Starting phenix.real_space_refine on Thu Mar 21 08:21:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pij_20351/03_2024/6pij_20351.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pij_20351/03_2024/6pij_20351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pij_20351/03_2024/6pij_20351.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pij_20351/03_2024/6pij_20351.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pij_20351/03_2024/6pij_20351.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pij_20351/03_2024/6pij_20351.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 95 5.49 5 S 142 5.16 5 C 18531 2.51 5 N 5143 2.21 5 O 5760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E GLU 169": "OE1" <-> "OE2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F GLU 292": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 85": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ARG 246": "NH1" <-> "NH2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "G ARG 506": "NH1" <-> "NH2" Residue "G GLU 578": "OE1" <-> "OE2" Residue "G ARG 587": "NH1" <-> "NH2" Residue "G GLU 595": "OE1" <-> "OE2" Residue "G ARG 631": "NH1" <-> "NH2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "H ARG 117": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H ARG 121": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "I ARG 8": "NH1" <-> "NH2" Residue "I GLU 18": "OE1" <-> "OE2" Residue "I PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 252": "NH1" <-> "NH2" Residue "I ARG 284": "NH1" <-> "NH2" Residue "I ARG 313": "NH1" <-> "NH2" Residue "I ARG 349": "NH1" <-> "NH2" Residue "I ARG 390": "NH1" <-> "NH2" Residue "J ARG 23": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 124": "NH1" <-> "NH2" Residue "J GLU 151": "OE1" <-> "OE2" Residue "J ARG 223": "NH1" <-> "NH2" Residue "J ARG 277": "NH1" <-> "NH2" Residue "J ARG 284": "NH1" <-> "NH2" Residue "J GLU 305": "OE1" <-> "OE2" Residue "J ARG 313": "NH1" <-> "NH2" Residue "J GLU 330": "OE1" <-> "OE2" Residue "J ARG 349": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29671 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2782 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 330} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2714 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2715 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2705 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 317} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 2710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2710 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2509 Classifications: {'peptide': 310} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 292} Chain breaks: 2 Chain: "G" Number of atoms: 4009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4009 Classifications: {'peptide': 511} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 486} Chain breaks: 2 Chain: "H" Number of atoms: 1606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1606 Classifications: {'peptide': 197} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 187} Chain: "I" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2928 Classifications: {'peptide': 358} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 336} Chain breaks: 3 Chain: "J" Number of atoms: 2983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2983 Classifications: {'peptide': 369} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 348} Chain breaks: 2 Chain: "1" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1271 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 15, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 24, 'rna3p': 35} Chain: "2" Number of atoms: 561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 561 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "3" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 178 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 15.73, per 1000 atoms: 0.53 Number of scatterers: 29671 At special positions: 0 Unit cell: (130.442, 156.954, 185.588, 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 142 16.00 P 95 15.00 O 5760 8.00 N 5143 7.00 C 18531 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: 11.34 Conformation dependent library (CDL) restraints added in 5.0 seconds 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6578 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 42 sheets defined 30.9% alpha, 15.4% beta 25 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 10.11 Creating SS restraints... Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 63 through 67 removed outlier: 3.856A pdb=" N GLN A 67 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 123 Processing helix chain 'A' and resid 125 through 135 removed outlier: 3.844A pdb=" N ASN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.502A pdb=" N LEU A 142 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.567A pdb=" N PHE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 261 through 269 Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.789A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 4.227A pdb=" N ASN A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.830A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.743A pdb=" N GLN B 67 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 123 removed outlier: 3.524A pdb=" N GLN B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.856A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 305 through 311 removed outlier: 3.525A pdb=" N GLN B 311 " --> pdb=" O PHE B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.514A pdb=" N SER B 321 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 344 removed outlier: 3.548A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.765A pdb=" N GLN C 67 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 99 removed outlier: 4.104A pdb=" N GLN C 99 " --> pdb=" O GLU C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 99' Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 125 through 135 removed outlier: 3.923A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 Processing helix chain 'C' and resid 177 through 182 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 261 through 269 removed outlier: 3.565A pdb=" N GLY C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 311 Processing helix chain 'C' and resid 312 through 320 Processing helix chain 'C' and resid 330 through 342 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.643A pdb=" N ALA D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 123 Processing helix chain 'D' and resid 125 through 138 removed outlier: 3.628A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 Processing helix chain 'D' and resid 177 through 182 Processing helix chain 'D' and resid 186 through 192 removed outlier: 3.764A pdb=" N ILE D 190 " --> pdb=" O ASN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 305 through 311 Processing helix chain 'D' and resid 312 through 321 Processing helix chain 'D' and resid 330 through 344 removed outlier: 3.558A pdb=" N PHE D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.651A pdb=" N ALA E 49 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 107 through 123 Processing helix chain 'E' and resid 125 through 138 removed outlier: 3.633A pdb=" N ASN E 135 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.725A pdb=" N LEU E 142 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.601A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 removed outlier: 4.668A pdb=" N TRP E 187 " --> pdb=" O ASN E 183 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER E 188 " --> pdb=" O ASN E 184 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 200 Processing helix chain 'E' and resid 260 through 269 removed outlier: 3.811A pdb=" N THR E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 311 Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.868A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 342 removed outlier: 3.506A pdb=" N PHE E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 123 removed outlier: 3.542A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 138 removed outlier: 3.748A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.742A pdb=" N PHE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 194 through 200 Processing helix chain 'F' and resid 262 through 269 removed outlier: 3.697A pdb=" N ILE F 268 " --> pdb=" O THR F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 311 Processing helix chain 'F' and resid 312 through 320 removed outlier: 4.216A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 343 removed outlier: 3.509A pdb=" N PHE F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 20 through 27 removed outlier: 3.608A pdb=" N PHE G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 47 removed outlier: 4.423A pdb=" N ILE G 45 " --> pdb=" O ASP G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 removed outlier: 3.888A pdb=" N ASN G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS G 81 " --> pdb=" O SER G 77 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL G 82 " --> pdb=" O CYS G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 119 Processing helix chain 'G' and resid 151 through 156 removed outlier: 3.779A pdb=" N LEU G 155 " --> pdb=" O CYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 170 Processing helix chain 'G' and resid 176 through 185 Processing helix chain 'G' and resid 221 through 232 removed outlier: 3.767A pdb=" N HIS G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 251 removed outlier: 3.662A pdb=" N MET G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.778A pdb=" N CYS G 257 " --> pdb=" O THR G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 431 removed outlier: 3.778A pdb=" N PHE G 418 " --> pdb=" O SER G 414 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG G 431 " --> pdb=" O ARG G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 502 Processing helix chain 'G' and resid 527 through 534 removed outlier: 3.521A pdb=" N ALA G 531 " --> pdb=" O THR G 527 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU G 533 " --> pdb=" O GLU G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 552 through 561 removed outlier: 3.548A pdb=" N LEU G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 31 removed outlier: 3.603A pdb=" N LEU H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 70 removed outlier: 3.817A pdb=" N LEU H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.739A pdb=" N GLN H 80 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 81' Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.547A pdb=" N SER H 137 " --> pdb=" O ASP H 134 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE H 138 " --> pdb=" O PRO H 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 134 through 138' Processing helix chain 'I' and resid 18 through 23 removed outlier: 3.970A pdb=" N ARG I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 48 removed outlier: 3.714A pdb=" N ILE I 47 " --> pdb=" O PHE I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.650A pdb=" N THR I 75 " --> pdb=" O SER I 71 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 148 removed outlier: 4.130A pdb=" N PHE I 147 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN I 148 " --> pdb=" O TRP I 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 144 through 148' Processing helix chain 'I' and resid 199 through 204 removed outlier: 3.736A pdb=" N VAL I 203 " --> pdb=" O ALA I 199 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER I 204 " --> pdb=" O ALA I 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 199 through 204' Processing helix chain 'I' and resid 219 through 230 removed outlier: 3.766A pdb=" N GLY I 225 " --> pdb=" O SER I 221 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP I 230 " --> pdb=" O LEU I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 268 removed outlier: 3.663A pdb=" N PHE I 254 " --> pdb=" O TRP I 250 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N HIS I 255 " --> pdb=" O PRO I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 288 Processing helix chain 'I' and resid 300 through 313 Processing helix chain 'I' and resid 327 through 336 removed outlier: 4.087A pdb=" N THR I 332 " --> pdb=" O ALA I 328 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL I 333 " --> pdb=" O LEU I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 348 removed outlier: 4.164A pdb=" N ALA I 343 " --> pdb=" O LEU I 339 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 383 Processing helix chain 'I' and resid 389 through 393 removed outlier: 3.757A pdb=" N PHE I 392 " --> pdb=" O ASN I 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 removed outlier: 3.638A pdb=" N LYS J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 46 Processing helix chain 'J' and resid 70 through 84 Processing helix chain 'J' and resid 199 through 209 Processing helix chain 'J' and resid 219 through 234 removed outlier: 4.100A pdb=" N GLY J 225 " --> pdb=" O SER J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 245 Processing helix chain 'J' and resid 249 through 263 removed outlier: 4.051A pdb=" N PHE J 254 " --> pdb=" O TRP J 250 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS J 255 " --> pdb=" O PRO J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 313 removed outlier: 3.531A pdb=" N GLY J 304 " --> pdb=" O ASN J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 336 Processing helix chain 'J' and resid 341 through 347 Processing helix chain 'J' and resid 372 through 383 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.567A pdb=" N CYS A 151 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 248 through 251 Processing sheet with id=AA4, first strand: chain 'A' and resid 289 through 290 removed outlier: 3.787A pdb=" N THR A 295 " --> pdb=" O HIS A 290 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.583A pdb=" N CYS B 151 " --> pdb=" O HIS B 214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 15 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 41 Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 251 Processing sheet with id=AB4, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AB6, first strand: chain 'D' and resid 13 through 15 Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 42 Processing sheet with id=AB8, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AB9, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC1, first strand: chain 'E' and resid 13 through 15 Processing sheet with id=AC2, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.511A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AC4, first strand: chain 'E' and resid 248 through 251 Processing sheet with id=AC5, first strand: chain 'E' and resid 270 through 272 Processing sheet with id=AC6, first strand: chain 'F' and resid 13 through 15 Processing sheet with id=AC7, first strand: chain 'F' and resid 13 through 15 removed outlier: 3.631A pdb=" N CYS F 151 " --> pdb=" O HIS F 214 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 72 through 75 removed outlier: 6.800A pdb=" N SER F 36 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N ILE H 146 " --> pdb=" O SER F 36 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR F 38 " --> pdb=" O ILE H 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AD2, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.272A pdb=" N ALA G 592 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER G 215 " --> pdb=" O ALA G 592 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA G 594 " --> pdb=" O SER G 215 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER G 217 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYS G 596 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.272A pdb=" N ALA G 592 " --> pdb=" O TYR G 213 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER G 215 " --> pdb=" O ALA G 592 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ALA G 594 " --> pdb=" O SER G 215 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N SER G 217 " --> pdb=" O ALA G 594 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N CYS G 596 " --> pdb=" O SER G 217 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE G 593 " --> pdb=" O LEU G 575 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU G 575 " --> pdb=" O ILE G 593 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU G 595 " --> pdb=" O TYR G 573 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR G 573 " --> pdb=" O GLU G 595 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE G 597 " --> pdb=" O VAL G 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 441 through 447 removed outlier: 6.545A pdb=" N PHE G 441 " --> pdb=" O ASN G 487 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN G 487 " --> pdb=" O PHE G 441 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE G 443 " --> pdb=" O ILE G 485 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE G 485 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL G 445 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER G 483 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 484 " --> pdb=" O PRO G 394 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU G 486 " --> pdb=" O VAL G 392 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL G 392 " --> pdb=" O LEU G 486 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER G 511 " --> pdb=" O CYS G 399 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 441 through 447 removed outlier: 6.545A pdb=" N PHE G 441 " --> pdb=" O ASN G 487 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN G 487 " --> pdb=" O PHE G 441 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE G 443 " --> pdb=" O ILE G 485 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE G 485 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL G 445 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N SER G 483 " --> pdb=" O VAL G 445 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU G 484 " --> pdb=" O PRO G 394 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU G 486 " --> pdb=" O VAL G 392 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N VAL G 392 " --> pdb=" O LEU G 486 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 401 through 402 Processing sheet with id=AD7, first strand: chain 'G' and resid 460 through 461 Processing sheet with id=AD8, first strand: chain 'G' and resid 618 through 619 Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'H' and resid 55 through 56 Processing sheet with id=AE2, first strand: chain 'H' and resid 100 through 103 Processing sheet with id=AE3, first strand: chain 'I' and resid 98 through 99 Processing sheet with id=AE4, first strand: chain 'I' and resid 325 through 326 Processing sheet with id=AE5, first strand: chain 'J' and resid 98 through 99 Processing sheet with id=AE6, first strand: chain 'J' and resid 325 through 326 890 hydrogen bonds defined for protein. 2418 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 65 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 9.72 Time building geometry restraints manager: 12.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5545 1.33 - 1.46: 8410 1.46 - 1.58: 16274 1.58 - 1.70: 188 1.70 - 1.82: 205 Bond restraints: 30622 Sorted by residual: bond pdb=" N ILE B 258 " pdb=" CA ILE B 258 " ideal model delta sigma weight residual 1.460 1.500 -0.040 8.60e-03 1.35e+04 2.16e+01 bond pdb=" N ILE C 258 " pdb=" CA ILE C 258 " ideal model delta sigma weight residual 1.460 1.500 -0.039 8.60e-03 1.35e+04 2.11e+01 bond pdb=" N ILE E 190 " pdb=" CA ILE E 190 " ideal model delta sigma weight residual 1.459 1.500 -0.041 9.10e-03 1.21e+04 2.03e+01 bond pdb=" N ILE F 258 " pdb=" CA ILE F 258 " ideal model delta sigma weight residual 1.456 1.499 -0.043 9.50e-03 1.11e+04 2.02e+01 bond pdb=" N GLU E 280 " pdb=" CA GLU E 280 " ideal model delta sigma weight residual 1.453 1.494 -0.041 9.20e-03 1.18e+04 1.99e+01 ... (remaining 30617 not shown) Histogram of bond angle deviations from ideal: 98.59 - 105.78: 1166 105.78 - 112.97: 15069 112.97 - 120.16: 14119 120.16 - 127.35: 11105 127.35 - 134.54: 535 Bond angle restraints: 41994 Sorted by residual: angle pdb=" O3' DA 2 40 " pdb=" C3' DA 2 40 " pdb=" C2' DA 2 40 " ideal model delta sigma weight residual 111.50 121.75 -10.25 1.50e+00 4.44e-01 4.67e+01 angle pdb=" CA GLY G 107 " pdb=" C GLY G 107 " pdb=" O GLY G 107 " ideal model delta sigma weight residual 122.45 118.45 4.00 7.20e-01 1.93e+00 3.08e+01 angle pdb=" N ASP G 234 " pdb=" CA ASP G 234 " pdb=" C ASP G 234 " ideal model delta sigma weight residual 112.26 105.03 7.23 1.32e+00 5.74e-01 3.00e+01 angle pdb=" O GLY D 54 " pdb=" C GLY D 54 " pdb=" N GLN D 55 " ideal model delta sigma weight residual 121.85 124.82 -2.97 5.60e-01 3.19e+00 2.82e+01 angle pdb=" O3' DG 2 36 " pdb=" C3' DG 2 36 " pdb=" C2' DG 2 36 " ideal model delta sigma weight residual 111.50 119.36 -7.86 1.50e+00 4.44e-01 2.74e+01 ... (remaining 41989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 17509 35.19 - 70.38: 628 70.38 - 105.57: 48 105.57 - 140.76: 2 140.76 - 175.95: 2 Dihedral angle restraints: 18189 sinusoidal: 8064 harmonic: 10125 Sorted by residual: dihedral pdb=" CA ILE H 180 " pdb=" C ILE H 180 " pdb=" N PHE H 181 " pdb=" CA PHE H 181 " ideal model delta harmonic sigma weight residual -180.00 -122.67 -57.33 0 5.00e+00 4.00e-02 1.31e+02 dihedral pdb=" CA LEU G 586 " pdb=" C LEU G 586 " pdb=" N ARG G 587 " pdb=" CA ARG G 587 " ideal model delta harmonic sigma weight residual 180.00 129.06 50.94 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA GLN G 233 " pdb=" C GLN G 233 " pdb=" N ASP G 234 " pdb=" CA ASP G 234 " ideal model delta harmonic sigma weight residual 180.00 133.84 46.16 0 5.00e+00 4.00e-02 8.52e+01 ... (remaining 18186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3182 0.088 - 0.176: 1328 0.176 - 0.265: 133 0.265 - 0.353: 0 0.353 - 0.441: 3 Chirality restraints: 4646 Sorted by residual: chirality pdb=" C3' DG 2 36 " pdb=" C4' DG 2 36 " pdb=" O3' DG 2 36 " pdb=" C2' DG 2 36 " both_signs ideal model delta sigma weight residual False -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C3' DA 2 40 " pdb=" C4' DA 2 40 " pdb=" O3' DA 2 40 " pdb=" C2' DA 2 40 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" C3' C 1 28 " pdb=" C4' C 1 28 " pdb=" O3' C 1 28 " pdb=" C2' C 1 28 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 4643 not shown) Planarity restraints: 5036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG 2 49 " -0.044 2.00e-02 2.50e+03 1.89e-02 1.08e+01 pdb=" N9 DG 2 49 " 0.046 2.00e-02 2.50e+03 pdb=" C8 DG 2 49 " 0.007 2.00e-02 2.50e+03 pdb=" N7 DG 2 49 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG 2 49 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG 2 49 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG 2 49 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG 2 49 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG 2 49 " 0.004 2.00e-02 2.50e+03 pdb=" N2 DG 2 49 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DG 2 49 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DG 2 49 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA 2 51 " -0.037 2.00e-02 2.50e+03 1.64e-02 7.41e+00 pdb=" N9 DA 2 51 " 0.037 2.00e-02 2.50e+03 pdb=" C8 DA 2 51 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA 2 51 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DA 2 51 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA 2 51 " -0.007 2.00e-02 2.50e+03 pdb=" N6 DA 2 51 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA 2 51 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA 2 51 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA 2 51 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DA 2 51 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG 2 44 " 0.034 2.00e-02 2.50e+03 1.53e-02 7.04e+00 pdb=" N9 DG 2 44 " -0.039 2.00e-02 2.50e+03 pdb=" C8 DG 2 44 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DG 2 44 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG 2 44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG 2 44 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG 2 44 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG 2 44 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG 2 44 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG 2 44 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG 2 44 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG 2 44 " -0.002 2.00e-02 2.50e+03 ... (remaining 5033 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4371 2.80 - 3.33: 28694 3.33 - 3.85: 46154 3.85 - 4.38: 62145 4.38 - 4.90: 98755 Nonbonded interactions: 240119 Sorted by model distance: nonbonded pdb=" O LYS G 520 " pdb=" N ILE G 522 " model vdw 2.277 2.520 nonbonded pdb=" O LEU I 218 " pdb=" NE ARG I 223 " model vdw 2.319 2.520 nonbonded pdb=" NZ LYS C 230 " pdb=" O4 U 1 21 " model vdw 2.330 2.520 nonbonded pdb=" O VAL J 33 " pdb=" N ARG J 35 " model vdw 2.346 2.520 nonbonded pdb=" O TYR F 9 " pdb=" O2' U 1 35 " model vdw 2.348 2.440 ... (remaining 240114 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' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'B' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 230 or resid 243 through \ 349)) selection = chain 'F' } ncs_group { reference = (chain 'I' and (resid 3 through 196 or resid 198 through 235 or resid 239 throug \ h 354 or resid 364 through 381 or resid 383 through 396)) selection = (chain 'J' and (resid 3 through 165 or resid 167 or resid 169 or resid 199 throu \ gh 354 or resid 364 through 381 or resid 383 through 396)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.360 Check model and map are aligned: 0.470 Set scattering table: 0.270 Process input model: 82.100 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.130 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:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.046 30622 Z= 0.878 Angle : 1.744 10.246 41994 Z= 1.241 Chirality : 0.084 0.441 4646 Planarity : 0.004 0.061 5036 Dihedral : 17.354 175.946 11611 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 3.44 % Allowed : 14.21 % Favored : 82.35 % Rotamer: Outliers : 0.66 % Allowed : 6.56 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 0.95 % 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: -4.59 (0.12), residues: 3406 helix: -2.69 (0.13), residues: 977 sheet: -1.95 (0.19), residues: 515 loop : -3.72 (0.12), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP J 379 HIS 0.009 0.002 HIS I 228 PHE 0.022 0.002 PHE E 227 TYR 0.026 0.002 TYR H 74 ARG 0.006 0.001 ARG H 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 453 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.7966 (t0) cc_final: 0.7687 (t0) REVERT: A 286 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7432 (mtp180) REVERT: B 55 GLN cc_start: 0.7753 (pm20) cc_final: 0.7455 (mp10) REVERT: B 99 GLN cc_start: 0.7986 (pm20) cc_final: 0.7713 (pt0) REVERT: B 110 GLN cc_start: 0.7859 (pt0) cc_final: 0.7596 (pp30) REVERT: B 210 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8210 (ttm170) REVERT: B 280 GLU cc_start: 0.8332 (pm20) cc_final: 0.8058 (pm20) REVERT: C 148 LYS cc_start: 0.8656 (mttt) cc_final: 0.8443 (mttp) REVERT: C 210 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7856 (ttp-110) REVERT: C 291 ARG cc_start: 0.7693 (ttp80) cc_final: 0.7198 (mmt90) REVERT: C 314 GLU cc_start: 0.8295 (mp0) cc_final: 0.8083 (mp0) REVERT: C 338 MET cc_start: 0.8823 (mmt) cc_final: 0.8597 (mmp) REVERT: D 63 GLU cc_start: 0.8073 (tt0) cc_final: 0.7558 (mp0) REVERT: D 99 GLN cc_start: 0.8387 (mt0) cc_final: 0.8169 (mt0) REVERT: D 170 ASP cc_start: 0.8129 (t0) cc_final: 0.7870 (t70) REVERT: D 220 MET cc_start: 0.7858 (ttp) cc_final: 0.7653 (ttp) REVERT: D 268 ILE cc_start: 0.8356 (pt) cc_final: 0.8050 (mt) REVERT: D 292 GLU cc_start: 0.7864 (tt0) cc_final: 0.7664 (tt0) REVERT: E 44 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7587 (mt-10) REVERT: E 99 GLN cc_start: 0.8235 (tt0) cc_final: 0.8006 (tt0) REVERT: E 162 ASN cc_start: 0.8258 (p0) cc_final: 0.7981 (p0) REVERT: E 210 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7318 (ttp80) REVERT: E 252 ASP cc_start: 0.7731 (t70) cc_final: 0.7143 (t0) REVERT: F 37 ARG cc_start: 0.7617 (mtm180) cc_final: 0.7258 (mtt90) REVERT: F 323 ASN cc_start: 0.7189 (t0) cc_final: 0.6916 (p0) REVERT: F 334 MET cc_start: 0.8607 (mmm) cc_final: 0.8237 (mmm) REVERT: G 237 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7878 (mtp85) REVERT: G 564 HIS cc_start: 0.7164 (p-80) cc_final: 0.6191 (m170) REVERT: G 582 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7837 (mmtm) REVERT: G 613 ASN cc_start: 0.7395 (t0) cc_final: 0.7114 (t0) REVERT: H 77 GLN cc_start: 0.7717 (tp-100) cc_final: 0.7460 (tp-100) REVERT: H 85 HIS cc_start: 0.6624 (t-90) cc_final: 0.6219 (t-170) REVERT: H 102 ARG cc_start: 0.6833 (ttp-110) cc_final: 0.6588 (ttm170) REVERT: I 55 PHE cc_start: 0.4448 (t80) cc_final: 0.4018 (t80) REVERT: I 61 ARG cc_start: 0.6060 (ttm170) cc_final: 0.5395 (mtt90) REVERT: I 250 TRP cc_start: 0.7736 (t-100) cc_final: 0.7515 (t-100) REVERT: I 264 PHE cc_start: 0.8138 (t80) cc_final: 0.7885 (t80) REVERT: I 291 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7031 (ttt180) REVERT: I 302 ILE cc_start: 0.8922 (mm) cc_final: 0.8689 (mt) REVERT: I 305 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7199 (mp0) REVERT: I 347 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7651 (tm-30) REVERT: I 348 GLN cc_start: 0.8531 (mt0) cc_final: 0.8192 (mt0) REVERT: J 122 LEU cc_start: 0.7364 (mp) cc_final: 0.7117 (mt) REVERT: J 136 ARG cc_start: 0.6239 (mmt-90) cc_final: 0.4823 (ttm170) REVERT: J 138 ASN cc_start: 0.6282 (OUTLIER) cc_final: 0.5940 (t0) REVERT: J 231 MET cc_start: 0.5804 (tpt) cc_final: 0.5558 (tpp) REVERT: J 257 ILE cc_start: 0.6408 (tp) cc_final: 0.6153 (mp) REVERT: J 312 ASN cc_start: 0.5148 (t0) cc_final: 0.4548 (p0) REVERT: J 368 TYR cc_start: 0.2569 (m-80) cc_final: 0.2335 (m-80) outliers start: 20 outliers final: 11 residues processed: 470 average time/residue: 1.4689 time to fit residues: 801.3335 Evaluate side-chains 296 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 284 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 276 PRO Chi-restraints excluded: chain B residue 276 PRO Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 276 PRO Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 276 PRO Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain F residue 276 PRO Chi-restraints excluded: chain J residue 138 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 90 optimal weight: 0.0070 chunk 177 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 272 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 316 optimal weight: 30.0000 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 114 GLN A 174 ASN A 218 ASN A 299 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN B 183 ASN C 174 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 311 GLN D 110 GLN D 135 ASN D 174 ASN D 183 ASN D 290 HIS ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN D 312 GLN E 153 ASN ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 GLN E 335 HIS F 183 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 312 GLN F 349 HIS ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 HIS G 225 GLN G 230 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 423 HIS G 621 ASN H 17 ASN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 158 GLN I 49 HIS I 255 HIS I 341 GLN J 45 GLN J 83 GLN J 146 HIS J 156 HIS J 157 ASN ** J 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 268 HIS J 354 ASN J 384 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30622 Z= 0.228 Angle : 0.790 12.251 41994 Z= 0.415 Chirality : 0.046 0.228 4646 Planarity : 0.005 0.089 5036 Dihedral : 17.730 173.586 5070 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.76 % Allowed : 13.98 % Favored : 85.26 % Rotamer: Outliers : 3.46 % Allowed : 11.93 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.64 % Twisted General : 1.26 % 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: -3.39 (0.13), residues: 3406 helix: -1.13 (0.16), residues: 1010 sheet: -1.10 (0.22), residues: 517 loop : -3.39 (0.13), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 152 HIS 0.006 0.001 HIS G 275 PHE 0.026 0.002 PHE J 372 TYR 0.024 0.001 TYR H 149 ARG 0.010 0.000 ARG G 70 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 317 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.7865 (ttm170) cc_final: 0.7497 (mtp180) REVERT: B 96 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: B 99 GLN cc_start: 0.7962 (pm20) cc_final: 0.7721 (pt0) REVERT: B 110 GLN cc_start: 0.7775 (pt0) cc_final: 0.7560 (pp30) REVERT: B 210 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8223 (ttm170) REVERT: C 44 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8183 (mt-10) REVERT: C 148 LYS cc_start: 0.8721 (mttt) cc_final: 0.8459 (mttp) REVERT: C 210 ARG cc_start: 0.8219 (ttm170) cc_final: 0.7964 (ttp80) REVERT: C 291 ARG cc_start: 0.7579 (ttp80) cc_final: 0.7038 (mmt90) REVERT: C 314 GLU cc_start: 0.8379 (mp0) cc_final: 0.8145 (mp0) REVERT: D 63 GLU cc_start: 0.8156 (tt0) cc_final: 0.7576 (mp0) REVERT: D 193 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8202 (ptm) REVERT: D 292 GLU cc_start: 0.7954 (tt0) cc_final: 0.7601 (tt0) REVERT: D 338 MET cc_start: 0.8765 (mmm) cc_final: 0.8268 (mmm) REVERT: D 347 PHE cc_start: 0.9000 (OUTLIER) cc_final: 0.7735 (p90) REVERT: E 44 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7552 (mt-10) REVERT: E 99 GLN cc_start: 0.8129 (tt0) cc_final: 0.7881 (tt0) REVERT: E 210 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7436 (ttp80) REVERT: E 252 ASP cc_start: 0.7647 (t70) cc_final: 0.7284 (t0) REVERT: F 222 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7463 (mtm180) REVERT: F 323 ASN cc_start: 0.6918 (t0) cc_final: 0.6655 (p0) REVERT: G 8 LYS cc_start: 0.6455 (mptt) cc_final: 0.6053 (tttt) REVERT: G 46 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7487 (mp) REVERT: G 66 LYS cc_start: 0.6643 (OUTLIER) cc_final: 0.6108 (mtmt) REVERT: G 237 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7911 (mtp85) REVERT: G 437 ARG cc_start: 0.7279 (mpt180) cc_final: 0.6932 (tpp-160) REVERT: G 439 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: G 447 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: G 538 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: G 582 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7797 (mmtm) REVERT: G 613 ASN cc_start: 0.7512 (t0) cc_final: 0.7270 (t0) REVERT: G 625 TYR cc_start: 0.7797 (p90) cc_final: 0.7578 (p90) REVERT: H 4 TYR cc_start: 0.6267 (m-80) cc_final: 0.5965 (m-80) REVERT: H 77 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7308 (tp-100) REVERT: I 61 ARG cc_start: 0.6171 (ttm170) cc_final: 0.5129 (mtt90) REVERT: I 144 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.4982 (mm) REVERT: I 157 ASN cc_start: 0.5639 (OUTLIER) cc_final: 0.5370 (m-40) REVERT: I 291 ARG cc_start: 0.7748 (mtp180) cc_final: 0.7035 (ttt180) REVERT: I 305 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7192 (mm-30) REVERT: I 348 GLN cc_start: 0.8477 (mt0) cc_final: 0.8223 (mt0) REVERT: I 352 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8772 (mttt) REVERT: J 34 HIS cc_start: 0.7413 (m170) cc_final: 0.6945 (t70) REVERT: J 136 ARG cc_start: 0.5542 (mmt-90) cc_final: 0.4293 (ttm170) REVERT: J 231 MET cc_start: 0.5633 (tpt) cc_final: 0.5385 (tpp) REVERT: J 264 PHE cc_start: 0.4210 (OUTLIER) cc_final: 0.3371 (t80) REVERT: J 312 ASN cc_start: 0.4931 (t0) cc_final: 0.4468 (p0) REVERT: J 368 TYR cc_start: 0.2406 (m-80) cc_final: 0.2076 (m-80) outliers start: 105 outliers final: 30 residues processed: 389 average time/residue: 1.3869 time to fit residues: 634.5406 Evaluate side-chains 293 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 439 GLU Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 352 LYS Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 279 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 316 optimal weight: 8.9990 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 2.9990 chunk 313 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 253 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN A 183 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 340 ASN F 72 GLN F 186 ASN F 299 HIS G 104 GLN G 225 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 521 HIS G 565 GLN ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 ASN I 341 GLN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 GLN J 83 GLN J 87 ASN ** J 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 30622 Z= 0.392 Angle : 0.830 11.242 41994 Z= 0.436 Chirality : 0.049 0.249 4646 Planarity : 0.006 0.091 5036 Dihedral : 17.778 172.451 5050 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.65 % Allowed : 16.50 % Favored : 82.85 % Rotamer: Outliers : 4.61 % Allowed : 13.77 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.03 % Twisted General : 1.32 % 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: -3.21 (0.13), residues: 3406 helix: -0.89 (0.16), residues: 1013 sheet: -0.88 (0.23), residues: 523 loop : -3.40 (0.13), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 152 HIS 0.007 0.001 HIS A 335 PHE 0.027 0.002 PHE I 241 TYR 0.037 0.002 TYR H 149 ARG 0.007 0.001 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 263 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7233 (p0) REVERT: A 286 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7556 (mtp180) REVERT: B 96 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: B 110 GLN cc_start: 0.7835 (pt0) cc_final: 0.7572 (pp30) REVERT: B 210 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.8205 (ttm170) REVERT: B 346 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7936 (mtp) REVERT: C 44 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 148 LYS cc_start: 0.8669 (mttt) cc_final: 0.8402 (mttp) REVERT: C 180 ASP cc_start: 0.8063 (m-30) cc_final: 0.7475 (m-30) REVERT: C 210 ARG cc_start: 0.8217 (ttm170) cc_final: 0.7928 (ttp80) REVERT: C 291 ARG cc_start: 0.7684 (ttp80) cc_final: 0.7155 (mmt90) REVERT: C 314 GLU cc_start: 0.8382 (mp0) cc_final: 0.8177 (mp0) REVERT: D 63 GLU cc_start: 0.8219 (tt0) cc_final: 0.7618 (mp0) REVERT: D 347 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8679 (p90) REVERT: E 44 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7615 (mt-10) REVERT: E 61 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7888 (p) REVERT: E 99 GLN cc_start: 0.8225 (tt0) cc_final: 0.8005 (tt0) REVERT: E 106 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8431 (p) REVERT: E 210 ARG cc_start: 0.8014 (ttm170) cc_final: 0.7451 (ttp80) REVERT: E 252 ASP cc_start: 0.7713 (t70) cc_final: 0.7370 (t0) REVERT: E 298 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6611 (mtt90) REVERT: F 147 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7459 (ttp80) REVERT: F 222 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7737 (mtm180) REVERT: G 46 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7556 (mp) REVERT: G 437 ARG cc_start: 0.7363 (mpt180) cc_final: 0.7003 (tpp-160) REVERT: G 439 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6500 (tm-30) REVERT: G 440 SER cc_start: 0.7560 (OUTLIER) cc_final: 0.7257 (m) REVERT: G 447 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7335 (mt0) REVERT: G 538 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: G 582 LYS cc_start: 0.8185 (mmtt) cc_final: 0.7907 (mmtm) REVERT: G 613 ASN cc_start: 0.7376 (t0) cc_final: 0.7120 (t0) REVERT: H 4 TYR cc_start: 0.6420 (m-80) cc_final: 0.6163 (m-80) REVERT: H 77 GLN cc_start: 0.7707 (tp-100) cc_final: 0.7412 (tp-100) REVERT: H 166 ASN cc_start: 0.6572 (OUTLIER) cc_final: 0.6266 (m-40) REVERT: I 34 HIS cc_start: 0.3863 (t70) cc_final: 0.3463 (m-70) REVERT: I 55 PHE cc_start: 0.4434 (t80) cc_final: 0.3950 (t80) REVERT: I 61 ARG cc_start: 0.5626 (ttm170) cc_final: 0.5147 (mtt90) REVERT: I 291 ARG cc_start: 0.7756 (mtp180) cc_final: 0.7133 (ttt180) REVERT: I 334 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7225 (tpp) REVERT: I 348 GLN cc_start: 0.8465 (mt0) cc_final: 0.8184 (mt0) REVERT: I 352 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8672 (mttt) REVERT: J 136 ARG cc_start: 0.5974 (mmt-90) cc_final: 0.4426 (ttm170) REVERT: J 231 MET cc_start: 0.5857 (tpt) cc_final: 0.5620 (tpp) REVERT: J 264 PHE cc_start: 0.4198 (OUTLIER) cc_final: 0.3471 (t80) REVERT: J 312 ASN cc_start: 0.5146 (t0) cc_final: 0.4665 (p0) outliers start: 140 outliers final: 66 residues processed: 364 average time/residue: 1.3298 time to fit residues: 573.0743 Evaluate side-chains 325 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 241 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 276 PRO Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 291 ARG Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 319 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 439 GLU Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain I residue 352 LYS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 279 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 212 optimal weight: 9.9990 chunk 317 optimal weight: 0.0870 chunk 336 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 301 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 225 GLN ** D 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS E 174 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS H 158 GLN ** I 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN J 45 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30622 Z= 0.232 Angle : 0.739 12.802 41994 Z= 0.385 Chirality : 0.045 0.239 4646 Planarity : 0.006 0.115 5036 Dihedral : 17.568 173.483 5050 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.62 % Allowed : 14.80 % Favored : 84.59 % Rotamer: Outliers : 4.42 % Allowed : 15.68 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 2.42 % Twisted General : 1.13 % 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: -2.83 (0.14), residues: 3406 helix: -0.46 (0.17), residues: 998 sheet: -0.58 (0.23), residues: 510 loop : -3.23 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 152 HIS 0.005 0.001 HIS F 315 PHE 0.024 0.002 PHE I 241 TYR 0.039 0.002 TYR H 149 ARG 0.006 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 287 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASN cc_start: 0.8095 (t0) cc_final: 0.7763 (t0) REVERT: A 286 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7545 (mtp180) REVERT: B 96 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: B 170 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7605 (p0) REVERT: B 210 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8177 (ttm170) REVERT: B 346 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7626 (mtp) REVERT: C 44 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8178 (mt-10) REVERT: C 148 LYS cc_start: 0.8715 (mttt) cc_final: 0.8421 (mttp) REVERT: C 180 ASP cc_start: 0.8031 (m-30) cc_final: 0.7651 (m-30) REVERT: C 210 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7832 (ttp80) REVERT: C 291 ARG cc_start: 0.7509 (ttp80) cc_final: 0.6984 (mmt90) REVERT: D 63 GLU cc_start: 0.8197 (tt0) cc_final: 0.7572 (mp0) REVERT: D 193 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8201 (ptm) REVERT: D 347 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8639 (p90) REVERT: E 43 MET cc_start: 0.8934 (mmt) cc_final: 0.8691 (mmm) REVERT: E 44 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7623 (mt-10) REVERT: E 99 GLN cc_start: 0.8062 (tt0) cc_final: 0.7797 (tt0) REVERT: E 210 ARG cc_start: 0.7986 (ttm170) cc_final: 0.7457 (ttp80) REVERT: E 252 ASP cc_start: 0.7607 (t70) cc_final: 0.7270 (t0) REVERT: E 298 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.6669 (mtt90) REVERT: F 6 ASN cc_start: 0.8117 (t0) cc_final: 0.7841 (m-40) REVERT: F 11 ARG cc_start: 0.8750 (ptt180) cc_final: 0.8413 (ptt180) REVERT: F 200 SER cc_start: 0.8708 (m) cc_final: 0.8482 (p) REVERT: F 222 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7612 (mtm180) REVERT: G 66 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6151 (ttpt) REVERT: G 234 ASP cc_start: 0.7126 (t70) cc_final: 0.6726 (t70) REVERT: G 437 ARG cc_start: 0.7337 (mpt180) cc_final: 0.6921 (tpp-160) REVERT: G 447 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: G 538 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: G 582 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7836 (mmtm) REVERT: H 4 TYR cc_start: 0.6367 (m-80) cc_final: 0.6033 (m-80) REVERT: H 77 GLN cc_start: 0.7640 (tp-100) cc_final: 0.7381 (tp-100) REVERT: H 142 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5297 (pp20) REVERT: I 34 HIS cc_start: 0.4014 (t70) cc_final: 0.3679 (m-70) REVERT: I 61 ARG cc_start: 0.5669 (ttm170) cc_final: 0.5154 (mtt90) REVERT: I 68 LYS cc_start: 0.6013 (ttpp) cc_final: 0.5795 (tttp) REVERT: I 157 ASN cc_start: 0.5467 (OUTLIER) cc_final: 0.5255 (m-40) REVERT: I 222 TYR cc_start: 0.7674 (m-80) cc_final: 0.7385 (m-80) REVERT: I 291 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7062 (ttt180) REVERT: I 348 GLN cc_start: 0.8393 (mt0) cc_final: 0.8154 (mt0) REVERT: J 136 ARG cc_start: 0.5776 (mmt-90) cc_final: 0.4362 (ttm170) REVERT: J 143 TYR cc_start: 0.5362 (t80) cc_final: 0.4863 (t80) REVERT: J 231 MET cc_start: 0.5851 (tpt) cc_final: 0.5651 (tpt) REVERT: J 261 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6465 (mp0) REVERT: J 264 PHE cc_start: 0.4117 (OUTLIER) cc_final: 0.3348 (t80) REVERT: J 278 LEU cc_start: 0.5422 (tp) cc_final: 0.4194 (pp) REVERT: J 312 ASN cc_start: 0.4997 (t0) cc_final: 0.4643 (p0) REVERT: J 326 MET cc_start: 0.1312 (mmt) cc_final: 0.0518 (mmt) outliers start: 134 outliers final: 63 residues processed: 384 average time/residue: 1.2433 time to fit residues: 570.4284 Evaluate side-chains 325 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 249 time to evaluate : 3.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 324 LYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 157 ASN Chi-restraints excluded: chain I residue 231 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 279 LYS Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 287 optimal weight: 20.0000 chunk 232 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 315 HIS ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 299 HIS E 99 GLN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN G 233 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 551 ASN ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 34 HIS I 312 ASN I 341 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.089 30622 Z= 0.586 Angle : 0.924 14.284 41994 Z= 0.483 Chirality : 0.055 0.272 4646 Planarity : 0.008 0.109 5036 Dihedral : 17.847 169.125 5049 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.73 % Allowed : 16.97 % Favored : 82.30 % Rotamer: Outliers : 5.73 % Allowed : 16.54 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 2.42 % Twisted General : 1.19 % 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: -3.13 (0.13), residues: 3406 helix: -0.83 (0.16), residues: 1001 sheet: -0.89 (0.22), residues: 550 loop : -3.34 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 152 HIS 0.008 0.002 HIS A 335 PHE 0.031 0.003 PHE A 89 TYR 0.043 0.003 TYR H 149 ARG 0.009 0.001 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 238 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7270 (p0) REVERT: A 104 ASN cc_start: 0.8214 (t0) cc_final: 0.7847 (t0) REVERT: A 286 ARG cc_start: 0.8044 (ttm170) cc_final: 0.7633 (mtp180) REVERT: B 96 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: B 210 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8384 (ttm170) REVERT: B 280 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: B 346 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8166 (mtp) REVERT: C 44 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8425 (mt-10) REVERT: C 193 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8259 (ptp) REVERT: C 210 ARG cc_start: 0.8182 (ttm170) cc_final: 0.7899 (ttp80) REVERT: C 222 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.7081 (mtm-85) REVERT: C 291 ARG cc_start: 0.7743 (ttp80) cc_final: 0.7284 (mmt90) REVERT: D 55 GLN cc_start: 0.7016 (tm-30) cc_final: 0.6740 (tm-30) REVERT: D 63 GLU cc_start: 0.8261 (tt0) cc_final: 0.7570 (mp0) REVERT: D 347 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8866 (p90) REVERT: D 348 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: E 44 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 99 GLN cc_start: 0.8331 (tt0) cc_final: 0.8058 (tt0) REVERT: E 210 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7496 (ttp80) REVERT: E 252 ASP cc_start: 0.7783 (t70) cc_final: 0.7430 (t0) REVERT: E 298 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.6875 (mtt90) REVERT: F 11 ARG cc_start: 0.8811 (ptt180) cc_final: 0.8549 (ptt180) REVERT: F 40 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6450 (tt) REVERT: F 147 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7488 (mtp85) REVERT: F 222 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.7822 (mtm180) REVERT: F 338 MET cc_start: 0.8391 (mmp) cc_final: 0.8088 (mmp) REVERT: F 348 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7257 (pp30) REVERT: G 66 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6182 (mtmt) REVERT: G 165 ASN cc_start: 0.7144 (p0) cc_final: 0.6477 (t0) REVERT: G 234 ASP cc_start: 0.7234 (t70) cc_final: 0.6808 (t70) REVERT: G 437 ARG cc_start: 0.7381 (mpt180) cc_final: 0.6941 (tpp-160) REVERT: G 447 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: G 538 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: G 564 HIS cc_start: 0.7263 (p-80) cc_final: 0.5893 (m170) REVERT: G 582 LYS cc_start: 0.8271 (mmtt) cc_final: 0.8017 (mmtm) REVERT: H 2 LYS cc_start: 0.5686 (OUTLIER) cc_final: 0.5057 (pmtt) REVERT: H 4 TYR cc_start: 0.6336 (m-80) cc_final: 0.6057 (m-80) REVERT: H 77 GLN cc_start: 0.7637 (tp-100) cc_final: 0.7245 (tp-100) REVERT: H 142 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5853 (pp20) REVERT: I 34 HIS cc_start: 0.4069 (OUTLIER) cc_final: 0.3757 (m-70) REVERT: I 61 ARG cc_start: 0.5556 (ttm170) cc_final: 0.5144 (mtt90) REVERT: I 144 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.4660 (mm) REVERT: I 147 PHE cc_start: 0.4687 (OUTLIER) cc_final: 0.3275 (OUTLIER) REVERT: I 334 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7286 (tpp) REVERT: J 116 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: J 136 ARG cc_start: 0.6105 (mmt-90) cc_final: 0.4526 (ttm170) REVERT: J 211 GLU cc_start: 0.4791 (OUTLIER) cc_final: 0.4467 (tt0) REVERT: J 231 MET cc_start: 0.5913 (tpt) cc_final: 0.5685 (tpt) REVERT: J 252 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7054 (tmm-80) REVERT: J 297 LEU cc_start: 0.5390 (OUTLIER) cc_final: 0.5024 (mm) REVERT: J 312 ASN cc_start: 0.5114 (t0) cc_final: 0.4595 (p0) outliers start: 174 outliers final: 86 residues processed: 377 average time/residue: 1.2767 time to fit residues: 574.3865 Evaluate side-chains 342 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 231 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 276 PRO Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 104 ASN Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 202 ASP Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain D residue 348 GLN Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 276 PRO Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 348 GLN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 433 THR Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 88 ASN Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 144 LEU Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 231 MET Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 374 ASP Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 84 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 211 GLU Chi-restraints excluded: chain J residue 252 ARG Chi-restraints excluded: chain J residue 279 LYS Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 308 CYS Chi-restraints excluded: chain J residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 336 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 chunk 155 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 183 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN E 99 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 551 ASN ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS I 148 GLN I 341 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30622 Z= 0.213 Angle : 0.743 15.050 41994 Z= 0.386 Chirality : 0.044 0.251 4646 Planarity : 0.006 0.103 5036 Dihedral : 17.452 170.672 5049 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.36 % Favored : 85.00 % Rotamer: Outliers : 4.18 % Allowed : 18.78 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 2.42 % Twisted General : 0.98 % 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: -2.68 (0.14), residues: 3406 helix: -0.36 (0.17), residues: 1001 sheet: -0.36 (0.24), residues: 493 loop : -3.14 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 152 HIS 0.017 0.001 HIS I 34 PHE 0.028 0.001 PHE I 43 TYR 0.042 0.001 TYR H 149 ARG 0.006 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 257 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7568 (mtp180) REVERT: B 39 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8799 (pp) REVERT: B 96 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: B 170 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7691 (p0) REVERT: B 210 ARG cc_start: 0.8537 (ttm-80) cc_final: 0.8154 (ttm170) REVERT: B 280 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7967 (pm20) REVERT: B 346 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7644 (mtp) REVERT: C 44 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8200 (mt-10) REVERT: C 148 LYS cc_start: 0.8731 (mttt) cc_final: 0.8457 (mttp) REVERT: C 180 ASP cc_start: 0.8012 (m-30) cc_final: 0.7646 (m-30) REVERT: C 210 ARG cc_start: 0.8068 (ttm170) cc_final: 0.7836 (ttp80) REVERT: C 291 ARG cc_start: 0.7547 (ttp80) cc_final: 0.7105 (mmt90) REVERT: D 55 GLN cc_start: 0.6635 (tm-30) cc_final: 0.6398 (tm-30) REVERT: D 63 GLU cc_start: 0.8224 (tt0) cc_final: 0.7606 (mp0) REVERT: E 44 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7634 (mt-10) REVERT: E 99 GLN cc_start: 0.8094 (tt0) cc_final: 0.7841 (tt0) REVERT: E 210 ARG cc_start: 0.7987 (ttm170) cc_final: 0.7475 (ttp80) REVERT: E 252 ASP cc_start: 0.7621 (t70) cc_final: 0.7257 (t0) REVERT: E 298 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6743 (mtt90) REVERT: F 6 ASN cc_start: 0.8123 (t0) cc_final: 0.7910 (m-40) REVERT: F 11 ARG cc_start: 0.8759 (ptt180) cc_final: 0.8511 (ptt180) REVERT: F 153 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8132 (m110) REVERT: F 222 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7529 (mtm180) REVERT: G 66 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.6003 (ttpt) REVERT: G 165 ASN cc_start: 0.7241 (p0) cc_final: 0.6538 (t0) REVERT: G 437 ARG cc_start: 0.7296 (mpt180) cc_final: 0.6870 (tpp-160) REVERT: G 447 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7246 (mt0) REVERT: G 538 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7085 (mp0) REVERT: G 564 HIS cc_start: 0.7366 (p-80) cc_final: 0.6093 (m170) REVERT: G 582 LYS cc_start: 0.8214 (mmtt) cc_final: 0.7887 (mmtm) REVERT: G 625 TYR cc_start: 0.8109 (p90) cc_final: 0.7616 (p90) REVERT: H 4 TYR cc_start: 0.6269 (m-80) cc_final: 0.5873 (m-80) REVERT: H 77 GLN cc_start: 0.7558 (tp-100) cc_final: 0.7311 (tp-100) REVERT: H 142 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5574 (pp20) REVERT: I 61 ARG cc_start: 0.5819 (ttm170) cc_final: 0.5285 (mtt90) REVERT: I 68 LYS cc_start: 0.5965 (ttpp) cc_final: 0.4902 (ttpt) REVERT: I 84 LEU cc_start: 0.4144 (OUTLIER) cc_final: 0.3889 (tp) REVERT: I 147 PHE cc_start: 0.4706 (OUTLIER) cc_final: 0.3261 (OUTLIER) REVERT: I 252 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7988 (mmm160) REVERT: I 341 GLN cc_start: 0.7921 (pt0) cc_final: 0.7092 (mm110) REVERT: J 116 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: J 136 ARG cc_start: 0.6004 (mmt-90) cc_final: 0.4570 (ttm170) REVERT: J 278 LEU cc_start: 0.5654 (tp) cc_final: 0.4085 (pp) REVERT: J 297 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.5169 (mm) REVERT: J 312 ASN cc_start: 0.4941 (t0) cc_final: 0.4670 (p0) REVERT: J 326 MET cc_start: 0.0873 (mmt) cc_final: 0.0275 (mmt) outliers start: 127 outliers final: 61 residues processed: 355 average time/residue: 1.2777 time to fit residues: 545.2415 Evaluate side-chains 315 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 239 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 153 ASN Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 252 VAL Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 447 GLN Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 35 TYR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 142 GLU Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 231 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 118 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 245 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 188 optimal weight: 3.9990 chunk 335 optimal weight: 7.9990 chunk 209 optimal weight: 0.0980 chunk 204 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN E 104 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30622 Z= 0.268 Angle : 0.769 16.654 41994 Z= 0.398 Chirality : 0.046 0.254 4646 Planarity : 0.006 0.101 5036 Dihedral : 17.392 172.801 5049 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.59 % Allowed : 15.15 % Favored : 84.26 % Rotamer: Outliers : 4.38 % Allowed : 19.11 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 2.42 % Twisted General : 1.01 % 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: -2.60 (0.14), residues: 3406 helix: -0.24 (0.17), residues: 996 sheet: -0.36 (0.23), residues: 508 loop : -3.12 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 152 HIS 0.014 0.001 HIS H 143 PHE 0.025 0.002 PHE I 43 TYR 0.037 0.002 TYR H 149 ARG 0.005 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 248 time to evaluate : 3.544 Fit side-chains REVERT: A 156 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8211 (pt) REVERT: A 286 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7598 (mtp180) REVERT: B 39 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8835 (pp) REVERT: B 96 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: B 170 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7530 (p0) REVERT: B 210 ARG cc_start: 0.8546 (ttm-80) cc_final: 0.8160 (ttm170) REVERT: B 280 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7914 (pm20) REVERT: B 346 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7748 (mtp) REVERT: C 44 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8279 (mt-10) REVERT: C 148 LYS cc_start: 0.8731 (mttt) cc_final: 0.8443 (mttp) REVERT: C 180 ASP cc_start: 0.8083 (m-30) cc_final: 0.7731 (m-30) REVERT: C 210 ARG cc_start: 0.8076 (ttm170) cc_final: 0.7840 (ttp80) REVERT: C 222 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7241 (mtm-85) REVERT: C 291 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7167 (mmt90) REVERT: D 63 GLU cc_start: 0.8221 (tt0) cc_final: 0.7546 (mp0) REVERT: E 44 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7613 (mt-10) REVERT: E 99 GLN cc_start: 0.8096 (tt0) cc_final: 0.7854 (tt0) REVERT: E 210 ARG cc_start: 0.8013 (ttm170) cc_final: 0.7470 (ttp80) REVERT: E 252 ASP cc_start: 0.7753 (t70) cc_final: 0.7381 (t0) REVERT: E 298 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.6794 (mtt90) REVERT: F 11 ARG cc_start: 0.8761 (ptt180) cc_final: 0.8494 (ptt180) REVERT: F 43 MET cc_start: 0.4400 (mpp) cc_final: 0.1073 (tpt) REVERT: F 172 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7310 (ttm170) REVERT: F 222 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7561 (mtm180) REVERT: G 66 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.6024 (ttpt) REVERT: G 165 ASN cc_start: 0.7241 (p0) cc_final: 0.6815 (p0) REVERT: G 437 ARG cc_start: 0.7327 (mpt180) cc_final: 0.6895 (tpp-160) REVERT: G 538 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: G 564 HIS cc_start: 0.7428 (p-80) cc_final: 0.6102 (m170) REVERT: G 582 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7882 (mmtm) REVERT: H 2 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5100 (pmtt) REVERT: H 4 TYR cc_start: 0.6340 (m-80) cc_final: 0.5969 (m-80) REVERT: H 77 GLN cc_start: 0.7552 (tp-100) cc_final: 0.7302 (tp-100) REVERT: H 143 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.7448 (m90) REVERT: I 61 ARG cc_start: 0.5828 (ttm170) cc_final: 0.5290 (mtt90) REVERT: I 68 LYS cc_start: 0.5966 (ttpp) cc_final: 0.4822 (ttmt) REVERT: I 147 PHE cc_start: 0.4718 (OUTLIER) cc_final: 0.3315 (OUTLIER) REVERT: I 252 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7944 (mmm160) REVERT: I 341 GLN cc_start: 0.7920 (pt0) cc_final: 0.7112 (mm110) REVERT: J 116 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: J 136 ARG cc_start: 0.5983 (mmt-90) cc_final: 0.4445 (ttm-80) REVERT: J 264 PHE cc_start: 0.4170 (OUTLIER) cc_final: 0.3655 (t80) REVERT: J 278 LEU cc_start: 0.5445 (tp) cc_final: 0.3960 (pp) REVERT: J 297 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5229 (mm) REVERT: J 312 ASN cc_start: 0.5000 (t0) cc_final: 0.4628 (p0) REVERT: J 326 MET cc_start: 0.1237 (mmt) cc_final: 0.0638 (mmt) outliers start: 133 outliers final: 73 residues processed: 357 average time/residue: 1.2459 time to fit residues: 532.3667 Evaluate side-chains 323 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 233 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 538 GLU Chi-restraints excluded: chain G residue 561 THR Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 231 MET Chi-restraints excluded: chain I residue 317 ASP Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 118 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 264 PHE Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.7980 chunk 133 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 165 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 263 optimal weight: 0.0030 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 143 HIS ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30622 Z= 0.228 Angle : 0.753 17.611 41994 Z= 0.388 Chirality : 0.045 0.247 4646 Planarity : 0.006 0.102 5036 Dihedral : 17.299 173.997 5049 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.59 % Allowed : 14.80 % Favored : 84.62 % Rotamer: Outliers : 4.09 % Allowed : 19.84 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 2.42 % Twisted General : 0.98 % 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: -2.49 (0.14), residues: 3406 helix: -0.09 (0.17), residues: 983 sheet: -0.25 (0.23), residues: 502 loop : -3.08 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 152 HIS 0.014 0.001 HIS H 143 PHE 0.028 0.001 PHE I 43 TYR 0.031 0.002 TYR H 149 ARG 0.005 0.000 ARG B 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 244 time to evaluate : 3.480 Fit side-chains REVERT: A 286 ARG cc_start: 0.7978 (ttm170) cc_final: 0.7589 (mtp180) REVERT: B 39 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8805 (pp) REVERT: B 96 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: B 170 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7602 (p0) REVERT: B 210 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8147 (ttm170) REVERT: B 280 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: B 346 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7615 (mtp) REVERT: C 44 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 148 LYS cc_start: 0.8717 (mttt) cc_final: 0.8436 (mttp) REVERT: C 180 ASP cc_start: 0.8059 (m-30) cc_final: 0.7709 (m-30) REVERT: C 210 ARG cc_start: 0.8053 (ttm170) cc_final: 0.7840 (ttp80) REVERT: C 222 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.7348 (mtm-85) REVERT: C 291 ARG cc_start: 0.7518 (ttp80) cc_final: 0.7132 (mmt90) REVERT: D 63 GLU cc_start: 0.8210 (tt0) cc_final: 0.7551 (mp0) REVERT: E 99 GLN cc_start: 0.8032 (tt0) cc_final: 0.7766 (pt0) REVERT: E 210 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7467 (ttp80) REVERT: E 252 ASP cc_start: 0.7675 (t70) cc_final: 0.7311 (t0) REVERT: E 298 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.6776 (mtt90) REVERT: F 6 ASN cc_start: 0.8147 (t0) cc_final: 0.7900 (m-40) REVERT: F 11 ARG cc_start: 0.8745 (ptt180) cc_final: 0.8503 (ptt180) REVERT: F 172 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7268 (ttm170) REVERT: F 200 SER cc_start: 0.8664 (m) cc_final: 0.8457 (p) REVERT: F 222 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7594 (mtm180) REVERT: G 66 LYS cc_start: 0.6443 (OUTLIER) cc_final: 0.5931 (ttpt) REVERT: G 165 ASN cc_start: 0.7270 (p0) cc_final: 0.6846 (p0) REVERT: G 437 ARG cc_start: 0.7315 (mpt180) cc_final: 0.6905 (tpp-160) REVERT: G 564 HIS cc_start: 0.7230 (p-80) cc_final: 0.6164 (m170) REVERT: G 577 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7510 (mt-10) REVERT: G 582 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7946 (mptt) REVERT: H 2 LYS cc_start: 0.5739 (OUTLIER) cc_final: 0.5111 (pmtt) REVERT: H 4 TYR cc_start: 0.6315 (m-80) cc_final: 0.5956 (m-80) REVERT: H 143 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.7575 (m90) REVERT: I 61 ARG cc_start: 0.5836 (ttm170) cc_final: 0.5309 (mtt90) REVERT: I 68 LYS cc_start: 0.6062 (ttpp) cc_final: 0.4864 (ttmt) REVERT: I 112 VAL cc_start: 0.0890 (OUTLIER) cc_final: 0.0658 (t) REVERT: I 147 PHE cc_start: 0.4702 (OUTLIER) cc_final: 0.3386 (t80) REVERT: I 334 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7517 (ttm) REVERT: I 341 GLN cc_start: 0.7891 (pt0) cc_final: 0.7079 (mm110) REVERT: J 27 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6791 (ptpp) REVERT: J 116 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: J 136 ARG cc_start: 0.5839 (mmt-90) cc_final: 0.4311 (ttm170) REVERT: J 278 LEU cc_start: 0.5458 (tp) cc_final: 0.4002 (pp) REVERT: J 297 LEU cc_start: 0.5529 (OUTLIER) cc_final: 0.5259 (mm) REVERT: J 312 ASN cc_start: 0.4987 (t0) cc_final: 0.4624 (p0) REVERT: J 386 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5939 (m-30) outliers start: 124 outliers final: 67 residues processed: 346 average time/residue: 1.2530 time to fit residues: 518.3913 Evaluate side-chains 320 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 234 time to evaluate : 3.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 297 TYR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 185 LYS Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 346 MET Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 172 ARG Chi-restraints excluded: chain F residue 222 ARG Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 264 THR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 143 HIS Chi-restraints excluded: chain H residue 150 HIS Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 27 LYS Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 308 CYS Chi-restraints excluded: chain J residue 386 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.8980 chunk 321 optimal weight: 7.9990 chunk 293 optimal weight: 0.0770 chunk 312 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 245 optimal weight: 0.2980 chunk 95 optimal weight: 0.7980 chunk 282 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 311 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN A 186 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** I 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 49 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30622 Z= 0.175 Angle : 0.724 18.852 41994 Z= 0.372 Chirality : 0.043 0.231 4646 Planarity : 0.005 0.100 5036 Dihedral : 17.106 177.090 5049 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.44 % Allowed : 14.27 % Favored : 85.29 % Rotamer: Outliers : 3.20 % Allowed : 20.92 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 3.64 % Twisted General : 0.95 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3406 helix: 0.13 (0.17), residues: 983 sheet: -0.17 (0.24), residues: 478 loop : -2.99 (0.13), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 152 HIS 0.024 0.001 HIS H 143 PHE 0.029 0.001 PHE I 43 TYR 0.033 0.001 TYR H 74 ARG 0.011 0.000 ARG I 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 280 time to evaluate : 3.611 Fit side-chains REVERT: A 286 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7597 (mtp180) REVERT: B 39 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8700 (pp) REVERT: B 170 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7728 (p0) REVERT: B 210 ARG cc_start: 0.8499 (ttm-80) cc_final: 0.8123 (ttm170) REVERT: B 280 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: B 346 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7669 (mtp) REVERT: C 44 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8191 (mt-10) REVERT: C 148 LYS cc_start: 0.8687 (mttt) cc_final: 0.8404 (mttp) REVERT: C 180 ASP cc_start: 0.8125 (m-30) cc_final: 0.7762 (m-30) REVERT: C 210 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7842 (ttp80) REVERT: C 222 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7423 (mtm-85) REVERT: C 291 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7158 (mmt90) REVERT: D 61 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7957 (p) REVERT: D 63 GLU cc_start: 0.8169 (tt0) cc_final: 0.7539 (mp0) REVERT: D 193 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8143 (ptm) REVERT: D 338 MET cc_start: 0.8815 (mmm) cc_final: 0.8349 (mmm) REVERT: E 99 GLN cc_start: 0.7832 (tt0) cc_final: 0.7592 (pm20) REVERT: E 210 ARG cc_start: 0.7973 (ttm170) cc_final: 0.7469 (ttp80) REVERT: E 252 ASP cc_start: 0.7689 (t70) cc_final: 0.7332 (t0) REVERT: F 11 ARG cc_start: 0.8698 (ptt180) cc_final: 0.8442 (ptt180) REVERT: F 43 MET cc_start: 0.4773 (mpp) cc_final: 0.1661 (tpt) REVERT: G 66 LYS cc_start: 0.6250 (OUTLIER) cc_final: 0.5853 (ttpt) REVERT: G 161 HIS cc_start: 0.3825 (t70) cc_final: 0.3614 (t-90) REVERT: G 165 ASN cc_start: 0.7210 (p0) cc_final: 0.6824 (p0) REVERT: G 437 ARG cc_start: 0.7274 (mpt180) cc_final: 0.6872 (tpp-160) REVERT: G 564 HIS cc_start: 0.7198 (p-80) cc_final: 0.6172 (m170) REVERT: G 577 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7498 (mt-10) REVERT: G 582 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7978 (mptt) REVERT: H 2 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.4970 (pmtt) REVERT: H 4 TYR cc_start: 0.6211 (m-80) cc_final: 0.5862 (m-80) REVERT: H 69 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6281 (pp) REVERT: I 61 ARG cc_start: 0.5805 (ttm170) cc_final: 0.5251 (mtt90) REVERT: I 68 LYS cc_start: 0.6038 (ttpp) cc_final: 0.4917 (ttpt) REVERT: I 147 PHE cc_start: 0.4573 (OUTLIER) cc_final: 0.3399 (t80) REVERT: I 334 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7482 (ttm) REVERT: I 341 GLN cc_start: 0.7878 (pt0) cc_final: 0.7096 (mm110) REVERT: J 7 GLN cc_start: 0.4596 (OUTLIER) cc_final: 0.4357 (pt0) REVERT: J 136 ARG cc_start: 0.5689 (mmt-90) cc_final: 0.4234 (ttm170) REVERT: J 278 LEU cc_start: 0.5139 (tp) cc_final: 0.3831 (pp) REVERT: J 372 PHE cc_start: 0.6891 (t80) cc_final: 0.6354 (t80) outliers start: 97 outliers final: 47 residues processed: 352 average time/residue: 1.2948 time to fit residues: 541.7981 Evaluate side-chains 307 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 247 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 222 ARG Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 193 MET Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain D residue 347 PHE Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 34 HIS Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 118 PHE Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 9.9990 chunk 330 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 346 optimal weight: 10.0000 chunk 319 optimal weight: 9.9990 chunk 276 optimal weight: 0.0270 chunk 28 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 205 ASN ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30622 Z= 0.306 Angle : 0.793 19.002 41994 Z= 0.408 Chirality : 0.046 0.242 4646 Planarity : 0.006 0.102 5036 Dihedral : 17.223 173.686 5046 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.53 % Allowed : 15.36 % Favored : 84.12 % Rotamer: Outliers : 2.80 % Allowed : 21.61 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 2.42 % Twisted General : 0.86 % 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: -2.39 (0.14), residues: 3406 helix: 0.00 (0.17), residues: 993 sheet: -0.22 (0.23), residues: 504 loop : -3.03 (0.13), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 152 HIS 0.008 0.001 HIS G 161 PHE 0.025 0.002 PHE I 43 TYR 0.032 0.002 TYR H 74 ARG 0.012 0.000 ARG I 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6812 Ramachandran restraints generated. 3406 Oldfield, 0 Emsley, 3406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 229 time to evaluate : 3.517 Fit side-chains revert: symmetry clash REVERT: A 286 ARG cc_start: 0.8057 (ttm170) cc_final: 0.7649 (mtm-85) REVERT: B 39 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8817 (pp) REVERT: B 170 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7537 (p0) REVERT: B 210 ARG cc_start: 0.8553 (ttm-80) cc_final: 0.8169 (ttm170) REVERT: B 280 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7963 (pt0) REVERT: B 346 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7708 (mtp) REVERT: C 44 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 148 LYS cc_start: 0.8727 (mttt) cc_final: 0.8437 (mttp) REVERT: C 180 ASP cc_start: 0.8137 (m-30) cc_final: 0.7798 (m-30) REVERT: C 210 ARG cc_start: 0.8054 (ttm170) cc_final: 0.7803 (ttp80) REVERT: C 291 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7256 (mmt90) REVERT: D 63 GLU cc_start: 0.8213 (tt0) cc_final: 0.7574 (mp0) REVERT: E 210 ARG cc_start: 0.8040 (ttm170) cc_final: 0.7484 (ttp80) REVERT: E 252 ASP cc_start: 0.7775 (t70) cc_final: 0.7417 (t0) REVERT: E 298 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.6754 (mtt90) REVERT: F 43 MET cc_start: 0.4785 (mpp) cc_final: 0.1642 (tpt) REVERT: F 338 MET cc_start: 0.8358 (mmp) cc_final: 0.8069 (mmp) REVERT: G 66 LYS cc_start: 0.6310 (OUTLIER) cc_final: 0.5853 (ttpt) REVERT: G 165 ASN cc_start: 0.7340 (p0) cc_final: 0.6925 (p0) REVERT: G 437 ARG cc_start: 0.7321 (mpt180) cc_final: 0.6922 (tpp-160) REVERT: G 564 HIS cc_start: 0.7103 (p-80) cc_final: 0.5992 (m170) REVERT: G 577 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7541 (mt-10) REVERT: G 582 LYS cc_start: 0.8264 (mmtt) cc_final: 0.8029 (mptt) REVERT: H 2 LYS cc_start: 0.5570 (OUTLIER) cc_final: 0.4978 (pmtt) REVERT: H 4 TYR cc_start: 0.6198 (m-80) cc_final: 0.5867 (m-80) REVERT: I 61 ARG cc_start: 0.5925 (ttm170) cc_final: 0.5385 (mtt90) REVERT: I 68 LYS cc_start: 0.6111 (ttpp) cc_final: 0.4955 (ttmt) REVERT: I 147 PHE cc_start: 0.4436 (OUTLIER) cc_final: 0.3487 (t80) REVERT: I 334 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7386 (ttm) REVERT: I 341 GLN cc_start: 0.7868 (pt0) cc_final: 0.7076 (mm110) REVERT: J 7 GLN cc_start: 0.4859 (OUTLIER) cc_final: 0.4575 (pt0) REVERT: J 136 ARG cc_start: 0.5719 (mmt-90) cc_final: 0.4147 (ttm170) REVERT: J 231 MET cc_start: 0.5708 (tpt) cc_final: 0.5099 (mmm) REVERT: J 252 ARG cc_start: 0.7530 (tpp-160) cc_final: 0.7120 (ppt170) REVERT: J 278 LEU cc_start: 0.5129 (tp) cc_final: 0.3754 (pp) REVERT: J 372 PHE cc_start: 0.6699 (t80) cc_final: 0.6252 (t80) outliers start: 85 outliers final: 55 residues processed: 301 average time/residue: 1.3708 time to fit residues: 491.4792 Evaluate side-chains 282 residues out of total 3042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 217 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 346 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 323 ASN Chi-restraints excluded: chain D residue 17 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 323 ASN Chi-restraints excluded: chain D residue 325 THR Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 26 ASP Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 271 SER Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 450 VAL Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 585 SER Chi-restraints excluded: chain G residue 610 THR Chi-restraints excluded: chain H residue 2 LYS Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 128 ILE Chi-restraints excluded: chain I residue 147 PHE Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain J residue 7 GLN Chi-restraints excluded: chain J residue 58 ASP Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 92 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain J residue 308 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 9.9990 chunk 294 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 276 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN A 241 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.146282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.109549 restraints weight = 47033.549| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.02 r_work: 0.3163 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30622 Z= 0.348 Angle : 0.818 18.743 41994 Z= 0.423 Chirality : 0.048 0.246 4646 Planarity : 0.006 0.102 5036 Dihedral : 17.322 172.662 5046 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.50 % Allowed : 15.83 % Favored : 83.68 % Rotamer: Outliers : 2.97 % Allowed : 21.68 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.70 % Twisted Proline : 2.42 % Twisted General : 0.89 % 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: -2.47 (0.14), residues: 3406 helix: -0.18 (0.17), residues: 997 sheet: -0.24 (0.23), residues: 511 loop : -3.04 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 152 HIS 0.004 0.001 HIS G 276 PHE 0.027 0.002 PHE A 89 TYR 0.036 0.002 TYR H 74 ARG 0.017 0.001 ARG G 70 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9929.09 seconds wall clock time: 176 minutes 58.23 seconds (10618.23 seconds total)