240 GLU Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 536 GLU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 831 THR Chi-restraints excluded: chain I residue 854 LYS Chi-restraints excluded: chain I residue 871 GLN Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 907 ILE Chi-restraints excluded: chain I residue 923 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 220 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 226 optimal weight: 0.7980 chunk 242 optimal weight: 0.0770 chunk 176 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 280 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 ASN A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 10 GLN D 267 ASN D 290 ASN E 10 GLN E 232 ASN E 267 ASN E 295 ASN F 43 ASN F 68 GLN G 68 GLN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 110 GLN H 119 ASN H 195 GLN I 35 HIS I 399 GLN I 871 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31399 Z= 0.258 Angle : 0.640 11.863 42781 Z= 0.327 Chirality : 0.043 0.175 4787 Planarity : 0.004 0.052 5308 Dihedral : 14.218 173.766 5019 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.96 % Allowed : 24.81 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.33 (0.14), residues: 3639 helix: 1.31 (0.14), residues: 1572 sheet: 0.04 (0.22), residues: 471 loop : -0.80 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 221 HIS 0.010 0.001 HIS I 246 PHE 0.019 0.001 PHE B 151 TYR 0.029 0.002 TYR I 446 ARG 0.010 0.001 ARG I 846 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 939 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 58 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7936 (tt) REVERT: A 65 LYS cc_start: 0.7800 (mtmm) cc_final: 0.7527 (mtmm) REVERT: A 87 SER cc_start: 0.8529 (t) cc_final: 0.8132 (p) REVERT: A 90 LYS cc_start: 0.8080 (mppt) cc_final: 0.7792 (mppt) REVERT: A 101 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6390 (mt-10) REVERT: A 139 GLU cc_start: 0.7814 (mp0) cc_final: 0.7310 (mp0) REVERT: A 194 TYR cc_start: 0.8491 (t80) cc_final: 0.8021 (t80) REVERT: A 209 GLU cc_start: 0.7387 (pt0) cc_final: 0.7142 (pt0) REVERT: A 210 SER cc_start: 0.8553 (m) cc_final: 0.8218 (p) REVERT: A 232 ASN cc_start: 0.8260 (m-40) cc_final: 0.8004 (m110) REVERT: A 283 ASP cc_start: 0.7414 (m-30) cc_final: 0.7099 (m-30) REVERT: A 287 GLN cc_start: 0.7437 (tm-30) cc_final: 0.7140 (tm-30) REVERT: A 298 GLU cc_start: 0.7716 (tp30) cc_final: 0.7453 (tp30) REVERT: A 301 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8078 (ttpp) REVERT: A 311 GLN cc_start: 0.8025 (tt0) cc_final: 0.7810 (tt0) REVERT: B 39 ASP cc_start: 0.5863 (t0) cc_final: 0.5641 (t0) REVERT: B 67 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7553 (mptp) REVERT: B 90 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8173 (mmtp) REVERT: B 109 ASP cc_start: 0.7652 (t70) cc_final: 0.7201 (t0) REVERT: B 123 GLU cc_start: 0.7699 (tp30) cc_final: 0.7337 (tp30) REVERT: B 226 ASP cc_start: 0.6918 (t0) cc_final: 0.6607 (t0) REVERT: B 268 LYS cc_start: 0.8654 (ttmm) cc_final: 0.8376 (mtpp) REVERT: B 269 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7172 (mm-30) REVERT: B 271 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8270 (p) REVERT: B 283 ASP cc_start: 0.7357 (p0) cc_final: 0.6838 (p0) REVERT: C 1 MET cc_start: 0.7573 (tpp) cc_final: 0.6914 (tpt) REVERT: C 32 SER cc_start: 0.7626 (m) cc_final: 0.7037 (p) REVERT: C 54 LYS cc_start: 0.8053 (mptt) cc_final: 0.7791 (mmmm) REVERT: C 109 ASP cc_start: 0.7751 (t0) cc_final: 0.7500 (t70) REVERT: C 139 GLU cc_start: 0.7553 (mp0) cc_final: 0.7174 (mp0) REVERT: C 151 PHE cc_start: 0.8285 (m-80) cc_final: 0.8034 (m-80) REVERT: C 156 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7220 (mtm) REVERT: C 199 LEU cc_start: 0.8604 (mt) cc_final: 0.8394 (mt) REVERT: C 283 ASP cc_start: 0.7274 (m-30) cc_final: 0.7009 (m-30) REVERT: D 65 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6867 (pttt) REVERT: D 72 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6869 (mt-10) REVERT: D 78 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6880 (tt0) REVERT: D 156 MET cc_start: 0.7624 (mtp) cc_final: 0.7219 (mtp) REVERT: D 182 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6676 (mt-10) REVERT: D 283 ASP cc_start: 0.7394 (m-30) cc_final: 0.7118 (m-30) REVERT: E 45 THR cc_start: 0.8464 (t) cc_final: 0.8187 (m) REVERT: E 46 ARG cc_start: 0.7995 (mtp-110) cc_final: 0.7609 (mmm160) REVERT: E 72 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6854 (mt-10) REVERT: E 89 ASP cc_start: 0.8554 (p0) cc_final: 0.8320 (p0) REVERT: E 141 SER cc_start: 0.8424 (m) cc_final: 0.8057 (p) REVERT: E 199 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8223 (mm) REVERT: E 209 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6680 (mt-10) REVERT: E 231 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8211 (t) REVERT: E 249 LYS cc_start: 0.7700 (mmpt) cc_final: 0.7439 (mmpt) REVERT: E 256 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7056 (mm-30) REVERT: E 264 ASP cc_start: 0.7619 (t70) cc_final: 0.7351 (t0) REVERT: E 275 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6857 (mt-10) REVERT: E 286 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8463 (mm) REVERT: E 308 GLN cc_start: 0.7569 (tp40) cc_final: 0.7137 (tp40) REVERT: E 312 ASP cc_start: 0.7606 (m-30) cc_final: 0.7329 (m-30) REVERT: F 67 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8070 (mtpp) REVERT: F 68 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6637 (tt0) REVERT: F 72 GLU cc_start: 0.7577 (mp0) cc_final: 0.6975 (mp0) REVERT: F 109 ASP cc_start: 0.7645 (t70) cc_final: 0.7378 (t0) REVERT: F 180 THR cc_start: 0.8308 (t) cc_final: 0.7891 (t) REVERT: F 190 GLU cc_start: 0.6926 (mp0) cc_final: 0.6659 (mp0) REVERT: F 242 GLN cc_start: 0.8415 (tp40) cc_final: 0.8016 (tm-30) REVERT: G 70 THR cc_start: 0.7177 (OUTLIER) cc_final: 0.6939 (p) REVERT: G 72 GLU cc_start: 0.7000 (mp0) cc_final: 0.6648 (mp0) REVERT: G 74 LEU cc_start: 0.7124 (mm) cc_final: 0.6854 (mt) REVERT: G 83 LEU cc_start: 0.8240 (tp) cc_final: 0.8003 (tm) REVERT: G 106 GLN cc_start: 0.6892 (pm20) cc_final: 0.6658 (pm20) REVERT: G 233 LEU cc_start: 0.8666 (tp) cc_final: 0.8361 (tm) REVERT: G 253 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6828 (mm-30) REVERT: G 254 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7285 (mm) REVERT: G 288 GLU cc_start: 0.7705 (tp30) cc_final: 0.7318 (tp30) REVERT: G 294 GLN cc_start: 0.4241 (tp40) cc_final: 0.4033 (mm110) REVERT: H 8 LYS cc_start: 0.8341 (ptmt) cc_final: 0.7910 (ptmt) REVERT: H 86 GLN cc_start: 0.7984 (tt0) cc_final: 0.7670 (tt0) REVERT: H 95 ASN cc_start: 0.8443 (m-40) cc_final: 0.8161 (m-40) REVERT: H 118 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8175 (mttp) REVERT: H 122 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7729 (pt) REVERT: H 137 LEU cc_start: 0.8424 (tp) cc_final: 0.8149 (tt) REVERT: H 205 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7777 (ttm) REVERT: H 217 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8154 (tp40) REVERT: H 227 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7905 (p) REVERT: I 20 ILE cc_start: 0.8653 (mt) cc_final: 0.8281 (mm) REVERT: I 26 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7713 (mt0) REVERT: I 78 LEU cc_start: 0.8247 (mt) cc_final: 0.7946 (mt) REVERT: I 82 ILE cc_start: 0.8622 (mt) cc_final: 0.8413 (mt) REVERT: I 86 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8360 (tt) REVERT: I 93 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7816 (tmm) REVERT: I 94 GLN cc_start: 0.8377 (mm110) cc_final: 0.8155 (mm-40) REVERT: I 105 ARG cc_start: 0.7802 (mtm-85) cc_final: 0.7571 (mtt180) REVERT: I 106 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.6817 (mtp180) REVERT: I 149 ASN cc_start: 0.7879 (m-40) cc_final: 0.7517 (m-40) REVERT: I 152 GLU cc_start: 0.7552 (mp0) cc_final: 0.7193 (mp0) REVERT: I 216 SER cc_start: 0.8225 (m) cc_final: 0.8015 (t) REVERT: I 229 ARG cc_start: 0.7337 (ptm160) cc_final: 0.6992 (ptm160) REVERT: I 233 LEU cc_start: 0.8292 (mt) cc_final: 0.7967 (mt) REVERT: I 294 GLU cc_start: 0.6905 (tp30) cc_final: 0.6648 (mm-30) REVERT: I 295 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7371 (ttt90) REVERT: I 298 ILE cc_start: 0.8687 (pp) cc_final: 0.8424 (mt) REVERT: I 346 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8160 (pp) REVERT: I 349 GLN cc_start: 0.8186 (tp40) cc_final: 0.7386 (tp-100) REVERT: I 351 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8539 (mp) REVERT: I 401 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6850 (mm-30) REVERT: I 460 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7117 (tm-30) REVERT: I 472 TRP cc_start: 0.8407 (t60) cc_final: 0.8130 (t60) REVERT: I 474 GLU cc_start: 0.6657 (pt0) cc_final: 0.6267 (pt0) REVERT: I 488 GLN cc_start: 0.7714 (tp40) cc_final: 0.6927 (tm-30) REVERT: I 504 GLU cc_start: 0.6728 (tp30) cc_final: 0.6418 (tp30) REVERT: I 544 ASP cc_start: 0.7470 (t70) cc_final: 0.7243 (t0) REVERT: I 576 GLU cc_start: 0.7407 (tp30) cc_final: 0.6902 (tp30) REVERT: I 590 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7708 (tmtt) REVERT: I 595 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7891 (mm-40) REVERT: I 606 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7919 (t) REVERT: I 632 LYS cc_start: 0.7901 (ttpt) cc_final: 0.7576 (ttpp) REVERT: I 642 THR cc_start: 0.8462 (m) cc_final: 0.8225 (p) REVERT: I 667 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6810 (mm-30) REVERT: I 668 ASP cc_start: 0.7113 (m-30) cc_final: 0.6899 (m-30) REVERT: I 686 ASP cc_start: 0.7565 (m-30) cc_final: 0.7161 (t0) REVERT: I 723 ARG cc_start: 0.7044 (mtp85) cc_final: 0.6704 (mtp85) REVERT: I 746 VAL cc_start: 0.8561 (p) cc_final: 0.8317 (t) REVERT: I 774 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7529 (mtm110) REVERT: I 777 ASP cc_start: 0.7452 (m-30) cc_final: 0.7121 (m-30) REVERT: I 780 LYS cc_start: 0.8296 (mttp) cc_final: 0.8014 (mttp) REVERT: I 788 ASP cc_start: 0.6828 (t0) cc_final: 0.6589 (t70) REVERT: I 797 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6889 (mm-30) REVERT: I 827 ASN cc_start: 0.7611 (t0) cc_final: 0.7335 (t0) REVERT: I 829 VAL cc_start: 0.8729 (m) cc_final: 0.8447 (p) REVERT: I 830 MET cc_start: 0.7395 (mmp) cc_final: 0.7193 (mmp) REVERT: I 832 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6967 (mt-10) REVERT: I 835 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8086 (mtpp) REVERT: I 870 GLU cc_start: 0.6843 (pp20) cc_final: 0.6572 (pp20) REVERT: I 927 ILE cc_start: 0.8488 (tt) cc_final: 0.8199 (pt) REVERT: I 934 ARG cc_start: 0.7622 (tpp80) cc_final: 0.7279 (mtm-85) REVERT: J 5 LEU cc_start: 0.5020 (OUTLIER) cc_final: 0.4508 (pt) REVERT: J 14 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7282 (mm-30) REVERT: J 33 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6605 (pp) REVERT: J 41 GLU cc_start: 0.7286 (tp30) cc_final: 0.6347 (tp30) REVERT: J 53 GLU cc_start: 0.7405 (mp0) cc_final: 0.6849 (mp0) REVERT: J 54 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6796 (tm-30) REVERT: J 121 GLU cc_start: 0.7273 (tm-30) cc_final: 0.7028 (tm-30) REVERT: J 135 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7753 (mtm-85) REVERT: K 100 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7115 (mtm) outliers start: 157 outliers final: 93 residues processed: 1006 average time/residue: 1.6505 time to fit residues: 1919.9378 Evaluate side-chains 1061 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 939 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 162 MET Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 232 ASN Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 162 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 217 GLN Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain H residue 228 PHE Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 831 THR Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain I residue 892 LEU Chi-restraints excluded: chain I residue 907 ILE Chi-restraints excluded: chain I residue 923 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 324 optimal weight: 0.6980 chunk 341 optimal weight: 0.1980 chunk 311 optimal weight: 0.3980 chunk 332 optimal weight: 0.2980 chunk 200 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 260 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 300 optimal weight: 0.5980 chunk 314 optimal weight: 0.7980 chunk 331 optimal weight: 0.9980 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 10 GLN D 267 ASN D 290 ASN E 10 GLN E 31 GLN E 48 GLN E 232 ASN E 267 ASN E 295 ASN F 43 ASN F 68 GLN G 68 GLN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 110 GLN H 195 GLN I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 871 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31399 Z= 0.196 Angle : 0.632 9.914 42781 Z= 0.321 Chirality : 0.041 0.205 4787 Planarity : 0.004 0.096 5308 Dihedral : 14.192 173.720 5016 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.51 % Allowed : 25.66 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.39 (0.14), residues: 3639 helix: 1.40 (0.14), residues: 1573 sheet: -0.06 (0.22), residues: 475 loop : -0.76 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 221 HIS 0.009 0.001 HIS I 246 PHE 0.034 0.001 PHE I 150 TYR 0.031 0.001 TYR I 446 ARG 0.021 0.001 ARG I 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 961 time to evaluate : 3.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8312 (m) REVERT: A 58 LEU cc_start: 0.8197 (tp) cc_final: 0.7917 (tt) REVERT: A 65 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7492 (mtmm) REVERT: A 72 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6844 (mt-10) REVERT: A 101 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6280 (mt-10) REVERT: A 139 GLU cc_start: 0.7820 (mp0) cc_final: 0.7308 (mp0) REVERT: A 194 TYR cc_start: 0.8474 (t80) cc_final: 0.8096 (t80) REVERT: A 209 GLU cc_start: 0.7364 (pt0) cc_final: 0.7136 (pt0) REVERT: A 210 SER cc_start: 0.8526 (m) cc_final: 0.8179 (p) REVERT: A 232 ASN cc_start: 0.8256 (m-40) cc_final: 0.7984 (m110) REVERT: A 271 VAL cc_start: 0.8220 (p) cc_final: 0.7940 (m) REVERT: A 283 ASP cc_start: 0.7404 (m-30) cc_final: 0.7072 (m-30) REVERT: A 287 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 298 GLU cc_start: 0.7706 (tp30) cc_final: 0.7452 (tp30) REVERT: A 301 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8073 (ttpp) REVERT: A 311 GLN cc_start: 0.7985 (tt0) cc_final: 0.7769 (tt0) REVERT: B 39 ASP cc_start: 0.5797 (t0) cc_final: 0.5563 (t0) REVERT: B 58 LEU cc_start: 0.8131 (tt) cc_final: 0.7828 (pt) REVERT: B 67 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7532 (mptp) REVERT: B 109 ASP cc_start: 0.7607 (t70) cc_final: 0.7175 (t0) REVERT: B 123 GLU cc_start: 0.7683 (tp30) cc_final: 0.7332 (tp30) REVERT: B 185 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8089 (mtp85) REVERT: B 226 ASP cc_start: 0.6876 (t0) cc_final: 0.6576 (t0) REVERT: B 230 PHE cc_start: 0.8468 (p90) cc_final: 0.8075 (p90) REVERT: B 268 LYS cc_start: 0.8658 (ttmm) cc_final: 0.8368 (mtpp) REVERT: B 283 ASP cc_start: 0.7343 (p0) cc_final: 0.6827 (p0) REVERT: C 1 MET cc_start: 0.7547 (tpp) cc_final: 0.6852 (tpt) REVERT: C 54 LYS cc_start: 0.8015 (mptt) cc_final: 0.7803 (mmmm) REVERT: C 97 GLU cc_start: 0.6825 (mm-30) cc_final: 0.6456 (mm-30) REVERT: C 139 GLU cc_start: 0.7529 (mp0) cc_final: 0.7162 (mp0) REVERT: C 151 PHE cc_start: 0.8292 (m-80) cc_final: 0.8047 (m-80) REVERT: C 156 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7223 (mtm) REVERT: C 199 LEU cc_start: 0.8572 (mt) cc_final: 0.8371 (mt) REVERT: C 283 ASP cc_start: 0.7258 (m-30) cc_final: 0.6992 (m-30) REVERT: D 15 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7020 (ttt-90) REVERT: D 65 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6812 (pttt) REVERT: D 72 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6846 (mt-10) REVERT: D 78 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6815 (tt0) REVERT: D 127 VAL cc_start: 0.8654 (OUTLIER) cc_final: 0.8348 (t) REVERT: D 156 MET cc_start: 0.7563 (mtp) cc_final: 0.7161 (mtp) REVERT: D 283 ASP cc_start: 0.7384 (m-30) cc_final: 0.7099 (m-30) REVERT: D 293 TYR cc_start: 0.8863 (m-80) cc_final: 0.7986 (m-80) REVERT: E 45 THR cc_start: 0.8451 (t) cc_final: 0.8188 (m) REVERT: E 46 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7583 (mmm160) REVERT: E 72 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6840 (mt-10) REVERT: E 89 ASP cc_start: 0.8559 (p0) cc_final: 0.8327 (p0) REVERT: E 141 SER cc_start: 0.8417 (m) cc_final: 0.8048 (p) REVERT: E 199 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8201 (mm) REVERT: E 209 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6661 (mt-10) REVERT: E 231 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8216 (t) REVERT: E 241 ASP cc_start: 0.7456 (m-30) cc_final: 0.7247 (m-30) REVERT: E 249 LYS cc_start: 0.7653 (mmpt) cc_final: 0.7381 (mmpt) REVERT: E 256 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7060 (mm-30) REVERT: E 264 ASP cc_start: 0.7621 (t70) cc_final: 0.7354 (t0) REVERT: E 286 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8462 (mm) REVERT: E 305 SER cc_start: 0.8698 (m) cc_final: 0.8271 (p) REVERT: E 308 GLN cc_start: 0.7561 (tp40) cc_final: 0.7115 (tp40) REVERT: E 312 ASP cc_start: 0.7569 (m-30) cc_final: 0.7304 (m-30) REVERT: F 26 MET cc_start: 0.7902 (ptm) cc_final: 0.7690 (ptt) REVERT: F 67 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8014 (mtpp) REVERT: F 68 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6717 (tt0) REVERT: F 72 GLU cc_start: 0.7548 (mp0) cc_final: 0.6979 (mp0) REVERT: F 89 ASP cc_start: 0.7069 (t0) cc_final: 0.6855 (t0) REVERT: F 139 GLU cc_start: 0.7158 (mp0) cc_final: 0.6750 (mp0) REVERT: F 190 GLU cc_start: 0.6885 (mp0) cc_final: 0.6616 (mp0) REVERT: F 242 GLN cc_start: 0.8367 (tp40) cc_final: 0.7968 (tm-30) REVERT: F 311 GLN cc_start: 0.8107 (tt0) cc_final: 0.7877 (tt0) REVERT: G 70 THR cc_start: 0.7188 (OUTLIER) cc_final: 0.6960 (p) REVERT: G 72 GLU cc_start: 0.6949 (mp0) cc_final: 0.6589 (mp0) REVERT: G 74 LEU cc_start: 0.7091 (mm) cc_final: 0.6825 (mt) REVERT: G 83 LEU cc_start: 0.8197 (tp) cc_final: 0.7964 (tm) REVERT: G 106 GLN cc_start: 0.6879 (pm20) cc_final: 0.6674 (pm20) REVERT: G 233 LEU cc_start: 0.8658 (tp) cc_final: 0.8364 (tm) REVERT: G 254 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7227 (mm) REVERT: G 287 GLN cc_start: 0.7496 (pp30) cc_final: 0.7227 (pp30) REVERT: G 288 GLU cc_start: 0.7694 (tp30) cc_final: 0.7258 (tp30) REVERT: G 294 GLN cc_start: 0.4227 (tp40) cc_final: 0.4019 (mm110) REVERT: G 295 ASN cc_start: 0.7239 (t0) cc_final: 0.6758 (t0) REVERT: H 8 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7876 (ptmt) REVERT: H 86 GLN cc_start: 0.7949 (tt0) cc_final: 0.7636 (tt0) REVERT: H 95 ASN cc_start: 0.8432 (m-40) cc_final: 0.8149 (m-40) REVERT: H 118 LYS cc_start: 0.8532 (mmtp) cc_final: 0.8164 (mttp) REVERT: H 122 ILE cc_start: 0.7959 (OUTLIER) cc_final: 0.7707 (pt) REVERT: H 137 LEU cc_start: 0.8397 (tp) cc_final: 0.8131 (tt) REVERT: H 153 ARG cc_start: 0.8600 (mtp85) cc_final: 0.8356 (mtt90) REVERT: H 201 ASN cc_start: 0.7416 (m-40) cc_final: 0.6936 (m-40) REVERT: H 205 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7726 (ttm) REVERT: H 217 GLN cc_start: 0.8361 (tt0) cc_final: 0.8127 (tp40) REVERT: H 227 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7890 (p) REVERT: I 18 ASP cc_start: 0.7090 (p0) cc_final: 0.6841 (p0) REVERT: I 20 ILE cc_start: 0.8643 (mt) cc_final: 0.8293 (mm) REVERT: I 22 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7728 (tp) REVERT: I 26 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7818 (mt0) REVERT: I 78 LEU cc_start: 0.8235 (mt) cc_final: 0.7927 (mt) REVERT: I 82 ILE cc_start: 0.8615 (mt) cc_final: 0.8395 (mt) REVERT: I 86 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8389 (tt) REVERT: I 93 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7836 (tmm) REVERT: I 94 GLN cc_start: 0.8369 (mm110) cc_final: 0.8131 (mm-40) REVERT: I 105 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7288 (mtt180) REVERT: I 106 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.6779 (mtp180) REVERT: I 109 CYS cc_start: 0.8069 (m) cc_final: 0.7550 (m) REVERT: I 149 ASN cc_start: 0.7867 (m-40) cc_final: 0.7491 (m-40) REVERT: I 152 GLU cc_start: 0.7552 (mp0) cc_final: 0.7170 (mp0) REVERT: I 229 ARG cc_start: 0.7334 (ptm160) cc_final: 0.7048 (ptm160) REVERT: I 233 LEU cc_start: 0.8306 (mt) cc_final: 0.7990 (mt) REVERT: I 294 GLU cc_start: 0.6835 (tp30) cc_final: 0.6609 (mm-30) REVERT: I 295 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7403 (ttt180) REVERT: I 298 ILE cc_start: 0.8667 (pp) cc_final: 0.8408 (mt) REVERT: I 346 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8130 (pp) REVERT: I 349 GLN cc_start: 0.8198 (tp40) cc_final: 0.7381 (tp-100) REVERT: I 351 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8504 (mm) REVERT: I 400 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7835 (mtpp) REVERT: I 401 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6888 (mm-30) REVERT: I 415 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7297 (ptmm) REVERT: I 460 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7083 (tm-30) REVERT: I 472 TRP cc_start: 0.8410 (t60) cc_final: 0.8127 (t60) REVERT: I 474 GLU cc_start: 0.6612 (pt0) cc_final: 0.6262 (pt0) REVERT: I 488 GLN cc_start: 0.7685 (tp40) cc_final: 0.6914 (tm-30) REVERT: I 504 GLU cc_start: 0.6729 (tp30) cc_final: 0.6458 (tp30) REVERT: I 544 ASP cc_start: 0.7483 (t70) cc_final: 0.7253 (t0) REVERT: I 576 GLU cc_start: 0.7363 (tp30) cc_final: 0.6893 (tp30) REVERT: I 590 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7702 (tmtt) REVERT: I 595 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7862 (mm-40) REVERT: I 606 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7731 (p) REVERT: I 632 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7574 (ttpp) REVERT: I 642 THR cc_start: 0.8413 (m) cc_final: 0.8183 (p) REVERT: I 667 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6808 (mm-30) REVERT: I 668 ASP cc_start: 0.7168 (m-30) cc_final: 0.6956 (m-30) REVERT: I 686 ASP cc_start: 0.7463 (m-30) cc_final: 0.7080 (t0) REVERT: I 723 ARG cc_start: 0.7035 (mtp85) cc_final: 0.6686 (mtp85) REVERT: I 746 VAL cc_start: 0.8556 (p) cc_final: 0.8313 (t) REVERT: I 774 ARG cc_start: 0.8030 (ttp-110) cc_final: 0.7673 (mtm110) REVERT: I 780 LYS cc_start: 0.8250 (mttp) cc_final: 0.7946 (mttp) REVERT: I 788 ASP cc_start: 0.6888 (t0) cc_final: 0.6674 (t70) REVERT: I 797 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6865 (mm-30) REVERT: I 807 ARG cc_start: 0.7500 (ptp-110) cc_final: 0.7288 (ptp-110) REVERT: I 827 ASN cc_start: 0.7601 (t0) cc_final: 0.7333 (t0) REVERT: I 829 VAL cc_start: 0.8738 (m) cc_final: 0.8452 (p) REVERT: I 832 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6959 (mt-10) REVERT: I 835 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8061 (mtpp) REVERT: I 870 GLU cc_start: 0.6753 (pp20) cc_final: 0.6477 (pp20) REVERT: I 871 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: I 927 ILE cc_start: 0.8472 (tt) cc_final: 0.8194 (pt) REVERT: I 934 ARG cc_start: 0.7598 (tpp80) cc_final: 0.7263 (mtm-85) REVERT: I 972 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7078 (pp30) REVERT: J 5 LEU cc_start: 0.5067 (OUTLIER) cc_final: 0.4497 (pt) REVERT: J 14 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7293 (mm-30) REVERT: J 33 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6567 (pp) REVERT: J 41 GLU cc_start: 0.7228 (tp30) cc_final: 0.6305 (tp30) REVERT: J 52 GLU cc_start: 0.6336 (tm-30) cc_final: 0.6096 (tm-30) REVERT: J 53 GLU cc_start: 0.7315 (mp0) cc_final: 0.6803 (mp0) REVERT: J 54 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6781 (tm-30) REVERT: J 121 GLU cc_start: 0.7260 (tm-30) cc_final: 0.7015 (tm-30) REVERT: J 135 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7737 (mtm-85) REVERT: K 100 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7121 (mtm) outliers start: 143 outliers final: 85 residues processed: 1019 average time/residue: 1.6371 time to fit residues: 1938.2541 Evaluate side-chains 1058 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 943 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 105 LYS Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 57 ASN Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 34 GLU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 705 LYS Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 831 THR Chi-restraints excluded: chain I residue 871 GLN Chi-restraints excluded: chain I residue 923 GLU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 218 optimal weight: 0.9980 chunk 351 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 368 optimal weight: 1.9990 chunk 339 optimal weight: 0.5980 chunk 293 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 GLN B 217 ASN B 232 ASN ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 311 GLN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 267 ASN D 290 ASN E 10 GLN E 232 ASN E 267 ASN E 295 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 HIS F 43 ASN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 34 ASN ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 110 GLN H 119 ASN I 35 HIS I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 871 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31399 Z= 0.304 Angle : 0.668 12.214 42781 Z= 0.339 Chirality : 0.044 0.191 4787 Planarity : 0.004 0.057 5308 Dihedral : 14.161 171.490 5016 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.10 % Allowed : 26.48 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3639 helix: 1.36 (0.14), residues: 1573 sheet: -0.05 (0.22), residues: 477 loop : -0.79 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 221 HIS 0.010 0.001 HIS I 246 PHE 0.034 0.002 PHE I 150 TYR 0.030 0.002 TYR I 844 ARG 0.014 0.001 ARG H 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7278 Ramachandran restraints generated. 3639 Oldfield, 0 Emsley, 3639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 944 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8296 (m) REVERT: A 58 LEU cc_start: 0.8205 (tp) cc_final: 0.7922 (tt) REVERT: A 65 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7520 (mtmm) REVERT: A 72 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6948 (mt-10) REVERT: A 87 SER cc_start: 0.8514 (t) cc_final: 0.8147 (p) REVERT: A 101 GLU cc_start: 0.6702 (mt-10) cc_final: 0.6368 (mt-10) REVERT: A 139 GLU cc_start: 0.7841 (mp0) cc_final: 0.7315 (mp0) REVERT: A 194 TYR cc_start: 0.8503 (t80) cc_final: 0.8075 (t80) REVERT: A 209 GLU cc_start: 0.7382 (pt0) cc_final: 0.7164 (pt0) REVERT: A 210 SER cc_start: 0.8554 (m) cc_final: 0.8225 (p) REVERT: A 232 ASN cc_start: 0.8267 (m-40) cc_final: 0.8017 (m110) REVERT: A 271 VAL cc_start: 0.8281 (p) cc_final: 0.8006 (m) REVERT: A 283 ASP cc_start: 0.7435 (m-30) cc_final: 0.7082 (m-30) REVERT: A 287 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 298 GLU cc_start: 0.7716 (tp30) cc_final: 0.7460 (tp30) REVERT: A 301 LYS cc_start: 0.8378 (ttpp) cc_final: 0.8080 (ttpp) REVERT: A 311 GLN cc_start: 0.8008 (tt0) cc_final: 0.7795 (tt0) REVERT: B 39 ASP cc_start: 0.5954 (t0) cc_final: 0.5719 (t0) REVERT: B 58 LEU cc_start: 0.8170 (tt) cc_final: 0.7805 (pt) REVERT: B 109 ASP cc_start: 0.7664 (t70) cc_final: 0.7221 (t0) REVERT: B 123 GLU cc_start: 0.7716 (tp30) cc_final: 0.7344 (tp30) REVERT: B 185 ARG cc_start: 0.8335 (mtp85) cc_final: 0.8095 (mtp85) REVERT: B 226 ASP cc_start: 0.6843 (t0) cc_final: 0.6556 (t0) REVERT: B 268 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8347 (mtpp) REVERT: B 283 ASP cc_start: 0.7338 (p0) cc_final: 0.6823 (p0) REVERT: C 1 MET cc_start: 0.7607 (tpp) cc_final: 0.6918 (tpt) REVERT: C 139 GLU cc_start: 0.7532 (mp0) cc_final: 0.7184 (mp0) REVERT: C 151 PHE cc_start: 0.8301 (m-80) cc_final: 0.8051 (m-80) REVERT: C 156 MET cc_start: 0.7591 (mmm) cc_final: 0.7227 (mtm) REVERT: C 199 LEU cc_start: 0.8633 (mt) cc_final: 0.8427 (mt) REVERT: C 283 ASP cc_start: 0.7282 (m-30) cc_final: 0.7020 (m-30) REVERT: D 65 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.7047 (pttt) REVERT: D 72 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6899 (mt-10) REVERT: D 78 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: D 156 MET cc_start: 0.7628 (mtp) cc_final: 0.7216 (mtp) REVERT: D 283 ASP cc_start: 0.7402 (m-30) cc_final: 0.7126 (m-30) REVERT: E 45 THR cc_start: 0.8453 (t) cc_final: 0.8175 (m) REVERT: E 46 ARG cc_start: 0.8018 (mtp-110) cc_final: 0.7609 (mmm160) REVERT: E 72 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6885 (mt-10) REVERT: E 89 ASP cc_start: 0.8568 (p0) cc_final: 0.8327 (p0) REVERT: E 141 SER cc_start: 0.8438 (m) cc_final: 0.8067 (p) REVERT: E 173 LEU cc_start: 0.8503 (mp) cc_final: 0.8208 (mm) REVERT: E 199 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8283 (mm) REVERT: E 209 GLU cc_start: 0.7003 (mt-10) cc_final: 0.6721 (mt-10) REVERT: E 231 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8200 (t) REVERT: E 241 ASP cc_start: 0.7507 (m-30) cc_final: 0.7281 (m-30) REVERT: E 249 LYS cc_start: 0.7740 (mmpt) cc_final: 0.7452 (mmpt) REVERT: E 256 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7061 (mm-30) REVERT: E 264 ASP cc_start: 0.7628 (t70) cc_final: 0.7357 (t0) REVERT: E 308 GLN cc_start: 0.7580 (tp40) cc_final: 0.7138 (tp40) REVERT: E 312 ASP cc_start: 0.7600 (m-30) cc_final: 0.7311 (m-30) REVERT: F 26 MET cc_start: 0.7882 (ptm) cc_final: 0.7621 (ptt) REVERT: F 67 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8082 (mtpp) REVERT: F 220 VAL cc_start: 0.8707 (p) cc_final: 0.8503 (t) REVERT: G 72 GLU cc_start: 0.7005 (mp0) cc_final: 0.6625 (mp0) REVERT: G 74 LEU cc_start: 0.7103 (mm) cc_final: 0.6827 (mt) REVERT: G 83 LEU cc_start: 0.8222 (tp) cc_final: 0.7987 (tm) REVERT: G 106 GLN cc_start: 0.6911 (pm20) cc_final: 0.6682 (pm20) REVERT: G 124 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6203 (tmm160) REVERT: G 233 LEU cc_start: 0.8726 (tp) cc_final: 0.8368 (tm) REVERT: G 254 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7238 (mm) REVERT: G 287 GLN cc_start: 0.7514 (pp30) cc_final: 0.7247 (pp30) REVERT: G 288 GLU cc_start: 0.7714 (tp30) cc_final: 0.7270 (tp30) REVERT: G 294 GLN cc_start: 0.4249 (tp40) cc_final: 0.4019 (mm110) REVERT: G 295 ASN cc_start: 0.7315 (t0) cc_final: 0.6848 (t0) REVERT: H 8 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7883 (ptmt) REVERT: H 86 GLN cc_start: 0.7989 (tt0) cc_final: 0.7693 (tt0) REVERT: H 118 LYS cc_start: 0.8537 (mmtp) cc_final: 0.8189 (mttp) REVERT: H 122 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7760 (pt) REVERT: H 137 LEU cc_start: 0.8416 (tp) cc_final: 0.8146 (tt) REVERT: H 153 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8384 (mtt90) REVERT: H 174 LYS cc_start: 0.7617 (ptpt) cc_final: 0.7359 (ptpt) REVERT: H 201 ASN cc_start: 0.7475 (m-40) cc_final: 0.6837 (m110) REVERT: H 205 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7805 (ttm) REVERT: H 217 GLN cc_start: 0.8391 (tt0) cc_final: 0.8150 (tp40) REVERT: H 227 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7896 (p) REVERT: I 18 ASP cc_start: 0.7102 (p0) cc_final: 0.6843 (p0) REVERT: I 20 ILE cc_start: 0.8645 (mt) cc_final: 0.8283 (mm) REVERT: I 22 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7642 (tp) REVERT: I 26 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7786 (mt0) REVERT: I 35 HIS cc_start: 0.8405 (OUTLIER) cc_final: 0.6854 (m-70) REVERT: I 78 LEU cc_start: 0.8248 (mt) cc_final: 0.7947 (mt) REVERT: I 82 ILE cc_start: 0.8624 (mt) cc_final: 0.8417 (mt) REVERT: I 86 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8377 (tt) REVERT: I 93 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7868 (tmm) REVERT: I 94 GLN cc_start: 0.8392 (mm110) cc_final: 0.8155 (mm-40) REVERT: I 106 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.6852 (mtp180) REVERT: I 147 ARG cc_start: 0.7470 (mtp85) cc_final: 0.6989 (mtp180) REVERT: I 149 ASN cc_start: 0.7830 (m-40) cc_final: 0.7479 (m-40) REVERT: I 152 GLU cc_start: 0.7560 (mp0) cc_final: 0.7191 (mp0) REVERT: I 206 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8157 (mm) REVERT: I 233 LEU cc_start: 0.8361 (mt) cc_final: 0.7989 (mt) REVERT: I 295 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7337 (ttt90) REVERT: I 298 ILE cc_start: 0.8696 (pp) cc_final: 0.8425 (mt) REVERT: I 346 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8184 (pp) REVERT: I 349 GLN cc_start: 0.8222 (tp40) cc_final: 0.7417 (tp-100) REVERT: I 351 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8548 (mm) REVERT: I 400 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7917 (mtpp) REVERT: I 415 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7356 (ptmm) REVERT: I 460 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7205 (tp30) REVERT: I 472 TRP cc_start: 0.8414 (t60) cc_final: 0.8050 (t60) REVERT: I 476 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7251 (mp0) REVERT: I 488 GLN cc_start: 0.7733 (tp40) cc_final: 0.7431 (tm-30) REVERT: I 492 ASP cc_start: 0.7096 (m-30) cc_final: 0.6207 (m-30) REVERT: I 504 GLU cc_start: 0.6761 (tp30) cc_final: 0.6449 (tp30) REVERT: I 544 ASP cc_start: 0.7500 (t70) cc_final: 0.7200 (t0) REVERT: I 590 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7700 (tmtt) REVERT: I 595 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7870 (mm-40) REVERT: I 606 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7899 (t) REVERT: I 632 LYS cc_start: 0.7899 (ttpt) cc_final: 0.7609 (ttpp) REVERT: I 642 THR cc_start: 0.8447 (m) cc_final: 0.8206 (p) REVERT: I 668 ASP cc_start: 0.7116 (m-30) cc_final: 0.6899 (m-30) REVERT: I 681 GLU cc_start: 0.7385 (mp0) cc_final: 0.6902 (mp0) REVERT: I 723 ARG cc_start: 0.7043 (mtp85) cc_final: 0.6687 (mtp85) REVERT: I 746 VAL cc_start: 0.8525 (p) cc_final: 0.8278 (t) REVERT: I 774 ARG cc_start: 0.8077 (ttp-110) cc_final: 0.7732 (mtm110) REVERT: I 780 LYS cc_start: 0.8284 (mttp) cc_final: 0.7992 (mttp) REVERT: I 797 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6869 (mm-30) REVERT: I 827 ASN cc_start: 0.7613 (t0) cc_final: 0.7322 (t0) REVERT: I 829 VAL cc_start: 0.8730 (m) cc_final: 0.8467 (p) REVERT: I 832 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6991 (mt-10) REVERT: I 835 LYS cc_start: 0.8426 (mtpt) cc_final: 0.8079 (mtpp) REVERT: I 842 GLU cc_start: 0.7601 (tm-30) cc_final: 0.6974 (tp30) REVERT: I 870 GLU cc_start: 0.6728 (pp20) cc_final: 0.6506 (pp20) REVERT: I 927 ILE cc_start: 0.8491 (tt) cc_final: 0.8178 (pt) REVERT: I 969 GLU cc_start: 0.7330 (tm-30) cc_final: 0.7006 (tm-30) REVERT: I 972 GLN cc_start: 0.7535 (tm-30) cc_final: 0.7083 (pp30) REVERT: J 5 LEU cc_start: 0.5222 (OUTLIER) cc_final: 0.4611 (pt) REVERT: J 14 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7360 (mm-30) REVERT: J 33 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6579 (pp) REVERT: J 41 GLU cc_start: 0.7279 (tp30) cc_final: 0.6343 (tp30) REVERT: J 53 GLU cc_start: 0.7300 (mp0) cc_final: 0.6843 (mp0) REVERT: J 54 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6775 (tm-30) REVERT: J 57 LEU cc_start: 0.8312 (mt) cc_final: 0.8108 (mp) REVERT: J 121 GLU cc_start: 0.7265 (tm-30) cc_final: 0.7014 (tm-30) REVERT: J 135 ARG cc_start: 0.8022 (mtt-85) cc_final: 0.7744 (mtm-85) REVERT: K 100 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7136 (mtm) outliers start: 130 outliers final: 83 residues processed: 998 average time/residue: 1.5776 time to fit residues: 1822.5534 Evaluate side-chains 1051 residues out of total 3172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 941 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 67 LYS Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 218 HIS Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 287 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 286 LEU Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 228 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 267 ASN Chi-restraints excluded: chain F residue 6 LYS Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 228 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 124 ARG Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain G residue 162 MET Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 236 THR Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 281 HIS Chi-restraints excluded: chain G residue 316 GLU Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 67 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 122 ILE Chi-restraints excluded: chain H residue 144 LYS Chi-restraints excluded: chain H residue 175 THR Chi-restraints excluded: chain H residue 205 MET Chi-restraints excluded: chain H residue 227 THR Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 35 HIS Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 93 MET Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 196 ARG Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 246 HIS Chi-restraints excluded: chain I residue 295 ARG Chi-restraints excluded: chain I residue 346 ILE Chi-restraints excluded: chain I residue 351 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 363 THR Chi-restraints excluded: chain I residue 368 GLU Chi-restraints excluded: chain I residue 415 LYS Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 461 PHE Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 479 PHE Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 590 LYS Chi-restraints excluded: chain I residue 606 VAL Chi-restraints excluded: chain I residue 641 LEU Chi-restraints excluded: chain I residue 650 LEU Chi-restraints excluded: chain I residue 689 VAL Chi-restraints excluded: chain I residue 705 LYS Chi-restraints excluded: chain I residue 748 ASP Chi-restraints excluded: chain I residue 750 THR Chi-restraints excluded: chain I residue 831 THR Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 131 GLU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain K residue 119 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 1.9990 chunk 312 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 270 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 293 optimal weight: 0.3980 chunk 123 optimal weight: 0.7980 chunk 301 optimal weight: 0.0980 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 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 43 ASN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN B 198 ASN B 217 ASN B 232 ASN C 10 GLN C 267 ASN C 290 ASN C 295 ASN D 10 GLN D 267 ASN D 290 ASN E 10 GLN E 48 GLN E 217 ASN E 232 ASN E 267 ASN E 295 ASN F 8 GLN F 20 HIS F 43 ASN G 68 GLN ** G 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 95 ASN H 110 GLN I 35 HIS I 399 GLN ** I 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.118953 restraints weight = 47633.227| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.94 r_work: 0.3434 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31399 Z= 0.246 Angle : 0.668 13.606 42781 Z= 0.337 Chirality : 0.043 0.261 4787 Planarity : 0.004 0.093 5308 Dihedral : 14.148 171.210 5016 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.42 % Allowed : 26.74 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.76 % 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: 0.36 (0.14), residues: 3639 helix: 1.37 (0.14), residues: 1574 sheet: -0.08 (0.22), residues: 477 loop : -0.78 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 221 HIS 0.009 0.001 HIS I 246 PHE 0.027 0.001 PHE I 150 TYR 0.028 0.001 TYR I 446 ARG 0.022 0.001 ARG I 846 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23347.88 seconds wall clock time: 410 minutes 34.86 seconds (24634.86 seconds total)