Starting phenix.real_space_refine on Fri Feb 23 06:05:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/02_2024/6qg0_4543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/02_2024/6qg0_4543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/02_2024/6qg0_4543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/02_2024/6qg0_4543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/02_2024/6qg0_4543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/02_2024/6qg0_4543_updated.pdb" } resolution = 4.15 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= -0.000 sd= 0.013 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 2 5.49 5 S 162 5.16 5 C 23526 2.51 5 N 6322 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G GLU 508": "OE1" <-> "OE2" Residue "G GLU 538": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H GLU 436": "OE1" <-> "OE2" Residue "H GLU 508": "OE1" <-> "OE2" Residue "H GLU 538": "OE1" <-> "OE2" Residue "H GLU 583": "OE1" <-> "OE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I GLU 370": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 494": "OE1" <-> "OE2" Residue "M GLU 506": "OE1" <-> "OE2" Residue "N GLU 231": "OE1" <-> "OE2" Residue "N PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N GLU 494": "OE1" <-> "OE2" Residue "N GLU 506": "OE1" <-> "OE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 93": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K GLU 159": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36980 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "F" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "G" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "N" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "K" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 19.19, per 1000 atoms: 0.52 Number of scatterers: 36980 At special positions: 0 Unit cell: (274.7, 167.5, 121.94, 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 162 16.00 P 2 15.00 O 6968 8.00 N 6322 7.00 C 23526 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: 14.58 Conformation dependent library (CDL) restraints added in 7.4 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 48 sheets defined 29.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.917A pdb=" N ILE A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.639A pdb=" N ASP A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.546A pdb=" N ALA A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.514A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.520A pdb=" N VAL A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.788A pdb=" N THR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.649A pdb=" N ASP B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 115 removed outlier: 4.257A pdb=" N GLY B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 101 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.534A pdb=" N VAL B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 82 through 107 removed outlier: 3.550A pdb=" N ILE D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 166 Processing helix chain 'D' and resid 169 through 176 removed outlier: 3.993A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 279 through 287 Processing helix chain 'D' and resid 309 through 312 No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'E' and resid 76 through 86 removed outlier: 4.119A pdb=" N VAL E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 258 through 261 No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.992A pdb=" N GLN E 286 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 287 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 288 " --> pdb=" O CYS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 411 removed outlier: 3.533A pdb=" N ASN E 405 " --> pdb=" O MET E 402 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 409 " --> pdb=" O ARG E 406 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE E 411 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 181 through 190 Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 282 through 288 removed outlier: 3.997A pdb=" N GLN F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 287 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F 288 " --> pdb=" O CYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 411 removed outlier: 3.559A pdb=" N ASN F 405 " --> pdb=" O MET F 402 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE F 407 " --> pdb=" O ALA F 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 411 " --> pdb=" O VAL F 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 removed outlier: 4.054A pdb=" N HIS G 283 " --> pdb=" O SER G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 306 removed outlier: 3.904A pdb=" N ILE G 294 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'G' and resid 338 through 353 Processing helix chain 'G' and resid 360 through 378 removed outlier: 3.704A pdb=" N ASP G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 393 removed outlier: 3.743A pdb=" N GLN G 393 " --> pdb=" O ASN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 418 Processing helix chain 'G' and resid 436 through 447 Processing helix chain 'G' and resid 490 through 498 Processing helix chain 'G' and resid 529 through 532 Processing helix chain 'H' and resid 272 through 283 removed outlier: 4.048A pdb=" N HIS H 283 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 306 removed outlier: 3.723A pdb=" N ILE H 294 " --> pdb=" O ILE H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'H' and resid 338 through 353 Processing helix chain 'H' and resid 360 through 378 removed outlier: 3.541A pdb=" N LYS H 365 " --> pdb=" O LYS H 361 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP H 366 " --> pdb=" O ALA H 362 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 393 removed outlier: 3.623A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 417 Processing helix chain 'H' and resid 436 through 447 Processing helix chain 'H' and resid 456 through 462 removed outlier: 3.571A pdb=" N LEU H 459 " --> pdb=" O ILE H 456 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP H 460 " --> pdb=" O THR H 457 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR H 461 " --> pdb=" O SER H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 498 Processing helix chain 'H' and resid 529 through 532 Processing helix chain 'H' and resid 583 through 588 removed outlier: 6.039A pdb=" N LYS H 587 " --> pdb=" O GLY H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 70 Processing helix chain 'I' and resid 83 through 91 Processing helix chain 'I' and resid 115 through 125 Processing helix chain 'I' and resid 146 through 156 Processing helix chain 'I' and resid 218 through 221 No H-bonds generated for 'chain 'I' and resid 218 through 221' Processing helix chain 'I' and resid 241 through 248 Processing helix chain 'I' and resid 259 through 264 Processing helix chain 'I' and resid 288 through 299 Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing helix chain 'J' and resid 59 through 70 removed outlier: 3.515A pdb=" N THR J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 91 Processing helix chain 'J' and resid 115 through 125 Processing helix chain 'J' and resid 146 through 156 Processing helix chain 'J' and resid 215 through 221 removed outlier: 4.175A pdb=" N LEU J 218 " --> pdb=" O PRO J 215 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP J 219 " --> pdb=" O GLU J 216 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN J 220 " --> pdb=" O LEU J 217 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL J 221 " --> pdb=" O LEU J 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 215 through 221' Processing helix chain 'J' and resid 241 through 248 Processing helix chain 'J' and resid 259 through 264 Processing helix chain 'J' and resid 288 through 299 Processing helix chain 'J' and resid 308 through 310 No H-bonds generated for 'chain 'J' and resid 308 through 310' Processing helix chain 'L' and resid 92 through 118 removed outlier: 4.150A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG L 113 " --> pdb=" O HIS L 109 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 141 through 150 removed outlier: 3.731A pdb=" N ILE L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 173 Processing helix chain 'L' and resid 198 through 208 Processing helix chain 'L' and resid 238 through 258 removed outlier: 3.545A pdb=" N ILE L 241 " --> pdb=" O GLN L 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU L 242 " --> pdb=" O LYS L 239 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN L 243 " --> pdb=" O GLY L 240 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU L 244 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU L 245 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 246 " --> pdb=" O GLN L 243 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE L 248 " --> pdb=" O GLU L 245 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS L 250 " --> pdb=" O ALA L 247 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 252 " --> pdb=" O GLU L 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 253 " --> pdb=" O LYS L 250 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE L 255 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR L 256 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR L 258 " --> pdb=" O ILE L 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 120 Processing helix chain 'M' and resid 202 through 210 removed outlier: 3.592A pdb=" N ALA M 209 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 238 Processing helix chain 'M' and resid 258 through 269 Processing helix chain 'M' and resid 291 through 301 removed outlier: 3.602A pdb=" N VAL M 299 " --> pdb=" O ASN M 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'N' and resid 113 through 120 Processing helix chain 'N' and resid 202 through 210 removed outlier: 3.570A pdb=" N ALA N 209 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 238 Processing helix chain 'N' and resid 256 through 269 removed outlier: 3.821A pdb=" N LEU N 260 " --> pdb=" O GLU N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 301 removed outlier: 3.566A pdb=" N VAL N 299 " --> pdb=" O ASN N 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 140 Processing helix chain 'K' and resid 92 through 118 removed outlier: 4.150A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 130 Processing helix chain 'K' and resid 141 through 150 removed outlier: 3.747A pdb=" N ILE K 150 " --> pdb=" O LYS K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'K' and resid 198 through 208 Processing helix chain 'K' and resid 238 through 258 removed outlier: 3.535A pdb=" N ILE K 241 " --> pdb=" O GLN K 238 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 242 " --> pdb=" O LYS K 239 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN K 243 " --> pdb=" O GLY K 240 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU K 245 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER K 246 " --> pdb=" O GLN K 243 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE K 248 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS K 250 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR K 252 " --> pdb=" O GLU K 249 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU K 253 " --> pdb=" O LYS K 250 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE K 255 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR K 256 " --> pdb=" O GLU K 253 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS K 257 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR K 258 " --> pdb=" O ILE K 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 61 through 77 Processing helix chain 'C' and resid 82 through 107 removed outlier: 3.548A pdb=" N ILE C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 169 through 176 removed outlier: 3.992A pdb=" N GLN C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 223 through 235 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 309 through 312 No H-bonds generated for 'chain 'C' and resid 309 through 312' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 361 through 366 Processing sheet with id= A, first strand: chain 'A' and resid 282 through 284 removed outlier: 7.389A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 154 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 207 through 209 Processing sheet with id= C, first strand: chain 'B' and resid 282 through 284 removed outlier: 3.637A pdb=" N THR B 154 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR B 177 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.516A pdb=" N ASN B 209 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 348 through 350 removed outlier: 3.964A pdb=" N ILE D 348 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY D 261 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 339 through 341 removed outlier: 3.638A pdb=" N ASP D 339 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 133 through 137 removed outlier: 7.685A pdb=" N ILE E 92 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLN E 136 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL E 94 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 5 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL E 95 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 7 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 194 through 199 Processing sheet with id= I, first strand: chain 'E' and resid 223 through 225 Processing sheet with id= J, first strand: chain 'F' and resid 133 through 137 removed outlier: 7.603A pdb=" N ILE F 92 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N GLN F 136 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL F 94 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA F 5 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL F 95 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL F 7 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 194 through 199 Processing sheet with id= L, first strand: chain 'F' and resid 223 through 225 Processing sheet with id= M, first strand: chain 'G' and resid 579 through 581 removed outlier: 8.045A pdb=" N VAL G 503 " --> pdb=" O LYS G 572 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN G 574 " --> pdb=" O VAL G 503 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 505 " --> pdb=" O ASN G 574 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE G 576 " --> pdb=" O VAL G 505 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL G 470 " --> pdb=" O LEU G 504 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N CYS G 506 " --> pdb=" O VAL G 470 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU G 472 " --> pdb=" O CYS G 506 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR G 403 " --> pdb=" O PHE G 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY G 473 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS G 425 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR G 402 " --> pdb=" O LYS G 425 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE G 427 " --> pdb=" O THR G 402 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 564 through 566 Processing sheet with id= O, first strand: chain 'H' and resid 571 through 575 removed outlier: 7.660A pdb=" N VAL H 503 " --> pdb=" O LYS H 572 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN H 574 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 505 " --> pdb=" O ASN H 574 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL H 470 " --> pdb=" O LEU H 504 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS H 506 " --> pdb=" O VAL H 470 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU H 472 " --> pdb=" O CYS H 506 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR H 403 " --> pdb=" O PHE H 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 473 " --> pdb=" O TYR H 403 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS H 425 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR H 402 " --> pdb=" O LYS H 425 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 427 " --> pdb=" O THR H 402 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 564 through 566 Processing sheet with id= Q, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.509A pdb=" N ILE I 237 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN I 28 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL I 135 " --> pdb=" O GLN I 28 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL I 30 " --> pdb=" O VAL I 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU I 74 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL I 31 " --> pdb=" O GLU I 74 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE I 76 " --> pdb=" O VAL I 31 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS I 103 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU I 77 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR I 105 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS I 79 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE I 107 " --> pdb=" O CYS I 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 139 through 141 removed outlier: 4.039A pdb=" N LEU I 140 " --> pdb=" O VAL I 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL I 283 " --> pdb=" O LEU I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 276 through 278 removed outlier: 3.594A pdb=" N LYS I 170 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER I 169 " --> pdb=" O ILE I 231 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 224 through 227 removed outlier: 3.635A pdb=" N GLN I 198 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I 186 " --> pdb=" O TYR I 196 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR I 196 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP I 188 " --> pdb=" O CYS I 194 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS I 194 " --> pdb=" O ASP I 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 319 through 321 removed outlier: 6.441A pdb=" N THR I 343 " --> pdb=" O TYR I 326 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 331 through 333 removed outlier: 5.804A pdb=" N THR I 349 " --> pdb=" O VAL I 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'I' and resid 356 through 358 Processing sheet with id= X, first strand: chain 'I' and resid 394 through 396 removed outlier: 6.255A pdb=" N CYS I 412 " --> pdb=" O LEU I 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'J' and resid 164 through 166 removed outlier: 3.510A pdb=" N ILE J 237 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN J 28 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N VAL J 135 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL J 30 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU J 74 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL J 31 " --> pdb=" O GLU J 74 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE J 76 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS J 103 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU J 77 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR J 105 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS J 79 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE J 107 " --> pdb=" O CYS J 79 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 139 through 141 removed outlier: 4.052A pdb=" N LEU J 140 " --> pdb=" O VAL J 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL J 283 " --> pdb=" O LEU J 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'J' and resid 276 through 278 removed outlier: 3.517A pdb=" N LYS J 170 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 169 " --> pdb=" O ILE J 231 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 185 through 188 Processing sheet with id= AC, first strand: chain 'J' and resid 319 through 321 removed outlier: 6.435A pdb=" N THR J 343 " --> pdb=" O TYR J 326 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 331 through 333 removed outlier: 5.788A pdb=" N THR J 349 " --> pdb=" O VAL J 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'J' and resid 356 through 358 Processing sheet with id= AF, first strand: chain 'J' and resid 394 through 396 removed outlier: 6.229A pdb=" N CYS J 412 " --> pdb=" O LEU J 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'L' and resid 262 through 264 Processing sheet with id= AH, first strand: chain 'L' and resid 72 through 77 removed outlier: 6.628A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL L 76 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR L 82 " --> pdb=" O VAL L 76 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 280 through 282 removed outlier: 8.636A pdb=" N VAL M 281 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE M 246 " --> pdb=" O VAL M 281 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA M 214 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU M 247 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU M 216 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE M 101 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER M 190 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR M 105 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL M 186 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE M 147 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N HIS M 188 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA M 145 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 143 " --> pdb=" O SER M 190 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 373 through 376 removed outlier: 4.352A pdb=" N ASN M 344 " --> pdb=" O ARG M 314 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE M 316 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE M 342 " --> pdb=" O ILE M 316 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE M 342 " --> pdb=" O GLY M 394 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY M 394 " --> pdb=" O ILE M 342 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 319 through 321 Processing sheet with id= AL, first strand: chain 'M' and resid 425 through 427 removed outlier: 3.756A pdb=" N ASN M 425 " --> pdb=" O THR M 493 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 482 through 486 removed outlier: 7.248A pdb=" N LEU M 501 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP M 514 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE M 499 " --> pdb=" O TRP M 514 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG M 504 " --> pdb=" O VAL M 461 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL M 461 " --> pdb=" O ARG M 504 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR M 471 " --> pdb=" O VAL M 464 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE M 466 " --> pdb=" O THR M 469 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG M 484 " --> pdb=" O VAL M 476 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 280 through 282 removed outlier: 8.591A pdb=" N VAL N 281 " --> pdb=" O VAL N 244 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE N 246 " --> pdb=" O VAL N 281 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA N 214 " --> pdb=" O ILE N 245 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU N 247 " --> pdb=" O ALA N 214 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU N 216 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE N 101 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER N 190 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR N 105 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL N 186 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE N 147 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N HIS N 188 " --> pdb=" O ALA N 145 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA N 145 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER N 190 " --> pdb=" O ALA N 143 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA N 143 " --> pdb=" O SER N 190 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 373 through 376 removed outlier: 4.336A pdb=" N ASN N 344 " --> pdb=" O ARG N 314 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE N 316 " --> pdb=" O ILE N 342 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE N 342 " --> pdb=" O ILE N 316 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE N 342 " --> pdb=" O GLY N 394 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY N 394 " --> pdb=" O ILE N 342 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 319 through 321 Processing sheet with id= AQ, first strand: chain 'N' and resid 425 through 427 removed outlier: 3.710A pdb=" N ASN N 425 " --> pdb=" O THR N 493 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 482 through 486 removed outlier: 7.259A pdb=" N LEU N 501 " --> pdb=" O ILE N 512 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP N 514 " --> pdb=" O ILE N 499 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE N 499 " --> pdb=" O TRP N 514 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG N 504 " --> pdb=" O VAL N 461 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL N 461 " --> pdb=" O ARG N 504 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 471 " --> pdb=" O VAL N 464 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 484 " --> pdb=" O VAL N 476 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'K' and resid 262 through 264 Processing sheet with id= AT, first strand: chain 'K' and resid 72 through 77 removed outlier: 6.629A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.965A pdb=" N ILE C 348 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 261 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 339 through 341 removed outlier: 3.636A pdb=" N ASP C 339 " --> pdb=" O SER C 273 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.38 Time building geometry restraints manager: 15.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6299 1.32 - 1.45: 9109 1.45 - 1.57: 21943 1.57 - 1.70: 5 1.70 - 1.83: 242 Bond restraints: 37598 Sorted by residual: bond pdb=" N ASN B 89 " pdb=" CA ASN B 89 " ideal model delta sigma weight residual 1.459 1.543 -0.085 1.28e-02 6.10e+03 4.37e+01 bond pdb=" O3P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.495 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C ALA B 68 " pdb=" N GLY B 69 " ideal model delta sigma weight residual 1.334 1.254 0.080 1.42e-02 4.96e+03 3.21e+01 bond pdb=" O1P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" O2P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 37593 not shown) Histogram of bond angle deviations from ideal: 96.44 - 103.99: 483 103.99 - 111.55: 13726 111.55 - 119.10: 16842 119.10 - 126.65: 19489 126.65 - 134.21: 350 Bond angle restraints: 50890 Sorted by residual: angle pdb=" N ARG N 356 " pdb=" CA ARG N 356 " pdb=" C ARG N 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ARG M 356 " pdb=" CA ARG M 356 " pdb=" C ARG M 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ILE H 501 " pdb=" CA ILE H 501 " pdb=" C ILE H 501 " ideal model delta sigma weight residual 109.02 114.80 -5.78 9.30e-01 1.16e+00 3.86e+01 angle pdb=" CA LEU C 125 " pdb=" C LEU C 125 " pdb=" N GLN C 126 " ideal model delta sigma weight residual 119.56 116.25 3.31 5.80e-01 2.97e+00 3.25e+01 angle pdb=" N ILE A 207 " pdb=" CA ILE A 207 " pdb=" C ILE A 207 " ideal model delta sigma weight residual 108.46 116.34 -7.88 1.49e+00 4.50e-01 2.79e+01 ... (remaining 50885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 19287 16.66 - 33.32: 2680 33.32 - 49.98: 612 49.98 - 66.63: 334 66.63 - 83.29: 69 Dihedral angle restraints: 22982 sinusoidal: 9164 harmonic: 13818 Sorted by residual: dihedral pdb=" C GLN I 289 " pdb=" N GLN I 289 " pdb=" CA GLN I 289 " pdb=" CB GLN I 289 " ideal model delta harmonic sigma weight residual -122.60 -136.49 13.89 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" C LEU J 202 " pdb=" N LEU J 202 " pdb=" CA LEU J 202 " pdb=" CB LEU J 202 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLN J 289 " pdb=" N GLN J 289 " pdb=" CA GLN J 289 " pdb=" CB GLN J 289 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 22979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5051 0.109 - 0.217: 800 0.217 - 0.326: 98 0.326 - 0.434: 15 0.434 - 0.543: 8 Chirality restraints: 5972 Sorted by residual: chirality pdb=" CA GLN I 289 " pdb=" N GLN I 289 " pdb=" C GLN I 289 " pdb=" CB GLN I 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CA GLN J 289 " pdb=" N GLN J 289 " pdb=" C GLN J 289 " pdb=" CB GLN J 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA ASN C 275 " pdb=" N ASN C 275 " pdb=" C ASN C 275 " pdb=" CB ASN C 275 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 5969 not shown) Planarity restraints: 6496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 51 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LEU L 51 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU L 51 " 0.022 2.00e-02 2.50e+03 pdb=" N SEP L 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 249 " -0.016 2.00e-02 2.50e+03 2.35e-02 9.66e+00 pdb=" CG PHE C 249 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE C 249 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE C 249 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 249 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 249 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE C 249 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 24 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C VAL K 24 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL K 24 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN K 25 " 0.018 2.00e-02 2.50e+03 ... (remaining 6493 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.60: 6 1.60 - 2.42: 17 2.42 - 3.25: 31767 3.25 - 4.07: 88855 4.07 - 4.90: 152385 Warning: very small nonbonded interaction distances. Nonbonded interactions: 273030 Sorted by model distance: nonbonded pdb=" NE2 GLN L 26 " pdb=" CB ALA L 32 " model vdw 0.775 3.540 nonbonded pdb=" NE2 GLN L 26 " pdb=" CA ALA L 32 " model vdw 0.867 3.550 nonbonded pdb=" CD GLN L 26 " pdb=" CA ALA L 32 " model vdw 1.219 3.700 nonbonded pdb=" ND2 ASN A 80 " pdb=" CD2 LEU A 94 " model vdw 1.552 3.540 nonbonded pdb=" ND2 ASN B 80 " pdb=" CG LEU B 94 " model vdw 1.572 3.550 ... (remaining 273025 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.040 Extract box with map and model: 7.050 Check model and map are aligned: 0.610 Set scattering table: 0.350 Process input model: 97.230 Find NCS groups from input model: 2.440 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.009 0.115 37598 Z= 0.589 Angle : 1.399 12.373 50890 Z= 0.896 Chirality : 0.083 0.543 5972 Planarity : 0.005 0.047 6496 Dihedral : 18.074 83.294 13990 Min Nonbonded Distance : 0.775 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.97 % Favored : 87.59 % Rotamer: Outliers : 5.91 % Allowed : 12.82 % Favored : 81.27 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % 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: -3.14 (0.10), residues: 4632 helix: -2.05 (0.10), residues: 1536 sheet: -0.65 (0.19), residues: 606 loop : -2.53 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 87 HIS 0.008 0.001 HIS H 475 PHE 0.042 0.003 PHE C 249 TYR 0.022 0.003 TYR G 469 ARG 0.018 0.001 ARG H 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1183 time to evaluate : 4.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5798 (tp) REVERT: A 41 THR cc_start: 0.7137 (p) cc_final: 0.5968 (t) REVERT: A 86 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.5310 (m-30) REVERT: A 96 GLU cc_start: 0.5832 (tt0) cc_final: 0.5455 (pt0) REVERT: A 123 ASP cc_start: 0.7709 (t70) cc_final: 0.7190 (t70) REVERT: A 151 CYS cc_start: 0.6279 (m) cc_final: 0.6060 (m) REVERT: A 207 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 228 TYR cc_start: 0.7590 (m-80) cc_final: 0.6559 (m-80) REVERT: A 237 VAL cc_start: 0.5030 (OUTLIER) cc_final: 0.4577 (t) REVERT: A 239 MET cc_start: 0.6408 (mtp) cc_final: 0.6038 (tpp) REVERT: A 249 MET cc_start: 0.6372 (mtm) cc_final: 0.5124 (ttp) REVERT: A 258 ARG cc_start: 0.8091 (mmp-170) cc_final: 0.7702 (tmt170) REVERT: B 20 MET cc_start: 0.2635 (mmt) cc_final: 0.2075 (tpt) REVERT: B 24 ILE cc_start: 0.5694 (OUTLIER) cc_final: 0.5304 (tp) REVERT: B 37 LYS cc_start: 0.3770 (OUTLIER) cc_final: 0.3421 (tptp) REVERT: B 41 THR cc_start: 0.7753 (p) cc_final: 0.6840 (t) REVERT: B 45 MET cc_start: 0.4029 (tpt) cc_final: 0.3564 (ptt) REVERT: B 91 LYS cc_start: 0.6899 (ttmt) cc_final: 0.6608 (mmtp) REVERT: B 106 LYS cc_start: 0.8062 (mttt) cc_final: 0.7850 (tmtt) REVERT: B 123 ASP cc_start: 0.7503 (t70) cc_final: 0.7026 (t0) REVERT: B 145 LYS cc_start: 0.9323 (mmtt) cc_final: 0.8993 (mmtp) REVERT: B 148 ARG cc_start: 0.6652 (ttp80) cc_final: 0.6385 (ptt180) REVERT: B 195 PHE cc_start: 0.6334 (m-80) cc_final: 0.5972 (m-10) REVERT: B 228 TYR cc_start: 0.7652 (m-80) cc_final: 0.6502 (m-80) REVERT: B 239 MET cc_start: 0.6813 (mtp) cc_final: 0.6017 (tpp) REVERT: B 249 MET cc_start: 0.5951 (mtm) cc_final: 0.5023 (ttp) REVERT: B 258 ARG cc_start: 0.8067 (mmp-170) cc_final: 0.7666 (tmt170) REVERT: D 63 LEU cc_start: 0.8713 (tp) cc_final: 0.8477 (tp) REVERT: D 76 LYS cc_start: 0.8315 (mttt) cc_final: 0.7914 (mttp) REVERT: D 150 TYR cc_start: 0.8750 (t80) cc_final: 0.8248 (p90) REVERT: D 169 ASP cc_start: 0.8853 (m-30) cc_final: 0.8309 (t0) REVERT: D 198 LYS cc_start: 0.6280 (OUTLIER) cc_final: 0.6009 (mmtt) REVERT: D 224 LYS cc_start: 0.8416 (ttmm) cc_final: 0.8059 (tptp) REVERT: D 227 HIS cc_start: 0.8106 (m170) cc_final: 0.7504 (m-70) REVERT: D 315 PHE cc_start: 0.7409 (m-80) cc_final: 0.7083 (m-80) REVERT: D 319 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8370 (tm-30) REVERT: D 330 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.5039 (mpp-170) REVERT: E 3 ILE cc_start: 0.1541 (OUTLIER) cc_final: 0.1341 (pt) REVERT: E 141 ILE cc_start: 0.4174 (OUTLIER) cc_final: 0.3480 (mm) REVERT: E 162 ARG cc_start: 0.5055 (mtt180) cc_final: 0.4505 (tpt170) REVERT: E 261 TRP cc_start: 0.8698 (m100) cc_final: 0.7848 (p-90) REVERT: E 272 LEU cc_start: 0.8418 (mt) cc_final: 0.8118 (mt) REVERT: E 302 LYS cc_start: 0.9135 (pttt) cc_final: 0.8509 (ptpp) REVERT: F 141 ILE cc_start: 0.3021 (OUTLIER) cc_final: 0.2557 (mp) REVERT: F 188 ARG cc_start: 0.8086 (mtt180) cc_final: 0.7858 (mtt180) REVERT: F 195 LEU cc_start: 0.6716 (tp) cc_final: 0.6454 (tp) REVERT: F 197 MET cc_start: 0.8450 (mmt) cc_final: 0.7977 (tpp) REVERT: F 261 TRP cc_start: 0.8848 (m100) cc_final: 0.7776 (p-90) REVERT: F 269 SER cc_start: 0.9022 (m) cc_final: 0.8806 (p) REVERT: F 294 SER cc_start: 0.7411 (p) cc_final: 0.6919 (t) REVERT: F 302 LYS cc_start: 0.8734 (ptmt) cc_final: 0.8407 (ptpp) REVERT: G 284 TYR cc_start: 0.7611 (t80) cc_final: 0.7188 (t80) REVERT: G 328 ASP cc_start: 0.5598 (m-30) cc_final: 0.5168 (m-30) REVERT: G 350 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7993 (mm-30) REVERT: G 365 LYS cc_start: 0.7796 (tttt) cc_final: 0.7293 (mmtm) REVERT: G 407 LYS cc_start: 0.7945 (tttt) cc_final: 0.7512 (tttp) REVERT: G 411 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8336 (mt-10) REVERT: G 456 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8168 (mt) REVERT: G 486 ARG cc_start: 0.7069 (mtm180) cc_final: 0.4778 (ttm-80) REVERT: G 495 SER cc_start: 0.8750 (p) cc_final: 0.8544 (p) REVERT: G 516 VAL cc_start: 0.5341 (OUTLIER) cc_final: 0.4891 (m) REVERT: G 528 ASP cc_start: 0.7731 (m-30) cc_final: 0.7458 (m-30) REVERT: G 529 PRO cc_start: 0.8583 (Cg_endo) cc_final: 0.8337 (Cg_exo) REVERT: G 550 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6406 (tp) REVERT: H 396 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7347 (mp0) REVERT: H 407 LYS cc_start: 0.7672 (tttt) cc_final: 0.7227 (tttp) REVERT: H 411 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8291 (mt-10) REVERT: H 435 PHE cc_start: 0.7990 (m-80) cc_final: 0.7725 (m-80) REVERT: H 436 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8709 (mt-10) REVERT: H 456 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8580 (mt) REVERT: H 461 THR cc_start: 0.8733 (p) cc_final: 0.7387 (p) REVERT: H 528 ASP cc_start: 0.8011 (m-30) cc_final: 0.7642 (m-30) REVERT: H 568 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8153 (tm-30) REVERT: H 593 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7111 (mp0) REVERT: I 32 LEU cc_start: 0.8355 (mt) cc_final: 0.7882 (mp) REVERT: I 59 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8921 (tp) REVERT: I 73 HIS cc_start: 0.8569 (m-70) cc_final: 0.8340 (m90) REVERT: I 74 GLU cc_start: 0.9364 (tt0) cc_final: 0.9047 (tp30) REVERT: I 114 CYS cc_start: 0.8465 (m) cc_final: 0.8187 (m) REVERT: I 119 MET cc_start: 0.7701 (mmm) cc_final: 0.7499 (tmm) REVERT: I 145 PHE cc_start: 0.8802 (t80) cc_final: 0.8586 (t80) REVERT: I 198 GLN cc_start: 0.9289 (tp40) cc_final: 0.8730 (tm-30) REVERT: I 211 ILE cc_start: 0.8785 (mp) cc_final: 0.8563 (mp) REVERT: I 212 GLN cc_start: 0.9293 (mt0) cc_final: 0.9018 (mt0) REVERT: I 237 ILE cc_start: 0.9093 (mt) cc_final: 0.8878 (mm) REVERT: I 313 GLN cc_start: 0.8885 (tt0) cc_final: 0.8254 (tm-30) REVERT: I 321 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6796 (tt0) REVERT: J 32 LEU cc_start: 0.8159 (mt) cc_final: 0.7649 (mp) REVERT: J 37 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8169 (mp0) REVERT: J 59 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8912 (tp) REVERT: J 73 HIS cc_start: 0.8595 (m-70) cc_final: 0.8193 (m90) REVERT: J 74 GLU cc_start: 0.9366 (tt0) cc_final: 0.9015 (tp30) REVERT: J 77 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7509 (mp) REVERT: J 84 ASN cc_start: 0.9405 (m110) cc_final: 0.9202 (p0) REVERT: J 94 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7803 (mmtt) REVERT: J 95 TRP cc_start: 0.8299 (m100) cc_final: 0.7531 (m100) REVERT: J 170 LYS cc_start: 0.7705 (mptt) cc_final: 0.7012 (tmtt) REVERT: J 198 GLN cc_start: 0.9155 (tp40) cc_final: 0.8572 (tm-30) REVERT: J 211 ILE cc_start: 0.9051 (mp) cc_final: 0.8849 (mp) REVERT: J 308 LEU cc_start: 0.8259 (mt) cc_final: 0.7883 (tp) REVERT: J 313 GLN cc_start: 0.8917 (tt0) cc_final: 0.8340 (tm-30) REVERT: J 321 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6735 (tt0) REVERT: L 6 CYS cc_start: 0.2664 (t) cc_final: 0.2329 (p) REVERT: L 9 TYR cc_start: 0.3665 (m-80) cc_final: 0.3295 (m-80) REVERT: L 84 ASP cc_start: 0.6182 (m-30) cc_final: 0.5377 (m-30) REVERT: L 124 GLU cc_start: 0.5709 (pp20) cc_final: 0.5437 (tp30) REVERT: L 125 GLU cc_start: 0.7036 (tt0) cc_final: 0.6493 (pp20) REVERT: L 163 LYS cc_start: 0.3387 (OUTLIER) cc_final: 0.3030 (mmtt) REVERT: L 238 GLN cc_start: 0.3607 (pt0) cc_final: 0.2934 (mm110) REVERT: M 187 ARG cc_start: 0.5351 (mtm-85) cc_final: 0.5096 (tpt170) REVERT: M 192 VAL cc_start: 0.1983 (t) cc_final: 0.1465 (p) REVERT: M 239 MET cc_start: -0.1996 (mtp) cc_final: -0.2659 (tpp) REVERT: M 318 ILE cc_start: 0.2884 (OUTLIER) cc_final: 0.2230 (mm) REVERT: M 331 GLU cc_start: -0.1318 (mt-10) cc_final: -0.1822 (mm-30) REVERT: M 354 GLU cc_start: -0.2161 (OUTLIER) cc_final: -0.2407 (pm20) REVERT: M 411 ARG cc_start: 0.4437 (mtt-85) cc_final: 0.4079 (tpt170) REVERT: M 430 ILE cc_start: 0.5647 (pt) cc_final: 0.5294 (mm) REVERT: M 443 VAL cc_start: -0.2522 (OUTLIER) cc_final: -0.2775 (p) REVERT: M 452 LYS cc_start: 0.0451 (tttt) cc_final: 0.0002 (ptpt) REVERT: M 462 LEU cc_start: 0.2263 (OUTLIER) cc_final: 0.1262 (mm) REVERT: M 463 MET cc_start: 0.0326 (ttp) cc_final: -0.1234 (mmm) REVERT: N 211 MET cc_start: -0.2662 (mtp) cc_final: -0.3074 (mtm) REVERT: N 228 GLN cc_start: -0.0994 (OUTLIER) cc_final: -0.1370 (tp40) REVERT: N 311 ILE cc_start: 0.2593 (OUTLIER) cc_final: 0.2315 (pt) REVERT: N 318 ILE cc_start: 0.0892 (OUTLIER) cc_final: 0.0444 (mm) REVERT: N 406 LEU cc_start: 0.0745 (OUTLIER) cc_final: 0.0340 (tp) REVERT: N 430 ILE cc_start: 0.5972 (pt) cc_final: 0.5738 (mm) REVERT: N 462 LEU cc_start: 0.3983 (OUTLIER) cc_final: 0.2573 (mm) REVERT: N 463 MET cc_start: 0.1461 (ttp) cc_final: -0.0156 (mmm) REVERT: N 499 ILE cc_start: -0.2999 (mt) cc_final: -0.3298 (mt) REVERT: K 6 CYS cc_start: 0.3285 (t) cc_final: 0.1808 (t) REVERT: K 60 GLN cc_start: 0.5401 (pt0) cc_final: 0.5068 (mm-40) REVERT: K 79 GLU cc_start: 0.5083 (OUTLIER) cc_final: 0.4823 (pt0) REVERT: K 84 ASP cc_start: 0.5118 (m-30) cc_final: 0.4369 (m-30) REVERT: K 124 GLU cc_start: 0.5219 (pp20) cc_final: 0.4907 (tp30) REVERT: K 220 VAL cc_start: 0.3485 (t) cc_final: 0.2735 (p) REVERT: C 56 ARG cc_start: 0.8990 (mmp80) cc_final: 0.8738 (tmm160) REVERT: C 63 LEU cc_start: 0.8431 (tp) cc_final: 0.8108 (tp) REVERT: C 76 LYS cc_start: 0.8514 (mttt) cc_final: 0.8034 (mttp) REVERT: C 150 TYR cc_start: 0.8852 (t80) cc_final: 0.8359 (p90) REVERT: C 169 ASP cc_start: 0.8826 (m-30) cc_final: 0.8278 (t0) REVERT: C 224 LYS cc_start: 0.8424 (ttmm) cc_final: 0.8153 (tptp) REVERT: C 227 HIS cc_start: 0.8131 (m170) cc_final: 0.6947 (m-70) REVERT: C 319 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8301 (tm-30) REVERT: C 330 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.5162 (mpp-170) outliers start: 241 outliers final: 54 residues processed: 1337 average time/residue: 0.4879 time to fit residues: 1040.8777 Evaluate side-chains 826 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 742 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 6.9990 chunk 353 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 365 optimal weight: 8.9990 chunk 141 optimal weight: 30.0000 chunk 222 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 423 optimal weight: 10.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 144 ASN A 222 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN D 10 HIS D 183 HIS D 221 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 237 ASN E 14 ASN E 59 GLN E 262 ASN E 308 ASN E 309 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN F 308 ASN G 280 HIS G 301 GLN G 384 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN H 384 GLN ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 475 HIS H 539 ASN I 73 HIS ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 HIS I 247 GLN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 GLN I 388 ASN I 429 ASN J 73 HIS J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 GLN J 371 ASN J 388 ASN J 409 ASN ** J 429 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 103 GLN M 98 GLN ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 HIS M 197 HIS M 286 GLN M 415 GLN N 98 GLN N 197 HIS N 425 ASN N 465 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN K 243 GLN C 10 HIS C 61 ASN C 183 HIS C 221 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 37598 Z= 0.307 Angle : 0.769 14.481 50890 Z= 0.404 Chirality : 0.050 0.395 5972 Planarity : 0.006 0.089 6496 Dihedral : 6.096 79.784 5048 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 1.08 % Allowed : 8.66 % Favored : 90.26 % Rotamer: Outliers : 0.22 % Allowed : 4.93 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.04 (0.11), residues: 4632 helix: -0.33 (0.12), residues: 1558 sheet: -0.35 (0.20), residues: 590 loop : -2.38 (0.11), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 302 HIS 0.011 0.002 HIS G 280 PHE 0.027 0.002 PHE H 554 TYR 0.036 0.002 TYR G 322 ARG 0.018 0.001 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 881 time to evaluate : 4.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ARG cc_start: 0.6202 (tmm160) cc_final: 0.5936 (tmm160) REVERT: A 96 GLU cc_start: 0.5826 (tt0) cc_final: 0.5474 (pt0) REVERT: A 207 ILE cc_start: 0.8972 (mm) cc_final: 0.8748 (mm) REVERT: A 228 TYR cc_start: 0.7606 (m-80) cc_final: 0.6540 (m-80) REVERT: A 239 MET cc_start: 0.6863 (mtp) cc_final: 0.6278 (tpp) REVERT: A 249 MET cc_start: 0.6606 (mtm) cc_final: 0.5375 (ttp) REVERT: A 258 ARG cc_start: 0.8414 (mmp80) cc_final: 0.8000 (tmt170) REVERT: A 275 THR cc_start: 0.8032 (t) cc_final: 0.7751 (m) REVERT: B 17 ASP cc_start: 0.1493 (OUTLIER) cc_final: 0.1202 (m-30) REVERT: B 27 ILE cc_start: 0.5743 (mt) cc_final: 0.5373 (mt) REVERT: B 41 THR cc_start: 0.7139 (p) cc_final: 0.6655 (t) REVERT: B 145 LYS cc_start: 0.9355 (mmtt) cc_final: 0.9154 (mmmm) REVERT: B 193 LYS cc_start: 0.7711 (mttp) cc_final: 0.7267 (mttp) REVERT: B 195 PHE cc_start: 0.6414 (m-80) cc_final: 0.6089 (m-10) REVERT: B 225 LYS cc_start: 0.7603 (mmtt) cc_final: 0.7352 (mmpt) REVERT: B 228 TYR cc_start: 0.7536 (m-80) cc_final: 0.6252 (m-80) REVERT: B 249 MET cc_start: 0.6190 (mtm) cc_final: 0.5331 (ttp) REVERT: B 275 THR cc_start: 0.8242 (t) cc_final: 0.7858 (m) REVERT: D 76 LYS cc_start: 0.8385 (mttt) cc_final: 0.8095 (mttp) REVERT: D 169 ASP cc_start: 0.8992 (m-30) cc_final: 0.8273 (t0) REVERT: D 222 ASN cc_start: 0.8679 (m-40) cc_final: 0.8449 (m-40) REVERT: D 319 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8316 (tm-30) REVERT: D 320 ARG cc_start: 0.8513 (ttm110) cc_final: 0.8226 (ttm110) REVERT: D 326 ASP cc_start: 0.6143 (m-30) cc_final: 0.5859 (m-30) REVERT: E 58 MET cc_start: -0.1216 (ttt) cc_final: -0.1420 (tpt) REVERT: E 76 MET cc_start: 0.6067 (ptt) cc_final: 0.5665 (ptm) REVERT: E 184 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.8038 (p) REVERT: E 197 MET cc_start: 0.7226 (mmm) cc_final: 0.6993 (tpp) REVERT: E 261 TRP cc_start: 0.8666 (m100) cc_final: 0.7799 (p-90) REVERT: E 302 LYS cc_start: 0.9061 (pttt) cc_final: 0.8467 (ptpp) REVERT: F 162 ARG cc_start: 0.5550 (mtt180) cc_final: 0.5301 (ptm-80) REVERT: F 195 LEU cc_start: 0.7263 (tp) cc_final: 0.7021 (tp) REVERT: F 261 TRP cc_start: 0.8763 (m100) cc_final: 0.7747 (p-90) REVERT: F 272 LEU cc_start: 0.8568 (mt) cc_final: 0.8337 (mt) REVERT: F 274 ASN cc_start: 0.7717 (m110) cc_final: 0.7475 (t0) REVERT: F 302 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8315 (ptpp) REVERT: G 257 ILE cc_start: 0.4852 (tt) cc_final: 0.4452 (tt) REVERT: G 284 TYR cc_start: 0.7556 (t80) cc_final: 0.7057 (t80) REVERT: G 328 ASP cc_start: 0.5461 (m-30) cc_final: 0.5035 (m-30) REVERT: G 350 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8001 (mm-30) REVERT: G 365 LYS cc_start: 0.8035 (tttt) cc_final: 0.7548 (mmtm) REVERT: G 409 LEU cc_start: 0.9569 (mt) cc_final: 0.9348 (mt) REVERT: G 411 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8966 (mt-10) REVERT: G 430 ASP cc_start: 0.7928 (t70) cc_final: 0.7329 (t0) REVERT: G 435 PHE cc_start: 0.8695 (m-80) cc_final: 0.8462 (m-80) REVERT: G 486 ARG cc_start: 0.6796 (mtt90) cc_final: 0.5830 (mtm-85) REVERT: G 528 ASP cc_start: 0.7277 (m-30) cc_final: 0.7048 (m-30) REVERT: G 534 ASN cc_start: 0.7079 (m110) cc_final: 0.6540 (t0) REVERT: H 328 ASP cc_start: 0.5379 (m-30) cc_final: 0.4992 (m-30) REVERT: H 411 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8877 (mt-10) REVERT: H 436 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8636 (mt-10) REVERT: H 515 ARG cc_start: 0.7245 (ptm160) cc_final: 0.6557 (ttt-90) REVERT: H 518 LEU cc_start: 0.8343 (mt) cc_final: 0.8063 (mp) REVERT: I 120 ARG cc_start: 0.8599 (mtt180) cc_final: 0.8160 (mtt-85) REVERT: I 313 GLN cc_start: 0.8848 (tt0) cc_final: 0.8360 (tm-30) REVERT: I 321 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6893 (mp0) REVERT: I 370 GLU cc_start: 0.8060 (mp0) cc_final: 0.7742 (mp0) REVERT: J 84 ASN cc_start: 0.9415 (m110) cc_final: 0.9170 (p0) REVERT: J 120 ARG cc_start: 0.8926 (mtt180) cc_final: 0.8603 (mtt180) REVERT: J 170 LYS cc_start: 0.7545 (mptt) cc_final: 0.7238 (tmtt) REVERT: J 198 GLN cc_start: 0.9092 (tp40) cc_final: 0.8496 (tm-30) REVERT: J 284 ARG cc_start: 0.8722 (ptm-80) cc_final: 0.8274 (ptm-80) REVERT: J 313 GLN cc_start: 0.8890 (tt0) cc_final: 0.8413 (tm-30) REVERT: J 321 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6862 (mp0) REVERT: L 6 CYS cc_start: 0.0403 (t) cc_final: -0.1154 (t) REVERT: L 21 MET cc_start: 0.0765 (mmp) cc_final: 0.0561 (mpp) REVERT: L 79 GLU cc_start: 0.5609 (tm-30) cc_final: 0.5078 (pt0) REVERT: L 124 GLU cc_start: 0.5606 (pp20) cc_final: 0.5241 (tp30) REVERT: L 125 GLU cc_start: 0.7321 (tt0) cc_final: 0.6856 (pp20) REVERT: L 238 GLN cc_start: 0.3948 (pt0) cc_final: 0.3402 (mm110) REVERT: M 187 ARG cc_start: 0.4997 (mtm-85) cc_final: 0.4703 (tpt170) REVERT: M 331 GLU cc_start: -0.1314 (mt-10) cc_final: -0.1593 (mm-30) REVERT: M 430 ILE cc_start: 0.5450 (pt) cc_final: 0.4987 (mm) REVERT: M 452 LYS cc_start: 0.0501 (tttt) cc_final: 0.0080 (ptpt) REVERT: M 462 LEU cc_start: 0.2269 (mt) cc_final: 0.1261 (mm) REVERT: M 463 MET cc_start: 0.0391 (ttp) cc_final: -0.1330 (mmm) REVERT: N 211 MET cc_start: -0.2694 (mtp) cc_final: -0.3002 (mtm) REVERT: N 331 GLU cc_start: -0.1521 (mt-10) cc_final: -0.1884 (mm-30) REVERT: N 430 ILE cc_start: 0.5622 (pt) cc_final: 0.5342 (mm) REVERT: N 462 LEU cc_start: 0.3744 (mt) cc_final: 0.2545 (mm) REVERT: N 463 MET cc_start: 0.1192 (ttp) cc_final: -0.0496 (mmm) REVERT: K 6 CYS cc_start: 0.2617 (t) cc_final: 0.0626 (t) REVERT: K 21 MET cc_start: 0.2745 (mmm) cc_final: 0.2498 (mpp) REVERT: K 79 GLU cc_start: 0.5904 (tm-30) cc_final: 0.5478 (pt0) REVERT: K 124 GLU cc_start: 0.5370 (pp20) cc_final: 0.4944 (tp30) REVERT: K 127 TYR cc_start: 0.3142 (t80) cc_final: 0.2877 (t80) REVERT: C 76 LYS cc_start: 0.8493 (mttt) cc_final: 0.8219 (mttm) REVERT: C 104 MET cc_start: 0.2530 (tmm) cc_final: 0.1903 (tpp) REVERT: C 169 ASP cc_start: 0.9012 (m-30) cc_final: 0.8276 (t0) REVERT: C 227 HIS cc_start: 0.8404 (m170) cc_final: 0.8089 (m-70) REVERT: C 319 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8044 (tm-30) outliers start: 9 outliers final: 0 residues processed: 888 average time/residue: 0.4956 time to fit residues: 718.4874 Evaluate side-chains 659 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 657 time to evaluate : 4.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 235 optimal weight: 6.9990 chunk 131 optimal weight: 0.3980 chunk 352 optimal weight: 10.0000 chunk 288 optimal weight: 0.0870 chunk 116 optimal weight: 9.9990 chunk 423 optimal weight: 20.0000 chunk 457 optimal weight: 0.6980 chunk 377 optimal weight: 20.0000 chunk 420 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 340 optimal weight: 20.0000 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 ASN I 56 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 ASN J 56 ASN J 241 HIS J 249 ASN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN L 25 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 HIS ** N 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN N 433 ASN K 25 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.4164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37598 Z= 0.193 Angle : 0.643 9.016 50890 Z= 0.330 Chirality : 0.046 0.321 5972 Planarity : 0.004 0.059 6496 Dihedral : 5.679 81.494 5048 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.02 % Favored : 90.00 % Rotamer: Outliers : 0.12 % Allowed : 3.29 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.52 (0.12), residues: 4632 helix: 0.44 (0.13), residues: 1548 sheet: -0.28 (0.19), residues: 644 loop : -2.29 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 303 HIS 0.009 0.001 HIS H 475 PHE 0.024 0.002 PHE B 236 TYR 0.020 0.002 TYR K 82 ARG 0.014 0.001 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 833 time to evaluate : 4.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8961 (m) cc_final: 0.8617 (p) REVERT: A 96 GLU cc_start: 0.5670 (tt0) cc_final: 0.5319 (pt0) REVERT: A 207 ILE cc_start: 0.9019 (mm) cc_final: 0.8731 (mm) REVERT: A 228 TYR cc_start: 0.7407 (m-80) cc_final: 0.5896 (m-80) REVERT: A 239 MET cc_start: 0.6734 (mtp) cc_final: 0.6464 (mtp) REVERT: A 249 MET cc_start: 0.6505 (mtm) cc_final: 0.5094 (ttp) REVERT: A 258 ARG cc_start: 0.8344 (mmp80) cc_final: 0.7971 (tmt170) REVERT: A 275 THR cc_start: 0.8420 (t) cc_final: 0.8200 (m) REVERT: B 228 TYR cc_start: 0.7324 (m-80) cc_final: 0.6952 (m-80) REVERT: B 239 MET cc_start: 0.6810 (mtp) cc_final: 0.6385 (mmt) REVERT: B 249 MET cc_start: 0.6314 (mtm) cc_final: 0.5473 (ttp) REVERT: B 297 GLU cc_start: 0.7322 (tt0) cc_final: 0.7064 (mm-30) REVERT: D 23 ASP cc_start: 0.7687 (m-30) cc_final: 0.7473 (m-30) REVERT: D 76 LYS cc_start: 0.8330 (mttt) cc_final: 0.8020 (mttm) REVERT: D 160 ASP cc_start: 0.8449 (p0) cc_final: 0.8228 (p0) REVERT: D 169 ASP cc_start: 0.8867 (m-30) cc_final: 0.8145 (t0) REVERT: D 246 SER cc_start: 0.9132 (p) cc_final: 0.8620 (t) REVERT: D 254 ARG cc_start: 0.8780 (mmt90) cc_final: 0.8334 (mmt90) REVERT: D 319 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8090 (tm-30) REVERT: D 326 ASP cc_start: 0.6079 (m-30) cc_final: 0.5865 (m-30) REVERT: E 76 MET cc_start: 0.6287 (ptt) cc_final: 0.6015 (pmm) REVERT: E 197 MET cc_start: 0.7425 (mmm) cc_final: 0.6858 (tpp) REVERT: E 261 TRP cc_start: 0.8656 (m100) cc_final: 0.7788 (p-90) REVERT: E 272 LEU cc_start: 0.8829 (mt) cc_final: 0.8594 (mt) REVERT: E 302 LYS cc_start: 0.8912 (pttt) cc_final: 0.8461 (ptpt) REVERT: F 188 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7775 (mtt180) REVERT: F 261 TRP cc_start: 0.8769 (m100) cc_final: 0.7744 (p-90) REVERT: F 272 LEU cc_start: 0.8497 (mt) cc_final: 0.8247 (mt) REVERT: F 274 ASN cc_start: 0.7684 (m110) cc_final: 0.7422 (t0) REVERT: F 302 LYS cc_start: 0.8593 (ptmt) cc_final: 0.8190 (ptpp) REVERT: G 257 ILE cc_start: 0.4884 (tt) cc_final: 0.4551 (tt) REVERT: G 284 TYR cc_start: 0.7218 (t80) cc_final: 0.6661 (t80) REVERT: G 328 ASP cc_start: 0.5469 (m-30) cc_final: 0.5092 (m-30) REVERT: G 365 LYS cc_start: 0.7891 (tttt) cc_final: 0.7355 (mmtm) REVERT: G 409 LEU cc_start: 0.9498 (mt) cc_final: 0.9283 (mt) REVERT: G 442 GLU cc_start: 0.9273 (tt0) cc_final: 0.9053 (tt0) REVERT: G 528 ASP cc_start: 0.7690 (m-30) cc_final: 0.7415 (m-30) REVERT: H 377 GLU cc_start: 0.9087 (pt0) cc_final: 0.8670 (mp0) REVERT: H 436 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8702 (mt-10) REVERT: H 568 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7888 (tm-30) REVERT: H 579 LYS cc_start: 0.8897 (tmmt) cc_final: 0.8586 (tmmt) REVERT: I 87 ASN cc_start: 0.8826 (m-40) cc_final: 0.8549 (m-40) REVERT: I 119 MET cc_start: 0.8032 (mmm) cc_final: 0.7789 (mmm) REVERT: I 123 ASP cc_start: 0.7599 (t70) cc_final: 0.7307 (t70) REVERT: I 145 PHE cc_start: 0.8530 (t80) cc_final: 0.8090 (t80) REVERT: I 198 GLN cc_start: 0.8852 (tp40) cc_final: 0.8433 (tm-30) REVERT: I 313 GLN cc_start: 0.8863 (tt0) cc_final: 0.8364 (tm-30) REVERT: I 370 GLU cc_start: 0.7915 (mp0) cc_final: 0.7562 (mp0) REVERT: I 394 SER cc_start: 0.7232 (p) cc_final: 0.7022 (p) REVERT: J 84 ASN cc_start: 0.9399 (m110) cc_final: 0.9174 (p0) REVERT: J 120 ARG cc_start: 0.9038 (mtt180) cc_final: 0.7320 (tpt90) REVERT: J 167 CYS cc_start: 0.6930 (m) cc_final: 0.6530 (m) REVERT: J 170 LYS cc_start: 0.7694 (mptt) cc_final: 0.7269 (tmtt) REVERT: J 185 PHE cc_start: 0.9297 (m-80) cc_final: 0.9064 (m-80) REVERT: J 198 GLN cc_start: 0.9122 (tp40) cc_final: 0.8479 (tm-30) REVERT: J 321 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6829 (mp0) REVERT: L 6 CYS cc_start: 0.0761 (t) cc_final: -0.0869 (t) REVERT: L 21 MET cc_start: 0.1232 (mmp) cc_final: 0.0561 (mpp) REVERT: L 79 GLU cc_start: 0.5734 (tm-30) cc_final: 0.5250 (pt0) REVERT: L 124 GLU cc_start: 0.5645 (pp20) cc_final: 0.5283 (tp30) REVERT: L 125 GLU cc_start: 0.7331 (tt0) cc_final: 0.6912 (pp20) REVERT: L 238 GLN cc_start: 0.4177 (pt0) cc_final: 0.3704 (mm110) REVERT: M 187 ARG cc_start: 0.4992 (mtm-85) cc_final: 0.4614 (mmm160) REVERT: M 331 GLU cc_start: -0.1228 (mt-10) cc_final: -0.1567 (mm-30) REVERT: M 430 ILE cc_start: 0.5270 (pt) cc_final: 0.4773 (mm) REVERT: M 452 LYS cc_start: 0.0459 (tttt) cc_final: 0.0010 (ptpt) REVERT: M 462 LEU cc_start: 0.2189 (mt) cc_final: 0.1288 (mm) REVERT: M 463 MET cc_start: 0.0333 (ttp) cc_final: -0.1450 (mmt) REVERT: N 331 GLU cc_start: -0.1234 (mt-10) cc_final: -0.1544 (mm-30) REVERT: N 430 ILE cc_start: 0.5671 (pt) cc_final: 0.5404 (mm) REVERT: N 462 LEU cc_start: 0.3550 (mt) cc_final: 0.2455 (mm) REVERT: N 463 MET cc_start: 0.1435 (ttp) cc_final: -0.0246 (mmm) REVERT: K 6 CYS cc_start: 0.2609 (t) cc_final: 0.0665 (t) REVERT: K 21 MET cc_start: 0.2721 (mmm) cc_final: 0.2428 (mpp) REVERT: K 79 GLU cc_start: 0.5482 (tm-30) cc_final: 0.5000 (pt0) REVERT: K 82 TYR cc_start: 0.4284 (m-80) cc_final: 0.4068 (m-80) REVERT: K 124 GLU cc_start: 0.5193 (pp20) cc_final: 0.4895 (tp30) REVERT: K 235 LEU cc_start: 0.3769 (tp) cc_final: 0.3382 (pp) REVERT: C 76 LYS cc_start: 0.8390 (mttt) cc_final: 0.8147 (mttm) REVERT: C 169 ASP cc_start: 0.8911 (m-30) cc_final: 0.8233 (t0) REVERT: C 181 HIS cc_start: 0.9022 (m90) cc_final: 0.8785 (m90) REVERT: C 227 HIS cc_start: 0.8231 (m170) cc_final: 0.7642 (m-70) REVERT: C 283 GLU cc_start: 0.8690 (tp30) cc_final: 0.8452 (tp30) REVERT: C 310 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7905 (mt-10) REVERT: C 319 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7955 (tm-30) outliers start: 5 outliers final: 3 residues processed: 837 average time/residue: 0.4699 time to fit residues: 639.6596 Evaluate side-chains 659 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 656 time to evaluate : 4.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 418 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 202 optimal weight: 0.0980 chunk 284 optimal weight: 7.9990 chunk 425 optimal weight: 50.0000 chunk 450 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 403 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN E 219 GLN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS G 301 GLN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN G 415 HIS ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 539 ASN H 416 ASN H 480 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 429 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37598 Z= 0.252 Angle : 0.664 7.867 50890 Z= 0.341 Chirality : 0.047 0.268 5972 Planarity : 0.005 0.059 6496 Dihedral : 5.700 83.081 5048 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.87 % Favored : 90.20 % Rotamer: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.12), residues: 4632 helix: 0.49 (0.13), residues: 1552 sheet: -0.13 (0.19), residues: 668 loop : -2.33 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 303 HIS 0.011 0.001 HIS H 475 PHE 0.023 0.002 PHE P 139 TYR 0.017 0.002 TYR I 274 ARG 0.010 0.001 ARG I 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 781 time to evaluate : 4.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8973 (m) cc_final: 0.8610 (p) REVERT: A 79 ARG cc_start: 0.6630 (tmm160) cc_final: 0.6181 (tmm-80) REVERT: A 96 GLU cc_start: 0.5809 (tt0) cc_final: 0.5422 (pt0) REVERT: A 195 PHE cc_start: 0.7032 (m-80) cc_final: 0.6703 (m-10) REVERT: A 207 ILE cc_start: 0.8918 (mm) cc_final: 0.8603 (mm) REVERT: A 228 TYR cc_start: 0.7838 (m-80) cc_final: 0.6198 (m-80) REVERT: A 236 PHE cc_start: 0.7761 (m-80) cc_final: 0.7521 (m-10) REVERT: A 239 MET cc_start: 0.6773 (mtp) cc_final: 0.6438 (mtp) REVERT: A 249 MET cc_start: 0.6511 (mtm) cc_final: 0.5108 (ttp) REVERT: A 275 THR cc_start: 0.8372 (t) cc_final: 0.8082 (m) REVERT: B 228 TYR cc_start: 0.7346 (m-80) cc_final: 0.7039 (m-80) REVERT: B 249 MET cc_start: 0.6507 (mtm) cc_final: 0.5585 (ttp) REVERT: B 258 ARG cc_start: 0.8409 (mmp80) cc_final: 0.7901 (tmt170) REVERT: D 23 ASP cc_start: 0.7788 (m-30) cc_final: 0.7531 (m-30) REVERT: D 76 LYS cc_start: 0.8401 (mttt) cc_final: 0.8142 (mttm) REVERT: D 160 ASP cc_start: 0.8422 (p0) cc_final: 0.8188 (p0) REVERT: D 169 ASP cc_start: 0.8805 (m-30) cc_final: 0.8244 (t0) REVERT: D 222 ASN cc_start: 0.8639 (m-40) cc_final: 0.8384 (m-40) REVERT: D 246 SER cc_start: 0.9195 (p) cc_final: 0.8711 (t) REVERT: D 319 GLN cc_start: 0.8800 (tm-30) cc_final: 0.8188 (tm-30) REVERT: D 326 ASP cc_start: 0.6151 (m-30) cc_final: 0.5931 (m-30) REVERT: E 186 GLN cc_start: 0.8512 (mp10) cc_final: 0.8296 (mp10) REVERT: E 197 MET cc_start: 0.7590 (mmm) cc_final: 0.7016 (tpp) REVERT: E 261 TRP cc_start: 0.8673 (m100) cc_final: 0.7795 (p-90) REVERT: E 302 LYS cc_start: 0.8962 (pttt) cc_final: 0.8348 (ptpt) REVERT: F 188 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7761 (mtt180) REVERT: F 261 TRP cc_start: 0.8771 (m100) cc_final: 0.7750 (p-90) REVERT: F 302 LYS cc_start: 0.8654 (ptmt) cc_final: 0.8229 (ptpp) REVERT: G 257 ILE cc_start: 0.4991 (tt) cc_final: 0.4702 (tt) REVERT: G 274 ILE cc_start: 0.8835 (mp) cc_final: 0.8624 (mp) REVERT: G 284 TYR cc_start: 0.7543 (t80) cc_final: 0.6834 (t80) REVERT: G 328 ASP cc_start: 0.5384 (m-30) cc_final: 0.5003 (m-30) REVERT: G 365 LYS cc_start: 0.8176 (tttt) cc_final: 0.7636 (mmtm) REVERT: G 430 ASP cc_start: 0.8206 (t70) cc_final: 0.7721 (t70) REVERT: G 436 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8650 (mt-10) REVERT: G 456 ILE cc_start: 0.9082 (mp) cc_final: 0.8874 (mt) REVERT: G 528 ASP cc_start: 0.8140 (m-30) cc_final: 0.7837 (m-30) REVERT: H 328 ASP cc_start: 0.5232 (m-30) cc_final: 0.4865 (m-30) REVERT: H 365 LYS cc_start: 0.8261 (tttt) cc_final: 0.7911 (mmtt) REVERT: H 436 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8699 (mt-10) REVERT: H 506 CYS cc_start: 0.7383 (m) cc_final: 0.7183 (m) REVERT: H 515 ARG cc_start: 0.7194 (ptm160) cc_final: 0.6809 (ptm160) REVERT: H 534 ASN cc_start: 0.5970 (p0) cc_final: 0.5742 (p0) REVERT: H 569 ASN cc_start: 0.8505 (p0) cc_final: 0.8217 (p0) REVERT: I 95 TRP cc_start: 0.8435 (m100) cc_final: 0.8218 (m100) REVERT: I 155 MET cc_start: 0.7439 (ptp) cc_final: 0.7026 (mmp) REVERT: I 278 THR cc_start: 0.8701 (t) cc_final: 0.8055 (t) REVERT: I 370 GLU cc_start: 0.7809 (mp0) cc_final: 0.7597 (mp0) REVERT: I 394 SER cc_start: 0.7282 (p) cc_final: 0.7061 (p) REVERT: J 84 ASN cc_start: 0.9438 (m110) cc_final: 0.9232 (p0) REVERT: J 145 PHE cc_start: 0.8535 (t80) cc_final: 0.8038 (t80) REVERT: J 198 GLN cc_start: 0.9065 (tp40) cc_final: 0.8705 (tm-30) REVERT: J 308 LEU cc_start: 0.8419 (mt) cc_final: 0.8202 (mt) REVERT: L 6 CYS cc_start: 0.0711 (t) cc_final: -0.0946 (t) REVERT: L 21 MET cc_start: 0.0851 (mmp) cc_final: 0.0597 (mmt) REVERT: L 30 MET cc_start: 0.2110 (tmm) cc_final: 0.0516 (ptp) REVERT: L 79 GLU cc_start: 0.5721 (tm-30) cc_final: 0.5276 (pt0) REVERT: L 124 GLU cc_start: 0.5515 (pp20) cc_final: 0.5125 (tp30) REVERT: L 125 GLU cc_start: 0.7340 (tt0) cc_final: 0.6925 (pp20) REVERT: L 238 GLN cc_start: 0.4175 (pt0) cc_final: 0.3725 (mm110) REVERT: M 187 ARG cc_start: 0.5002 (mtm-85) cc_final: 0.4640 (tpt170) REVERT: M 331 GLU cc_start: -0.1196 (mt-10) cc_final: -0.1555 (mm-30) REVERT: M 430 ILE cc_start: 0.5275 (pt) cc_final: 0.4796 (mm) REVERT: M 452 LYS cc_start: -0.0211 (tttt) cc_final: -0.0665 (ptpt) REVERT: N 331 GLU cc_start: -0.1311 (mt-10) cc_final: -0.1564 (mm-30) REVERT: N 430 ILE cc_start: 0.5685 (pt) cc_final: 0.5384 (mm) REVERT: N 462 LEU cc_start: 0.3634 (mt) cc_final: 0.2544 (mm) REVERT: N 463 MET cc_start: 0.0444 (ttp) cc_final: -0.0994 (mmm) REVERT: K 21 MET cc_start: 0.2948 (mmm) cc_final: 0.2518 (mpp) REVERT: K 22 VAL cc_start: 0.6410 (t) cc_final: 0.5940 (p) REVERT: K 79 GLU cc_start: 0.5969 (tm-30) cc_final: 0.5567 (pt0) REVERT: K 124 GLU cc_start: 0.5161 (pp20) cc_final: 0.4919 (tm-30) REVERT: K 235 LEU cc_start: 0.3648 (tp) cc_final: 0.3248 (pp) REVERT: C 76 LYS cc_start: 0.8509 (mttt) cc_final: 0.8258 (mttm) REVERT: C 169 ASP cc_start: 0.8802 (m-30) cc_final: 0.8299 (t0) REVERT: C 319 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8092 (tm-30) outliers start: 2 outliers final: 1 residues processed: 782 average time/residue: 0.4778 time to fit residues: 618.9467 Evaluate side-chains 665 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 664 time to evaluate : 4.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 375 optimal weight: 0.8980 chunk 255 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 335 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 384 optimal weight: 30.0000 chunk 311 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 404 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 ASN G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN I 249 ASN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN N 415 GLN N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37598 Z= 0.262 Angle : 0.665 8.237 50890 Z= 0.341 Chirality : 0.046 0.235 5972 Planarity : 0.005 0.099 6496 Dihedral : 5.708 79.567 5048 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.22 % Favored : 89.96 % Rotamer: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.12), residues: 4632 helix: 0.49 (0.13), residues: 1554 sheet: -0.13 (0.20), residues: 648 loop : -2.33 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 303 HIS 0.010 0.001 HIS B 129 PHE 0.021 0.002 PHE I 250 TYR 0.019 0.002 TYR K 33 ARG 0.012 0.001 ARG D 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 780 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 779 time to evaluate : 4.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8981 (m) cc_final: 0.8612 (p) REVERT: A 79 ARG cc_start: 0.6702 (tmm160) cc_final: 0.6458 (tmm-80) REVERT: A 96 GLU cc_start: 0.5669 (tt0) cc_final: 0.5289 (pt0) REVERT: A 195 PHE cc_start: 0.7132 (m-80) cc_final: 0.6738 (m-10) REVERT: A 207 ILE cc_start: 0.9002 (mm) cc_final: 0.8679 (mm) REVERT: A 228 TYR cc_start: 0.7879 (m-80) cc_final: 0.6430 (m-80) REVERT: A 239 MET cc_start: 0.7073 (mtp) cc_final: 0.6438 (mtp) REVERT: A 249 MET cc_start: 0.6350 (mtm) cc_final: 0.4995 (ttp) REVERT: A 286 ASP cc_start: 0.8066 (p0) cc_final: 0.7272 (t0) REVERT: B 228 TYR cc_start: 0.7370 (m-80) cc_final: 0.7123 (m-10) REVERT: B 249 MET cc_start: 0.6468 (mtm) cc_final: 0.5564 (ttp) REVERT: D 23 ASP cc_start: 0.7769 (m-30) cc_final: 0.7507 (m-30) REVERT: D 76 LYS cc_start: 0.8494 (mttt) cc_final: 0.8218 (mttm) REVERT: D 169 ASP cc_start: 0.8869 (m-30) cc_final: 0.8317 (t0) REVERT: D 222 ASN cc_start: 0.8689 (m-40) cc_final: 0.8450 (m-40) REVERT: D 263 LYS cc_start: 0.8235 (tttt) cc_final: 0.7976 (tmtt) REVERT: D 307 PHE cc_start: 0.9082 (p90) cc_final: 0.8837 (p90) REVERT: D 326 ASP cc_start: 0.5828 (m-30) cc_final: 0.5608 (m-30) REVERT: E 162 ARG cc_start: 0.6453 (ptm-80) cc_final: 0.6035 (tmm-80) REVERT: E 186 GLN cc_start: 0.8646 (mp10) cc_final: 0.8262 (mm-40) REVERT: E 261 TRP cc_start: 0.8707 (m100) cc_final: 0.7787 (p-90) REVERT: E 302 LYS cc_start: 0.8798 (pttt) cc_final: 0.8353 (ptpt) REVERT: F 261 TRP cc_start: 0.8757 (m100) cc_final: 0.7732 (p-90) REVERT: F 302 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8150 (ptpp) REVERT: G 257 ILE cc_start: 0.4685 (tt) cc_final: 0.4459 (tt) REVERT: G 328 ASP cc_start: 0.5455 (m-30) cc_final: 0.5059 (m-30) REVERT: G 365 LYS cc_start: 0.7947 (tttt) cc_final: 0.7457 (mmtm) REVERT: G 430 ASP cc_start: 0.8309 (t70) cc_final: 0.7745 (t0) REVERT: G 436 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8520 (mt-10) REVERT: G 486 ARG cc_start: 0.6718 (mtt90) cc_final: 0.4494 (mtt90) REVERT: G 528 ASP cc_start: 0.8346 (m-30) cc_final: 0.8077 (m-30) REVERT: H 328 ASP cc_start: 0.5629 (m-30) cc_final: 0.5266 (m-30) REVERT: H 396 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7501 (mp0) REVERT: H 510 LEU cc_start: 0.9166 (tp) cc_final: 0.8895 (tp) REVERT: H 534 ASN cc_start: 0.6349 (p0) cc_final: 0.6105 (p0) REVERT: H 579 LYS cc_start: 0.8875 (tmmt) cc_final: 0.8610 (tmmt) REVERT: I 95 TRP cc_start: 0.8550 (m100) cc_final: 0.8206 (m100) REVERT: I 134 LEU cc_start: 0.8974 (tp) cc_final: 0.8626 (tp) REVERT: I 224 PHE cc_start: 0.8275 (m-80) cc_final: 0.8014 (m-10) REVERT: I 394 SER cc_start: 0.7330 (p) cc_final: 0.7107 (p) REVERT: J 134 LEU cc_start: 0.9016 (tp) cc_final: 0.8779 (tp) REVERT: J 138 ASP cc_start: 0.6088 (m-30) cc_final: 0.5803 (m-30) REVERT: J 198 GLN cc_start: 0.9078 (tp40) cc_final: 0.8742 (tm-30) REVERT: J 308 LEU cc_start: 0.8527 (mt) cc_final: 0.8318 (mt) REVERT: L 6 CYS cc_start: 0.0660 (t) cc_final: -0.1996 (t) REVERT: L 21 MET cc_start: 0.1115 (mmp) cc_final: 0.0489 (mmt) REVERT: L 79 GLU cc_start: 0.5768 (tm-30) cc_final: 0.5321 (pt0) REVERT: L 124 GLU cc_start: 0.5520 (pp20) cc_final: 0.5043 (tp30) REVERT: L 125 GLU cc_start: 0.7344 (tt0) cc_final: 0.6930 (pp20) REVERT: L 127 TYR cc_start: 0.3302 (t80) cc_final: 0.2937 (t80) REVERT: L 238 GLN cc_start: 0.4187 (pt0) cc_final: 0.3788 (mm-40) REVERT: M 118 ARG cc_start: 0.3324 (tmm-80) cc_final: 0.3053 (mtp-110) REVERT: M 187 ARG cc_start: 0.5003 (mtm-85) cc_final: 0.4691 (tpt170) REVERT: M 331 GLU cc_start: -0.1165 (mt-10) cc_final: -0.1526 (mm-30) REVERT: M 430 ILE cc_start: 0.5522 (pt) cc_final: 0.5155 (mm) REVERT: N 331 GLU cc_start: -0.1273 (mt-10) cc_final: -0.1519 (mm-30) REVERT: N 430 ILE cc_start: 0.5676 (pt) cc_final: 0.5409 (mm) REVERT: N 462 LEU cc_start: 0.3652 (mt) cc_final: 0.2598 (mm) REVERT: N 463 MET cc_start: 0.0695 (ttp) cc_final: -0.0654 (mmt) REVERT: K 21 MET cc_start: 0.2948 (mmm) cc_final: 0.2546 (mpp) REVERT: K 79 GLU cc_start: 0.5769 (tm-30) cc_final: 0.5445 (pt0) REVERT: K 124 GLU cc_start: 0.5210 (pp20) cc_final: 0.4934 (tp30) REVERT: C 23 ASP cc_start: 0.7897 (m-30) cc_final: 0.7610 (m-30) REVERT: C 76 LYS cc_start: 0.8554 (mttt) cc_final: 0.8276 (mttm) REVERT: C 169 ASP cc_start: 0.8841 (m-30) cc_final: 0.8310 (t0) REVERT: C 319 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8176 (tm-30) outliers start: 1 outliers final: 1 residues processed: 780 average time/residue: 0.4593 time to fit residues: 586.9896 Evaluate side-chains 641 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 640 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 151 optimal weight: 2.9990 chunk 405 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 264 optimal weight: 9.9990 chunk 111 optimal weight: 0.2980 chunk 450 optimal weight: 0.7980 chunk 374 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 524 ASN H 416 ASN ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 87 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 GLN J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 313 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37598 Z= 0.195 Angle : 0.625 8.214 50890 Z= 0.317 Chirality : 0.046 0.230 5972 Planarity : 0.004 0.079 6496 Dihedral : 5.521 78.545 5048 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.40 % Favored : 90.85 % Rotamer: Outliers : 0.05 % Allowed : 1.81 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.12), residues: 4632 helix: 0.72 (0.13), residues: 1540 sheet: -0.10 (0.20), residues: 652 loop : -2.26 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 303 HIS 0.009 0.001 HIS H 280 PHE 0.019 0.001 PHE H 435 TYR 0.020 0.001 TYR L 33 ARG 0.008 0.000 ARG G 486 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 771 time to evaluate : 4.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8993 (m) cc_final: 0.8536 (p) REVERT: A 79 ARG cc_start: 0.6656 (tmm160) cc_final: 0.6345 (tmm160) REVERT: A 96 GLU cc_start: 0.5684 (tt0) cc_final: 0.5287 (pt0) REVERT: A 195 PHE cc_start: 0.7128 (m-80) cc_final: 0.6898 (m-80) REVERT: A 207 ILE cc_start: 0.8966 (mm) cc_final: 0.8662 (mm) REVERT: A 228 TYR cc_start: 0.7604 (m-80) cc_final: 0.6226 (m-80) REVERT: A 239 MET cc_start: 0.7067 (mtp) cc_final: 0.6482 (ttp) REVERT: A 249 MET cc_start: 0.6342 (mtm) cc_final: 0.4927 (ttp) REVERT: A 286 ASP cc_start: 0.8051 (p0) cc_final: 0.7233 (t0) REVERT: B 239 MET cc_start: 0.6404 (mtp) cc_final: 0.6143 (mmt) REVERT: B 249 MET cc_start: 0.6372 (mtm) cc_final: 0.5504 (ttp) REVERT: D 76 LYS cc_start: 0.8442 (mttt) cc_final: 0.8172 (mttm) REVERT: D 150 TYR cc_start: 0.8173 (t80) cc_final: 0.7271 (m-10) REVERT: D 169 ASP cc_start: 0.8854 (m-30) cc_final: 0.8316 (t0) REVERT: E 162 ARG cc_start: 0.6557 (ptm-80) cc_final: 0.6159 (tmm-80) REVERT: E 261 TRP cc_start: 0.8726 (m100) cc_final: 0.7801 (p-90) REVERT: E 302 LYS cc_start: 0.8799 (pttt) cc_final: 0.8338 (ptpt) REVERT: F 162 ARG cc_start: 0.6185 (ptm160) cc_final: 0.5893 (tmm-80) REVERT: F 261 TRP cc_start: 0.8773 (m100) cc_final: 0.7740 (p-90) REVERT: F 278 TYR cc_start: 0.2363 (m-80) cc_final: 0.1468 (m-10) REVERT: F 302 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8172 (ptpp) REVERT: G 257 ILE cc_start: 0.4652 (tt) cc_final: 0.4341 (tt) REVERT: G 274 ILE cc_start: 0.8675 (mp) cc_final: 0.8461 (mp) REVERT: G 284 TYR cc_start: 0.7117 (t80) cc_final: 0.6632 (t80) REVERT: G 328 ASP cc_start: 0.5438 (m-30) cc_final: 0.5051 (m-30) REVERT: G 340 MET cc_start: 0.7842 (mtp) cc_final: 0.6808 (mmm) REVERT: G 365 LYS cc_start: 0.7959 (tttt) cc_final: 0.7456 (mmtm) REVERT: G 430 ASP cc_start: 0.8500 (t70) cc_final: 0.7836 (t0) REVERT: G 486 ARG cc_start: 0.6877 (mtt90) cc_final: 0.4426 (mtt90) REVERT: G 528 ASP cc_start: 0.8350 (m-30) cc_final: 0.8129 (m-30) REVERT: H 284 TYR cc_start: 0.7507 (t80) cc_final: 0.6963 (t80) REVERT: H 328 ASP cc_start: 0.5706 (m-30) cc_final: 0.5366 (m-30) REVERT: H 340 MET cc_start: 0.6561 (ptm) cc_final: 0.5908 (ppp) REVERT: H 366 ASP cc_start: 0.9310 (t0) cc_final: 0.9050 (t0) REVERT: H 436 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8818 (mt-10) REVERT: H 486 ARG cc_start: 0.7206 (mmt-90) cc_final: 0.6647 (mmt180) REVERT: H 510 LEU cc_start: 0.9150 (tp) cc_final: 0.8859 (tp) REVERT: I 134 LEU cc_start: 0.9149 (tp) cc_final: 0.8890 (tp) REVERT: I 224 PHE cc_start: 0.8287 (m-80) cc_final: 0.8029 (m-10) REVERT: I 370 GLU cc_start: 0.8121 (mp0) cc_final: 0.7811 (mp0) REVERT: J 198 GLN cc_start: 0.9100 (tp40) cc_final: 0.8762 (tm-30) REVERT: J 370 GLU cc_start: 0.8210 (mp0) cc_final: 0.7918 (mp0) REVERT: L 6 CYS cc_start: 0.0705 (t) cc_final: -0.0333 (t) REVERT: L 21 MET cc_start: 0.1971 (mmp) cc_final: 0.1471 (mmt) REVERT: L 30 MET cc_start: 0.2999 (tmm) cc_final: 0.0700 (ptp) REVERT: L 79 GLU cc_start: 0.5759 (tm-30) cc_final: 0.5318 (pt0) REVERT: L 125 GLU cc_start: 0.7340 (tt0) cc_final: 0.7102 (pt0) REVERT: L 238 GLN cc_start: 0.4360 (pt0) cc_final: 0.3894 (mm110) REVERT: M 118 ARG cc_start: 0.3642 (tmm-80) cc_final: 0.3388 (mtp-110) REVERT: M 187 ARG cc_start: 0.5061 (mtm-85) cc_final: 0.4714 (tpt170) REVERT: M 331 GLU cc_start: -0.1504 (mt-10) cc_final: -0.1769 (mm-30) REVERT: M 430 ILE cc_start: 0.5458 (pt) cc_final: 0.5124 (mm) REVERT: N 211 MET cc_start: -0.2073 (mtm) cc_final: -0.2437 (mtm) REVERT: N 430 ILE cc_start: 0.5833 (pt) cc_final: 0.5569 (mm) REVERT: N 462 LEU cc_start: 0.3659 (mt) cc_final: 0.2599 (mm) REVERT: N 463 MET cc_start: 0.0688 (ttp) cc_final: -0.0664 (mmt) REVERT: K 21 MET cc_start: 0.2810 (mmm) cc_final: 0.2481 (mpp) REVERT: K 79 GLU cc_start: 0.5846 (tm-30) cc_final: 0.5466 (pt0) REVERT: K 124 GLU cc_start: 0.5188 (pp20) cc_final: 0.4947 (tp30) REVERT: K 235 LEU cc_start: 0.3212 (tp) cc_final: 0.2779 (pp) REVERT: C 23 ASP cc_start: 0.7794 (m-30) cc_final: 0.7549 (m-30) REVERT: C 76 LYS cc_start: 0.8511 (mttt) cc_final: 0.8204 (mttm) REVERT: C 169 ASP cc_start: 0.8809 (m-30) cc_final: 0.8318 (t0) REVERT: C 319 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8155 (tm-30) outliers start: 2 outliers final: 1 residues processed: 773 average time/residue: 0.4818 time to fit residues: 618.4651 Evaluate side-chains 651 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 650 time to evaluate : 4.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 434 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 255 optimal weight: 0.9980 chunk 379 optimal weight: 0.2980 chunk 251 optimal weight: 7.9990 chunk 449 optimal weight: 10.0000 chunk 281 optimal weight: 0.9980 chunk 273 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37598 Z= 0.181 Angle : 0.619 8.966 50890 Z= 0.312 Chirality : 0.045 0.224 5972 Planarity : 0.004 0.056 6496 Dihedral : 5.387 77.957 5048 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.55 % Favored : 90.76 % Rotamer: Outliers : 0.05 % Allowed : 1.20 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.21 (0.12), residues: 4632 helix: 0.89 (0.14), residues: 1526 sheet: -0.30 (0.19), residues: 692 loop : -2.18 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 303 HIS 0.007 0.001 HIS A 129 PHE 0.033 0.001 PHE C 356 TYR 0.016 0.001 TYR K 33 ARG 0.016 0.000 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 769 time to evaluate : 4.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ILE cc_start: 0.5964 (mt) cc_final: 0.5579 (mt) REVERT: A 70 CYS cc_start: 0.8986 (m) cc_final: 0.8526 (p) REVERT: A 79 ARG cc_start: 0.6713 (tmm160) cc_final: 0.6468 (tmm-80) REVERT: A 96 GLU cc_start: 0.6310 (tt0) cc_final: 0.5941 (pt0) REVERT: A 195 PHE cc_start: 0.7118 (m-80) cc_final: 0.6847 (m-80) REVERT: A 207 ILE cc_start: 0.8928 (mm) cc_final: 0.8632 (mm) REVERT: A 228 TYR cc_start: 0.7627 (m-80) cc_final: 0.6325 (m-80) REVERT: A 239 MET cc_start: 0.7096 (mtp) cc_final: 0.6301 (mtp) REVERT: A 249 MET cc_start: 0.6477 (mtm) cc_final: 0.5246 (ttp) REVERT: A 286 ASP cc_start: 0.8043 (p0) cc_final: 0.7204 (t0) REVERT: B 239 MET cc_start: 0.6525 (mtp) cc_final: 0.6310 (mmt) REVERT: B 249 MET cc_start: 0.6321 (mtm) cc_final: 0.5499 (ttp) REVERT: B 286 ASP cc_start: 0.8326 (p0) cc_final: 0.8068 (t0) REVERT: D 23 ASP cc_start: 0.7617 (m-30) cc_final: 0.7295 (m-30) REVERT: D 76 LYS cc_start: 0.8432 (mttt) cc_final: 0.8162 (mttm) REVERT: D 150 TYR cc_start: 0.8187 (t80) cc_final: 0.7258 (m-10) REVERT: D 160 ASP cc_start: 0.8440 (p0) cc_final: 0.8175 (p0) REVERT: D 169 ASP cc_start: 0.8857 (m-30) cc_final: 0.8447 (t0) REVERT: D 237 ASN cc_start: 0.6784 (t0) cc_final: 0.6500 (t0) REVERT: D 266 PHE cc_start: 0.8004 (m-10) cc_final: 0.7600 (m-10) REVERT: D 326 ASP cc_start: 0.5808 (m-30) cc_final: 0.5494 (m-30) REVERT: E 162 ARG cc_start: 0.6604 (ptm-80) cc_final: 0.6192 (tmm-80) REVERT: E 239 LEU cc_start: 0.6838 (mp) cc_final: 0.6608 (mp) REVERT: E 261 TRP cc_start: 0.8678 (m100) cc_final: 0.7792 (p-90) REVERT: E 302 LYS cc_start: 0.8819 (pttt) cc_final: 0.8322 (ptpt) REVERT: F 162 ARG cc_start: 0.6181 (ptm160) cc_final: 0.5904 (tmm-80) REVERT: F 261 TRP cc_start: 0.8747 (m100) cc_final: 0.7736 (p-90) REVERT: F 278 TYR cc_start: 0.2394 (m-80) cc_final: 0.1421 (m-10) REVERT: F 302 LYS cc_start: 0.8651 (ptmt) cc_final: 0.8215 (ptpp) REVERT: G 257 ILE cc_start: 0.4654 (tt) cc_final: 0.4444 (tt) REVERT: G 284 TYR cc_start: 0.7115 (t80) cc_final: 0.6632 (t80) REVERT: G 296 MET cc_start: 0.9054 (tmm) cc_final: 0.8006 (tmm) REVERT: G 328 ASP cc_start: 0.5440 (m-30) cc_final: 0.5056 (m-30) REVERT: G 340 MET cc_start: 0.7738 (mtp) cc_final: 0.6712 (mmm) REVERT: G 365 LYS cc_start: 0.7960 (tttt) cc_final: 0.7487 (mmtm) REVERT: G 436 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8570 (mt-10) REVERT: G 486 ARG cc_start: 0.6954 (mtt90) cc_final: 0.4470 (mtt90) REVERT: G 528 ASP cc_start: 0.8363 (m-30) cc_final: 0.8106 (m-30) REVERT: H 284 TYR cc_start: 0.7291 (t80) cc_final: 0.6928 (t80) REVERT: H 328 ASP cc_start: 0.5700 (m-30) cc_final: 0.5368 (m-30) REVERT: H 340 MET cc_start: 0.6429 (ptm) cc_final: 0.5857 (ppp) REVERT: H 436 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8965 (mt-10) REVERT: H 506 CYS cc_start: 0.7441 (m) cc_final: 0.7203 (m) REVERT: H 507 CYS cc_start: 0.8726 (t) cc_final: 0.8237 (t) REVERT: H 510 LEU cc_start: 0.9109 (tp) cc_final: 0.8848 (tp) REVERT: I 134 LEU cc_start: 0.9099 (tp) cc_final: 0.8827 (tp) REVERT: I 224 PHE cc_start: 0.8274 (m-80) cc_final: 0.8027 (m-80) REVERT: I 370 GLU cc_start: 0.8076 (mp0) cc_final: 0.7701 (mp0) REVERT: I 394 SER cc_start: 0.7233 (p) cc_final: 0.7003 (p) REVERT: J 95 TRP cc_start: 0.8501 (m100) cc_final: 0.8093 (m100) REVERT: J 198 GLN cc_start: 0.9131 (tp40) cc_final: 0.8810 (tm-30) REVERT: J 308 LEU cc_start: 0.8339 (mt) cc_final: 0.8128 (mt) REVERT: J 370 GLU cc_start: 0.8207 (mp0) cc_final: 0.7907 (mp0) REVERT: L 21 MET cc_start: 0.1623 (mmp) cc_final: 0.1289 (mmt) REVERT: L 30 MET cc_start: 0.2278 (tmm) cc_final: 0.0248 (ptp) REVERT: L 79 GLU cc_start: 0.5834 (tm-30) cc_final: 0.5451 (pt0) REVERT: L 238 GLN cc_start: 0.4357 (pt0) cc_final: 0.3896 (mm110) REVERT: M 118 ARG cc_start: 0.3423 (tmm-80) cc_final: 0.3138 (mtp-110) REVERT: M 187 ARG cc_start: 0.5059 (mtm-85) cc_final: 0.4716 (tpt170) REVERT: M 331 GLU cc_start: -0.1495 (mt-10) cc_final: -0.1766 (mm-30) REVERT: M 430 ILE cc_start: 0.5402 (pt) cc_final: 0.5103 (mm) REVERT: N 211 MET cc_start: -0.2238 (mtm) cc_final: -0.2494 (mtm) REVERT: N 430 ILE cc_start: 0.5828 (pt) cc_final: 0.5564 (mm) REVERT: N 462 LEU cc_start: 0.3666 (mt) cc_final: 0.2588 (mm) REVERT: N 463 MET cc_start: 0.0800 (ttp) cc_final: -0.0536 (mmt) REVERT: K 21 MET cc_start: 0.2856 (mmm) cc_final: 0.2601 (mpp) REVERT: K 79 GLU cc_start: 0.5583 (tm-30) cc_final: 0.5240 (pt0) REVERT: K 235 LEU cc_start: 0.3202 (tp) cc_final: 0.2791 (pp) REVERT: C 76 LYS cc_start: 0.8503 (mttt) cc_final: 0.8194 (mttm) REVERT: C 169 ASP cc_start: 0.8835 (m-30) cc_final: 0.8325 (t0) REVERT: C 237 ASN cc_start: 0.6764 (t0) cc_final: 0.6485 (t0) REVERT: C 307 PHE cc_start: 0.8997 (p90) cc_final: 0.8772 (p90) REVERT: C 319 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8158 (tm-30) outliers start: 2 outliers final: 1 residues processed: 770 average time/residue: 0.4548 time to fit residues: 580.0557 Evaluate side-chains 641 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 640 time to evaluate : 4.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 277 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 0.0010 chunk 285 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 353 optimal weight: 30.0000 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 GLN H 301 GLN H 416 ASN ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.5412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37598 Z= 0.177 Angle : 0.611 9.835 50890 Z= 0.307 Chirality : 0.045 0.213 5972 Planarity : 0.004 0.057 6496 Dihedral : 5.268 76.924 5048 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.57 % Favored : 90.78 % Rotamer: Outliers : 0.05 % Allowed : 0.83 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.12), residues: 4632 helix: 1.04 (0.14), residues: 1522 sheet: -0.18 (0.20), residues: 672 loop : -2.16 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 303 HIS 0.005 0.001 HIS A 129 PHE 0.029 0.001 PHE D 356 TYR 0.017 0.001 TYR K 33 ARG 0.012 0.000 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 772 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 CYS cc_start: 0.8989 (m) cc_final: 0.8532 (p) REVERT: A 96 GLU cc_start: 0.6310 (tt0) cc_final: 0.5949 (pt0) REVERT: A 195 PHE cc_start: 0.7155 (m-80) cc_final: 0.6838 (m-80) REVERT: A 228 TYR cc_start: 0.7406 (m-80) cc_final: 0.6256 (m-80) REVERT: A 239 MET cc_start: 0.7170 (mtp) cc_final: 0.6378 (mtp) REVERT: A 249 MET cc_start: 0.6581 (mtm) cc_final: 0.5659 (ttp) REVERT: A 286 ASP cc_start: 0.8022 (p0) cc_final: 0.7399 (t70) REVERT: B 249 MET cc_start: 0.6372 (mtm) cc_final: 0.5673 (ttp) REVERT: D 23 ASP cc_start: 0.7499 (m-30) cc_final: 0.7233 (m-30) REVERT: D 76 LYS cc_start: 0.8446 (mttt) cc_final: 0.8171 (mttm) REVERT: D 86 ASN cc_start: 0.8874 (m110) cc_final: 0.8430 (m110) REVERT: D 150 TYR cc_start: 0.8331 (t80) cc_final: 0.7339 (m-10) REVERT: D 160 ASP cc_start: 0.8376 (p0) cc_final: 0.8091 (p0) REVERT: D 169 ASP cc_start: 0.8857 (m-30) cc_final: 0.8452 (t0) REVERT: D 237 ASN cc_start: 0.6761 (t0) cc_final: 0.6468 (t0) REVERT: D 326 ASP cc_start: 0.5538 (m-30) cc_final: 0.5310 (m-30) REVERT: E 162 ARG cc_start: 0.6517 (ptm-80) cc_final: 0.6156 (tmm-80) REVERT: E 261 TRP cc_start: 0.8659 (m100) cc_final: 0.7781 (p-90) REVERT: E 302 LYS cc_start: 0.8977 (pttt) cc_final: 0.8415 (ptpt) REVERT: F 261 TRP cc_start: 0.8710 (m100) cc_final: 0.7726 (p-90) REVERT: F 278 TYR cc_start: 0.2488 (m-80) cc_final: 0.1510 (m-10) REVERT: F 302 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8227 (ptpp) REVERT: G 257 ILE cc_start: 0.4577 (tt) cc_final: 0.4340 (tt) REVERT: G 284 TYR cc_start: 0.7030 (t80) cc_final: 0.6484 (t80) REVERT: G 296 MET cc_start: 0.9065 (tmm) cc_final: 0.8485 (tmm) REVERT: G 328 ASP cc_start: 0.5441 (m-30) cc_final: 0.5054 (m-30) REVERT: G 340 MET cc_start: 0.7753 (mtp) cc_final: 0.6783 (mmm) REVERT: G 365 LYS cc_start: 0.7983 (tttt) cc_final: 0.7496 (mmtm) REVERT: G 436 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8640 (mt-10) REVERT: G 486 ARG cc_start: 0.6872 (mtt90) cc_final: 0.6586 (mtt90) REVERT: G 528 ASP cc_start: 0.8313 (m-30) cc_final: 0.8079 (m-30) REVERT: G 569 ASN cc_start: 0.8429 (p0) cc_final: 0.8000 (p0) REVERT: H 284 TYR cc_start: 0.7248 (t80) cc_final: 0.6873 (t80) REVERT: H 328 ASP cc_start: 0.5198 (m-30) cc_final: 0.4853 (m-30) REVERT: H 340 MET cc_start: 0.6621 (ptm) cc_final: 0.6091 (ppp) REVERT: H 430 ASP cc_start: 0.8062 (t70) cc_final: 0.7515 (t70) REVERT: H 436 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8985 (mt-10) REVERT: H 506 CYS cc_start: 0.7286 (m) cc_final: 0.7066 (m) REVERT: H 507 CYS cc_start: 0.8689 (t) cc_final: 0.8204 (t) REVERT: H 510 LEU cc_start: 0.9137 (tp) cc_final: 0.8877 (tp) REVERT: H 534 ASN cc_start: 0.5989 (p0) cc_final: 0.5757 (p0) REVERT: H 579 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8475 (tmtt) REVERT: I 134 LEU cc_start: 0.8969 (tp) cc_final: 0.8671 (tp) REVERT: I 224 PHE cc_start: 0.8327 (m-80) cc_final: 0.8105 (m-80) REVERT: I 370 GLU cc_start: 0.8066 (mp0) cc_final: 0.7682 (mp0) REVERT: I 394 SER cc_start: 0.7135 (p) cc_final: 0.6915 (p) REVERT: J 95 TRP cc_start: 0.8426 (m100) cc_final: 0.7985 (m100) REVERT: J 134 LEU cc_start: 0.9065 (tp) cc_final: 0.8838 (tp) REVERT: J 198 GLN cc_start: 0.9143 (tp40) cc_final: 0.8803 (tm-30) REVERT: J 308 LEU cc_start: 0.8278 (mt) cc_final: 0.8078 (mt) REVERT: J 370 GLU cc_start: 0.8071 (mp0) cc_final: 0.7781 (mp0) REVERT: L 30 MET cc_start: 0.2652 (tmm) cc_final: 0.0373 (ptp) REVERT: L 79 GLU cc_start: 0.5804 (tm-30) cc_final: 0.5447 (pt0) REVERT: L 238 GLN cc_start: 0.4754 (pt0) cc_final: 0.4319 (mm110) REVERT: M 118 ARG cc_start: 0.3607 (tmm-80) cc_final: 0.3325 (mtp-110) REVERT: M 187 ARG cc_start: 0.5058 (mtm-85) cc_final: 0.4716 (tpt170) REVERT: M 331 GLU cc_start: -0.1486 (mt-10) cc_final: -0.1764 (mm-30) REVERT: M 430 ILE cc_start: 0.5404 (pt) cc_final: 0.5111 (mm) REVERT: N 430 ILE cc_start: 0.5854 (pt) cc_final: 0.5601 (mm) REVERT: N 462 LEU cc_start: 0.3697 (mt) cc_final: 0.2616 (mm) REVERT: N 463 MET cc_start: 0.0682 (ttp) cc_final: -0.0671 (mmt) REVERT: K 21 MET cc_start: 0.3045 (mmm) cc_final: 0.2766 (mpp) REVERT: K 79 GLU cc_start: 0.5642 (tm-30) cc_final: 0.5274 (pt0) REVERT: K 235 LEU cc_start: 0.3165 (tp) cc_final: 0.2764 (pp) REVERT: C 23 ASP cc_start: 0.7469 (m-30) cc_final: 0.7257 (m-30) REVERT: C 76 LYS cc_start: 0.8493 (mttt) cc_final: 0.8184 (mttm) REVERT: C 86 ASN cc_start: 0.9067 (m-40) cc_final: 0.8841 (m-40) REVERT: C 169 ASP cc_start: 0.8956 (m-30) cc_final: 0.8377 (t0) REVERT: C 237 ASN cc_start: 0.6768 (t0) cc_final: 0.6454 (t0) outliers start: 2 outliers final: 0 residues processed: 773 average time/residue: 0.4569 time to fit residues: 585.4542 Evaluate side-chains 639 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 408 optimal weight: 30.0000 chunk 430 optimal weight: 40.0000 chunk 392 optimal weight: 20.0000 chunk 418 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 378 optimal weight: 0.0870 chunk 395 optimal weight: 6.9990 chunk 417 optimal weight: 5.9990 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN B 161 GLN B 164 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS E 254 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 GLN F 312 GLN ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 301 GLN ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 ASN H 539 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN I 198 GLN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 ASN J 158 GLN ** J 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 376 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN M 197 HIS ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN M 433 ASN ** N 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 465 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 37598 Z= 0.531 Angle : 0.962 12.178 50890 Z= 0.498 Chirality : 0.056 0.395 5972 Planarity : 0.007 0.101 6496 Dihedral : 6.635 75.721 5048 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.70 % Favored : 87.59 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % 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: -2.23 (0.12), residues: 4632 helix: -0.42 (0.12), residues: 1538 sheet: -0.65 (0.19), residues: 710 loop : -2.55 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.004 TRP A 303 HIS 0.021 0.002 HIS A 129 PHE 0.039 0.003 PHE D 229 TYR 0.049 0.004 TYR G 284 ARG 0.018 0.001 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 735 time to evaluate : 4.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.8713 (mmp) cc_final: 0.8285 (mmm) REVERT: A 79 ARG cc_start: 0.4482 (ptt90) cc_final: 0.4278 (ptp90) REVERT: A 96 GLU cc_start: 0.6101 (tt0) cc_final: 0.5714 (pt0) REVERT: A 120 ILE cc_start: 0.7966 (mp) cc_final: 0.7142 (tt) REVERT: A 195 PHE cc_start: 0.7399 (m-80) cc_final: 0.7086 (m-10) REVERT: A 228 TYR cc_start: 0.7520 (m-80) cc_final: 0.5639 (m-80) REVERT: A 239 MET cc_start: 0.6806 (mtp) cc_final: 0.5892 (mtp) REVERT: A 249 MET cc_start: 0.6952 (mtm) cc_final: 0.6207 (ttm) REVERT: B 120 ILE cc_start: 0.8050 (mp) cc_final: 0.7329 (tt) REVERT: B 249 MET cc_start: 0.6729 (mtm) cc_final: 0.6424 (ttm) REVERT: D 23 ASP cc_start: 0.7981 (m-30) cc_final: 0.7625 (m-30) REVERT: D 86 ASN cc_start: 0.8798 (m110) cc_final: 0.8431 (m110) REVERT: D 92 LEU cc_start: 0.9128 (mt) cc_final: 0.8879 (mt) REVERT: D 169 ASP cc_start: 0.8913 (m-30) cc_final: 0.8478 (t0) REVERT: E 197 MET cc_start: 0.7300 (tpt) cc_final: 0.6978 (tpp) REVERT: E 261 TRP cc_start: 0.8534 (m100) cc_final: 0.7769 (t60) REVERT: E 302 LYS cc_start: 0.8705 (pttt) cc_final: 0.8347 (ptpt) REVERT: F 261 TRP cc_start: 0.8657 (m100) cc_final: 0.7630 (t60) REVERT: F 302 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8131 (ptpp) REVERT: G 284 TYR cc_start: 0.7519 (t80) cc_final: 0.7023 (t80) REVERT: G 365 LYS cc_start: 0.8040 (tttt) cc_final: 0.7666 (mmtt) REVERT: G 411 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8930 (tm-30) REVERT: G 430 ASP cc_start: 0.8448 (t70) cc_final: 0.8015 (t70) REVERT: G 436 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8833 (mt-10) REVERT: G 486 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6582 (mtt90) REVERT: G 515 ARG cc_start: 0.7877 (ptm160) cc_final: 0.7371 (ptm160) REVERT: H 284 TYR cc_start: 0.7843 (t80) cc_final: 0.7041 (t80) REVERT: H 340 MET cc_start: 0.7589 (ptm) cc_final: 0.7117 (ppp) REVERT: H 430 ASP cc_start: 0.8220 (t70) cc_final: 0.7782 (t0) REVERT: H 436 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8726 (mt-10) REVERT: H 510 LEU cc_start: 0.9216 (tp) cc_final: 0.9012 (tp) REVERT: I 119 MET cc_start: 0.8321 (ptm) cc_final: 0.8114 (ptm) REVERT: I 318 TYR cc_start: 0.8163 (m-10) cc_final: 0.7860 (m-10) REVERT: I 357 ILE cc_start: 0.8658 (mt) cc_final: 0.8411 (mp) REVERT: I 370 GLU cc_start: 0.8103 (mp0) cc_final: 0.7612 (mt-10) REVERT: I 394 SER cc_start: 0.7705 (p) cc_final: 0.7468 (p) REVERT: J 49 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6371 (tmm-80) REVERT: J 94 LYS cc_start: 0.8838 (mptt) cc_final: 0.8619 (mmtm) REVERT: J 95 TRP cc_start: 0.8717 (m100) cc_final: 0.8275 (m100) REVERT: J 134 LEU cc_start: 0.9088 (tp) cc_final: 0.8827 (tp) REVERT: J 318 TYR cc_start: 0.8323 (m-10) cc_final: 0.7787 (m-10) REVERT: J 370 GLU cc_start: 0.7869 (mp0) cc_final: 0.7662 (mp0) REVERT: J 394 SER cc_start: 0.7744 (p) cc_final: 0.7540 (p) REVERT: L 21 MET cc_start: -0.1512 (mmt) cc_final: -0.1774 (mmt) REVERT: L 30 MET cc_start: 0.2299 (tmm) cc_final: -0.0410 (ptp) REVERT: L 79 GLU cc_start: 0.5773 (tm-30) cc_final: 0.5398 (tt0) REVERT: L 221 LYS cc_start: -0.0148 (pptt) cc_final: -0.0503 (tppt) REVERT: L 238 GLN cc_start: 0.5024 (pt0) cc_final: 0.4643 (mm-40) REVERT: M 118 ARG cc_start: 0.2744 (tmm-80) cc_final: 0.2414 (mtp-110) REVERT: M 187 ARG cc_start: 0.4950 (mtm-85) cc_final: 0.4477 (tpt170) REVERT: M 406 LEU cc_start: 0.3626 (mt) cc_final: 0.3241 (tt) REVERT: M 430 ILE cc_start: 0.5372 (pt) cc_final: 0.5114 (mm) REVERT: N 430 ILE cc_start: 0.5808 (pt) cc_final: 0.5576 (mm) REVERT: N 462 LEU cc_start: 0.4136 (mt) cc_final: 0.3790 (mm) REVERT: K 21 MET cc_start: 0.3132 (mmm) cc_final: 0.2890 (mpp) REVERT: K 30 MET cc_start: 0.4326 (tmm) cc_final: 0.2729 (ptp) REVERT: K 235 LEU cc_start: 0.3464 (tp) cc_final: 0.3001 (pp) REVERT: C 23 ASP cc_start: 0.8077 (m-30) cc_final: 0.7744 (m-30) REVERT: C 69 ASP cc_start: 0.7481 (m-30) cc_final: 0.6556 (p0) REVERT: C 92 LEU cc_start: 0.9158 (mt) cc_final: 0.8916 (mt) REVERT: C 104 MET cc_start: 0.3022 (tmm) cc_final: 0.2728 (tpp) REVERT: C 169 ASP cc_start: 0.9024 (m-30) cc_final: 0.8569 (t0) REVERT: C 211 PHE cc_start: 0.8062 (p90) cc_final: 0.7791 (p90) REVERT: C 263 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7996 (tmtt) REVERT: C 287 GLU cc_start: 0.8805 (tp30) cc_final: 0.8497 (tp30) outliers start: 0 outliers final: 0 residues processed: 735 average time/residue: 0.4636 time to fit residues: 563.3432 Evaluate side-chains 618 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 618 time to evaluate : 4.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 274 optimal weight: 0.6980 chunk 442 optimal weight: 50.0000 chunk 270 optimal weight: 5.9990 chunk 209 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 464 optimal weight: 2.9990 chunk 427 optimal weight: 20.0000 chunk 369 optimal weight: 40.0000 chunk 38 optimal weight: 0.0030 chunk 285 optimal weight: 0.9990 chunk 226 optimal weight: 0.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 GLN ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 415 HIS ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 GLN ** J 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 GLN N 415 GLN ** N 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37598 Z= 0.213 Angle : 0.682 9.876 50890 Z= 0.347 Chirality : 0.047 0.204 5972 Planarity : 0.004 0.061 6496 Dihedral : 5.765 73.334 5048 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.51 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.12), residues: 4632 helix: 0.33 (0.13), residues: 1514 sheet: -0.38 (0.19), residues: 700 loop : -2.38 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 303 HIS 0.015 0.001 HIS A 129 PHE 0.028 0.002 PHE D 356 TYR 0.041 0.002 TYR H 537 ARG 0.013 0.001 ARG E 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 768 time to evaluate : 4.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 96 GLU cc_start: 0.6199 (tt0) cc_final: 0.5812 (pt0) REVERT: A 120 ILE cc_start: 0.7692 (mp) cc_final: 0.7362 (mt) REVERT: A 249 MET cc_start: 0.6735 (mtm) cc_final: 0.6100 (ttm) REVERT: A 286 ASP cc_start: 0.8257 (p0) cc_final: 0.7743 (t0) REVERT: B 123 ASP cc_start: 0.7959 (t70) cc_final: 0.7753 (t70) REVERT: B 249 MET cc_start: 0.7051 (mtm) cc_final: 0.6292 (ttp) REVERT: D 23 ASP cc_start: 0.7725 (m-30) cc_final: 0.7468 (m-30) REVERT: D 86 ASN cc_start: 0.8782 (m110) cc_final: 0.8259 (m110) REVERT: D 150 TYR cc_start: 0.8196 (t80) cc_final: 0.7348 (m-10) REVERT: D 169 ASP cc_start: 0.8909 (m-30) cc_final: 0.8522 (t0) REVERT: D 357 ASN cc_start: 0.8782 (t0) cc_final: 0.8357 (t0) REVERT: E 295 MET cc_start: 0.7077 (mmm) cc_final: 0.6340 (tpt) REVERT: E 302 LYS cc_start: 0.8924 (pttt) cc_final: 0.8557 (ptpt) REVERT: F 197 MET cc_start: 0.7957 (mmp) cc_final: 0.7329 (tpp) REVERT: F 261 TRP cc_start: 0.8763 (m100) cc_final: 0.7586 (t60) REVERT: F 272 LEU cc_start: 0.8299 (mm) cc_final: 0.7982 (mm) REVERT: F 302 LYS cc_start: 0.8590 (ptmt) cc_final: 0.8050 (ptpp) REVERT: G 284 TYR cc_start: 0.7692 (t80) cc_final: 0.7050 (t80) REVERT: G 365 LYS cc_start: 0.7827 (tttt) cc_final: 0.7367 (mmtm) REVERT: G 436 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8823 (mt-10) REVERT: H 284 TYR cc_start: 0.7555 (t80) cc_final: 0.6879 (t80) REVERT: H 328 ASP cc_start: 0.5684 (m-30) cc_final: 0.5342 (m-30) REVERT: H 340 MET cc_start: 0.6781 (ptm) cc_final: 0.6246 (ppp) REVERT: H 430 ASP cc_start: 0.8043 (t70) cc_final: 0.7577 (t0) REVERT: H 436 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8889 (mt-10) REVERT: H 495 SER cc_start: 0.9033 (p) cc_final: 0.8786 (p) REVERT: H 507 CYS cc_start: 0.8626 (t) cc_final: 0.8302 (t) REVERT: H 510 LEU cc_start: 0.9200 (tp) cc_final: 0.8971 (tp) REVERT: I 95 TRP cc_start: 0.8769 (m100) cc_final: 0.8303 (m100) REVERT: I 134 LEU cc_start: 0.9112 (tp) cc_final: 0.8858 (tp) REVERT: I 145 PHE cc_start: 0.8908 (t80) cc_final: 0.8679 (t80) REVERT: I 288 TRP cc_start: 0.8131 (m100) cc_final: 0.7733 (m100) REVERT: I 370 GLU cc_start: 0.8103 (mp0) cc_final: 0.7723 (mp0) REVERT: I 394 SER cc_start: 0.7310 (p) cc_final: 0.7077 (p) REVERT: J 49 ARG cc_start: 0.6995 (ttp80) cc_final: 0.6152 (tmm-80) REVERT: J 95 TRP cc_start: 0.8562 (m100) cc_final: 0.8003 (m100) REVERT: J 119 MET cc_start: 0.8330 (ptm) cc_final: 0.7722 (ppp) REVERT: J 308 LEU cc_start: 0.8670 (mt) cc_final: 0.8418 (mt) REVERT: J 370 GLU cc_start: 0.8108 (mp0) cc_final: 0.7773 (mp0) REVERT: J 394 SER cc_start: 0.7462 (p) cc_final: 0.7195 (p) REVERT: L 21 MET cc_start: -0.1192 (mmt) cc_final: -0.2154 (mmt) REVERT: L 45 MET cc_start: 0.4642 (ptm) cc_final: 0.4415 (ptm) REVERT: L 79 GLU cc_start: 0.5899 (tm-30) cc_final: 0.5511 (mt-10) REVERT: L 221 LYS cc_start: 0.0022 (pptt) cc_final: -0.0400 (tppt) REVERT: L 238 GLN cc_start: 0.4824 (pt0) cc_final: 0.4471 (mm-40) REVERT: M 118 ARG cc_start: 0.3012 (tmm-80) cc_final: 0.2718 (mtp-110) REVERT: M 187 ARG cc_start: 0.4865 (mtm-85) cc_final: 0.4419 (tpt170) REVERT: M 294 VAL cc_start: 0.2907 (t) cc_final: 0.2653 (t) REVERT: M 406 LEU cc_start: 0.3928 (mt) cc_final: 0.3430 (tp) REVERT: M 430 ILE cc_start: 0.5541 (pt) cc_final: 0.5209 (mm) REVERT: N 406 LEU cc_start: -0.0055 (tp) cc_final: -0.0261 (tp) REVERT: N 430 ILE cc_start: 0.5692 (pt) cc_final: 0.5442 (mm) REVERT: N 462 LEU cc_start: 0.3894 (mt) cc_final: 0.2630 (mm) REVERT: N 463 MET cc_start: -0.1051 (ttp) cc_final: -0.2103 (mmp) REVERT: K 21 MET cc_start: 0.3660 (mmm) cc_final: 0.2940 (mpp) REVERT: K 30 MET cc_start: 0.4467 (tmm) cc_final: 0.2762 (ptp) REVERT: K 235 LEU cc_start: 0.3320 (tp) cc_final: 0.2889 (pp) REVERT: C 23 ASP cc_start: 0.7776 (m-30) cc_final: 0.7470 (m-30) REVERT: C 86 ASN cc_start: 0.8833 (m-40) cc_final: 0.8532 (m-40) REVERT: C 92 LEU cc_start: 0.9194 (mt) cc_final: 0.8908 (mt) REVERT: C 104 MET cc_start: 0.2991 (tmm) cc_final: 0.2701 (tpp) REVERT: C 169 ASP cc_start: 0.8910 (m-30) cc_final: 0.8539 (t0) REVERT: C 254 ARG cc_start: 0.8826 (mmm-85) cc_final: 0.8594 (mtm-85) REVERT: C 357 ASN cc_start: 0.8919 (t0) cc_final: 0.8709 (t0) outliers start: 0 outliers final: 0 residues processed: 768 average time/residue: 0.4850 time to fit residues: 618.1098 Evaluate side-chains 631 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 631 time to evaluate : 4.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 293 optimal weight: 3.9990 chunk 393 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 chunk 54 optimal weight: 0.0040 chunk 102 optimal weight: 20.0000 chunk 370 optimal weight: 30.0000 chunk 154 optimal weight: 1.9990 chunk 380 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4936 r_free = 0.4936 target = 0.237820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.189330 restraints weight = 70130.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.185822 restraints weight = 63867.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.186899 restraints weight = 51006.341| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37598 Z= 0.202 Angle : 0.660 9.780 50890 Z= 0.334 Chirality : 0.046 0.220 5972 Planarity : 0.004 0.083 6496 Dihedral : 5.536 72.153 5048 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.02 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.42 (0.12), residues: 4632 helix: 0.68 (0.14), residues: 1504 sheet: -0.37 (0.19), residues: 700 loop : -2.28 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 303 HIS 0.010 0.001 HIS A 129 PHE 0.026 0.002 PHE D 199 TYR 0.024 0.002 TYR C 305 ARG 0.013 0.001 ARG E 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10375.67 seconds wall clock time: 188 minutes 38.58 seconds (11318.58 seconds total)