Starting phenix.real_space_refine on Sat Dec 16 23:12:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/12_2023/6qg0_4543_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/12_2023/6qg0_4543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/12_2023/6qg0_4543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/12_2023/6qg0_4543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/12_2023/6qg0_4543_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qg0_4543/12_2023/6qg0_4543_updated.pdb" } resolution = 4.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 162 5.16 5 C 23526 2.51 5 N 6322 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B ARG 79": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D GLU 98": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D GLU 344": "OE1" <-> "OE2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G GLU 436": "OE1" <-> "OE2" Residue "G GLU 508": "OE1" <-> "OE2" Residue "G GLU 538": "OE1" <-> "OE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H GLU 436": "OE1" <-> "OE2" Residue "H GLU 508": "OE1" <-> "OE2" Residue "H GLU 538": "OE1" <-> "OE2" Residue "H GLU 583": "OE1" <-> "OE2" Residue "I TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 91": "OE1" <-> "OE2" Residue "I ARG 113": "NH1" <-> "NH2" Residue "I GLU 216": "OE1" <-> "OE2" Residue "I GLU 358": "OE1" <-> "OE2" Residue "I GLU 370": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 113": "NH1" <-> "NH2" Residue "J GLU 216": "OE1" <-> "OE2" Residue "J GLU 358": "OE1" <-> "OE2" Residue "J GLU 370": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L GLU 29": "OE1" <-> "OE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L ARG 88": "NH1" <-> "NH2" Residue "L GLU 93": "OE1" <-> "OE2" Residue "L GLU 100": "OE1" <-> "OE2" Residue "L GLU 125": "OE1" <-> "OE2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L GLU 159": "OE1" <-> "OE2" Residue "L GLU 168": "OE1" <-> "OE2" Residue "L GLU 209": "OE1" <-> "OE2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M GLU 383": "OE1" <-> "OE2" Residue "M PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 494": "OE1" <-> "OE2" Residue "M GLU 506": "OE1" <-> "OE2" Residue "N GLU 231": "OE1" <-> "OE2" Residue "N PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 383": "OE1" <-> "OE2" Residue "N GLU 494": "OE1" <-> "OE2" Residue "N GLU 506": "OE1" <-> "OE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K GLU 93": "OE1" <-> "OE2" Residue "K GLU 100": "OE1" <-> "OE2" Residue "K GLU 125": "OE1" <-> "OE2" Residue "K GLU 152": "OE1" <-> "OE2" Residue "K GLU 159": "OE1" <-> "OE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K GLU 209": "OE1" <-> "OE2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C GLU 98": "OE1" <-> "OE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 164": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 239": "OE1" <-> "OE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 36980 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "F" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "G" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "N" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 50 Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "K" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1973 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Time building chain proxies: 18.85, per 1000 atoms: 0.51 Number of scatterers: 36980 At special positions: 0 Unit cell: (274.7, 167.5, 121.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 162 16.00 P 2 15.00 O 6968 8.00 N 6322 7.00 C 23526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.48 Conformation dependent library (CDL) restraints added in 7.4 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 127 helices and 48 sheets defined 29.1% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.47 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 22 through 36 removed outlier: 3.917A pdb=" N ILE A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 59 Processing helix chain 'A' and resid 65 through 82 removed outlier: 3.639A pdb=" N ASP A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N HIS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 96 Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.546A pdb=" N ALA A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.514A pdb=" N ALA A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.520A pdb=" N VAL A 187 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 223 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'B' and resid 7 through 11 Processing helix chain 'B' and resid 22 through 34 Processing helix chain 'B' and resid 44 through 59 removed outlier: 3.788A pdb=" N THR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 83 removed outlier: 3.649A pdb=" N ASP B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 72 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 115 removed outlier: 4.257A pdb=" N GLY B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLN B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 101 " --> pdb=" O ASN B 97 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 143 Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.534A pdb=" N VAL B 187 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'D' and resid 21 through 30 Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 82 through 107 removed outlier: 3.550A pdb=" N ILE D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 104 " --> pdb=" O GLU D 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER D 105 " --> pdb=" O GLU D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 166 Processing helix chain 'D' and resid 169 through 176 removed outlier: 3.993A pdb=" N GLN D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ILE D 175 " --> pdb=" O GLY D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 279 through 287 Processing helix chain 'D' and resid 309 through 312 No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'E' and resid 76 through 86 removed outlier: 4.119A pdb=" N VAL E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 Processing helix chain 'E' and resid 153 through 158 Processing helix chain 'E' and resid 181 through 190 Processing helix chain 'E' and resid 258 through 261 No H-bonds generated for 'chain 'E' and resid 258 through 261' Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.992A pdb=" N GLN E 286 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 287 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU E 288 " --> pdb=" O CYS E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 411 removed outlier: 3.533A pdb=" N ASN E 405 " --> pdb=" O MET E 402 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU E 409 " --> pdb=" O ARG E 406 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE E 411 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 86 Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 153 through 158 Processing helix chain 'F' and resid 181 through 190 Processing helix chain 'F' and resid 257 through 261 Processing helix chain 'F' and resid 282 through 288 removed outlier: 3.997A pdb=" N GLN F 286 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU F 287 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU F 288 " --> pdb=" O CYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 411 removed outlier: 3.559A pdb=" N ASN F 405 " --> pdb=" O MET F 402 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE F 407 " --> pdb=" O ALA F 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 411 " --> pdb=" O VAL F 408 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 283 removed outlier: 4.054A pdb=" N HIS G 283 " --> pdb=" O SER G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 306 removed outlier: 3.904A pdb=" N ILE G 294 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'G' and resid 338 through 353 Processing helix chain 'G' and resid 360 through 378 removed outlier: 3.704A pdb=" N ASP G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 393 removed outlier: 3.743A pdb=" N GLN G 393 " --> pdb=" O ASN G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 407 through 418 Processing helix chain 'G' and resid 436 through 447 Processing helix chain 'G' and resid 490 through 498 Processing helix chain 'G' and resid 529 through 532 Processing helix chain 'H' and resid 272 through 283 removed outlier: 4.048A pdb=" N HIS H 283 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 306 removed outlier: 3.723A pdb=" N ILE H 294 " --> pdb=" O ILE H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 319 through 333 Processing helix chain 'H' and resid 338 through 353 Processing helix chain 'H' and resid 360 through 378 removed outlier: 3.541A pdb=" N LYS H 365 " --> pdb=" O LYS H 361 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP H 366 " --> pdb=" O ALA H 362 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 393 removed outlier: 3.623A pdb=" N GLN H 393 " --> pdb=" O ASN H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 417 Processing helix chain 'H' and resid 436 through 447 Processing helix chain 'H' and resid 456 through 462 removed outlier: 3.571A pdb=" N LEU H 459 " --> pdb=" O ILE H 456 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASP H 460 " --> pdb=" O THR H 457 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR H 461 " --> pdb=" O SER H 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 498 Processing helix chain 'H' and resid 529 through 532 Processing helix chain 'H' and resid 583 through 588 removed outlier: 6.039A pdb=" N LYS H 587 " --> pdb=" O GLY H 584 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 70 Processing helix chain 'I' and resid 83 through 91 Processing helix chain 'I' and resid 115 through 125 Processing helix chain 'I' and resid 146 through 156 Processing helix chain 'I' and resid 218 through 221 No H-bonds generated for 'chain 'I' and resid 218 through 221' Processing helix chain 'I' and resid 241 through 248 Processing helix chain 'I' and resid 259 through 264 Processing helix chain 'I' and resid 288 through 299 Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing helix chain 'J' and resid 59 through 70 removed outlier: 3.515A pdb=" N THR J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 91 Processing helix chain 'J' and resid 115 through 125 Processing helix chain 'J' and resid 146 through 156 Processing helix chain 'J' and resid 215 through 221 removed outlier: 4.175A pdb=" N LEU J 218 " --> pdb=" O PRO J 215 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ASP J 219 " --> pdb=" O GLU J 216 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN J 220 " --> pdb=" O LEU J 217 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL J 221 " --> pdb=" O LEU J 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 215 through 221' Processing helix chain 'J' and resid 241 through 248 Processing helix chain 'J' and resid 259 through 264 Processing helix chain 'J' and resid 288 through 299 Processing helix chain 'J' and resid 308 through 310 No H-bonds generated for 'chain 'J' and resid 308 through 310' Processing helix chain 'L' and resid 92 through 118 removed outlier: 4.150A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG L 113 " --> pdb=" O HIS L 109 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TYR L 114 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 130 Processing helix chain 'L' and resid 141 through 150 removed outlier: 3.731A pdb=" N ILE L 150 " --> pdb=" O LYS L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 173 Processing helix chain 'L' and resid 198 through 208 Processing helix chain 'L' and resid 238 through 258 removed outlier: 3.545A pdb=" N ILE L 241 " --> pdb=" O GLN L 238 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU L 242 " --> pdb=" O LYS L 239 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN L 243 " --> pdb=" O GLY L 240 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU L 244 " --> pdb=" O ILE L 241 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU L 245 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER L 246 " --> pdb=" O GLN L 243 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE L 248 " --> pdb=" O GLU L 245 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS L 250 " --> pdb=" O ALA L 247 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 252 " --> pdb=" O GLU L 249 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 253 " --> pdb=" O LYS L 250 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE L 255 " --> pdb=" O THR L 252 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR L 256 " --> pdb=" O GLU L 253 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS L 257 " --> pdb=" O VAL L 254 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR L 258 " --> pdb=" O ILE L 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 120 Processing helix chain 'M' and resid 202 through 210 removed outlier: 3.592A pdb=" N ALA M 209 " --> pdb=" O LEU M 205 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 227 through 238 Processing helix chain 'M' and resid 258 through 269 Processing helix chain 'M' and resid 291 through 301 removed outlier: 3.602A pdb=" N VAL M 299 " --> pdb=" O ASN M 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 140 Processing helix chain 'N' and resid 113 through 120 Processing helix chain 'N' and resid 202 through 210 removed outlier: 3.570A pdb=" N ALA N 209 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 238 Processing helix chain 'N' and resid 256 through 269 removed outlier: 3.821A pdb=" N LEU N 260 " --> pdb=" O GLU N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 301 removed outlier: 3.566A pdb=" N VAL N 299 " --> pdb=" O ASN N 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 140 Processing helix chain 'K' and resid 92 through 118 removed outlier: 4.150A pdb=" N ILE K 96 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYR K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N CYS K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ALA K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 130 Processing helix chain 'K' and resid 141 through 150 removed outlier: 3.747A pdb=" N ILE K 150 " --> pdb=" O LYS K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 173 Processing helix chain 'K' and resid 198 through 208 Processing helix chain 'K' and resid 238 through 258 removed outlier: 3.535A pdb=" N ILE K 241 " --> pdb=" O GLN K 238 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 242 " --> pdb=" O LYS K 239 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN K 243 " --> pdb=" O GLY K 240 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU K 245 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER K 246 " --> pdb=" O GLN K 243 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE K 248 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS K 250 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR K 252 " --> pdb=" O GLU K 249 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU K 253 " --> pdb=" O LYS K 250 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE K 255 " --> pdb=" O THR K 252 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR K 256 " --> pdb=" O GLU K 253 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS K 257 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR K 258 " --> pdb=" O ILE K 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 61 through 77 Processing helix chain 'C' and resid 82 through 107 removed outlier: 3.548A pdb=" N ILE C 88 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET C 104 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 169 through 176 removed outlier: 3.992A pdb=" N GLN C 174 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE C 175 " --> pdb=" O GLY C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 223 through 235 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 309 through 312 No H-bonds generated for 'chain 'C' and resid 309 through 312' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 361 through 366 Processing sheet with id= A, first strand: chain 'A' and resid 282 through 284 removed outlier: 7.389A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A 154 " --> pdb=" O VAL A 128 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 207 through 209 Processing sheet with id= C, first strand: chain 'B' and resid 282 through 284 removed outlier: 3.637A pdb=" N THR B 154 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR B 177 " --> pdb=" O CYS B 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 207 through 209 removed outlier: 3.516A pdb=" N ASN B 209 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 348 through 350 removed outlier: 3.964A pdb=" N ILE D 348 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY D 261 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 339 through 341 removed outlier: 3.638A pdb=" N ASP D 339 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 133 through 137 removed outlier: 7.685A pdb=" N ILE E 92 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N GLN E 136 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL E 94 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA E 5 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL E 95 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL E 7 " --> pdb=" O VAL E 95 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 194 through 199 Processing sheet with id= I, first strand: chain 'E' and resid 223 through 225 Processing sheet with id= J, first strand: chain 'F' and resid 133 through 137 removed outlier: 7.603A pdb=" N ILE F 92 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N GLN F 136 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL F 94 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA F 5 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VAL F 95 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL F 7 " --> pdb=" O VAL F 95 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 194 through 199 Processing sheet with id= L, first strand: chain 'F' and resid 223 through 225 Processing sheet with id= M, first strand: chain 'G' and resid 579 through 581 removed outlier: 8.045A pdb=" N VAL G 503 " --> pdb=" O LYS G 572 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN G 574 " --> pdb=" O VAL G 503 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL G 505 " --> pdb=" O ASN G 574 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ILE G 576 " --> pdb=" O VAL G 505 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL G 470 " --> pdb=" O LEU G 504 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N CYS G 506 " --> pdb=" O VAL G 470 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU G 472 " --> pdb=" O CYS G 506 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR G 403 " --> pdb=" O PHE G 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY G 473 " --> pdb=" O TYR G 403 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LYS G 425 " --> pdb=" O ILE G 400 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N THR G 402 " --> pdb=" O LYS G 425 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE G 427 " --> pdb=" O THR G 402 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 564 through 566 Processing sheet with id= O, first strand: chain 'H' and resid 571 through 575 removed outlier: 7.660A pdb=" N VAL H 503 " --> pdb=" O LYS H 572 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN H 574 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 505 " --> pdb=" O ASN H 574 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL H 470 " --> pdb=" O LEU H 504 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS H 506 " --> pdb=" O VAL H 470 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU H 472 " --> pdb=" O CYS H 506 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR H 403 " --> pdb=" O PHE H 471 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 473 " --> pdb=" O TYR H 403 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N LYS H 425 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR H 402 " --> pdb=" O LYS H 425 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 427 " --> pdb=" O THR H 402 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 564 through 566 Processing sheet with id= Q, first strand: chain 'I' and resid 164 through 166 removed outlier: 3.509A pdb=" N ILE I 237 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N GLN I 28 " --> pdb=" O ILE I 133 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N VAL I 135 " --> pdb=" O GLN I 28 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL I 30 " --> pdb=" O VAL I 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU I 74 " --> pdb=" O ALA I 29 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL I 31 " --> pdb=" O GLU I 74 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE I 76 " --> pdb=" O VAL I 31 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS I 103 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N LEU I 77 " --> pdb=" O LYS I 103 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR I 105 " --> pdb=" O LEU I 77 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS I 79 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ILE I 107 " --> pdb=" O CYS I 79 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 139 through 141 removed outlier: 4.039A pdb=" N LEU I 140 " --> pdb=" O VAL I 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL I 283 " --> pdb=" O LEU I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 276 through 278 removed outlier: 3.594A pdb=" N LYS I 170 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER I 169 " --> pdb=" O ILE I 231 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 224 through 227 removed outlier: 3.635A pdb=" N GLN I 198 " --> pdb=" O ALA I 184 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL I 186 " --> pdb=" O TYR I 196 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR I 196 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP I 188 " --> pdb=" O CYS I 194 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS I 194 " --> pdb=" O ASP I 188 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 319 through 321 removed outlier: 6.441A pdb=" N THR I 343 " --> pdb=" O TYR I 326 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 331 through 333 removed outlier: 5.804A pdb=" N THR I 349 " --> pdb=" O VAL I 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'I' and resid 356 through 358 Processing sheet with id= X, first strand: chain 'I' and resid 394 through 396 removed outlier: 6.255A pdb=" N CYS I 412 " --> pdb=" O LEU I 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'J' and resid 164 through 166 removed outlier: 3.510A pdb=" N ILE J 237 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N GLN J 28 " --> pdb=" O ILE J 133 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N VAL J 135 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL J 30 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU J 74 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL J 31 " --> pdb=" O GLU J 74 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE J 76 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS J 103 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU J 77 " --> pdb=" O LYS J 103 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR J 105 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS J 79 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE J 107 " --> pdb=" O CYS J 79 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'J' and resid 139 through 141 removed outlier: 4.052A pdb=" N LEU J 140 " --> pdb=" O VAL J 283 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL J 283 " --> pdb=" O LEU J 140 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'J' and resid 276 through 278 removed outlier: 3.517A pdb=" N LYS J 170 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 169 " --> pdb=" O ILE J 231 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 185 through 188 Processing sheet with id= AC, first strand: chain 'J' and resid 319 through 321 removed outlier: 6.435A pdb=" N THR J 343 " --> pdb=" O TYR J 326 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 331 through 333 removed outlier: 5.788A pdb=" N THR J 349 " --> pdb=" O VAL J 332 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'J' and resid 356 through 358 Processing sheet with id= AF, first strand: chain 'J' and resid 394 through 396 removed outlier: 6.229A pdb=" N CYS J 412 " --> pdb=" O LEU J 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'L' and resid 262 through 264 Processing sheet with id= AH, first strand: chain 'L' and resid 72 through 77 removed outlier: 6.628A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL L 76 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR L 82 " --> pdb=" O VAL L 76 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 280 through 282 removed outlier: 8.636A pdb=" N VAL M 281 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE M 246 " --> pdb=" O VAL M 281 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA M 214 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU M 247 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU M 216 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE M 101 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER M 190 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR M 105 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL M 186 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE M 147 " --> pdb=" O VAL M 186 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N HIS M 188 " --> pdb=" O ALA M 145 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA M 145 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER M 190 " --> pdb=" O ALA M 143 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA M 143 " --> pdb=" O SER M 190 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 373 through 376 removed outlier: 4.352A pdb=" N ASN M 344 " --> pdb=" O ARG M 314 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE M 316 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE M 342 " --> pdb=" O ILE M 316 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE M 342 " --> pdb=" O GLY M 394 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY M 394 " --> pdb=" O ILE M 342 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 319 through 321 Processing sheet with id= AL, first strand: chain 'M' and resid 425 through 427 removed outlier: 3.756A pdb=" N ASN M 425 " --> pdb=" O THR M 493 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 482 through 486 removed outlier: 7.248A pdb=" N LEU M 501 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N TRP M 514 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE M 499 " --> pdb=" O TRP M 514 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ARG M 504 " --> pdb=" O VAL M 461 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL M 461 " --> pdb=" O ARG M 504 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR M 471 " --> pdb=" O VAL M 464 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE M 466 " --> pdb=" O THR M 469 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG M 484 " --> pdb=" O VAL M 476 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 280 through 282 removed outlier: 8.591A pdb=" N VAL N 281 " --> pdb=" O VAL N 244 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE N 246 " --> pdb=" O VAL N 281 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA N 214 " --> pdb=" O ILE N 245 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU N 247 " --> pdb=" O ALA N 214 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU N 216 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE N 101 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER N 190 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR N 105 " --> pdb=" O VAL N 192 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL N 186 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE N 147 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N HIS N 188 " --> pdb=" O ALA N 145 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA N 145 " --> pdb=" O HIS N 188 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N SER N 190 " --> pdb=" O ALA N 143 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA N 143 " --> pdb=" O SER N 190 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 373 through 376 removed outlier: 4.336A pdb=" N ASN N 344 " --> pdb=" O ARG N 314 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE N 316 " --> pdb=" O ILE N 342 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ILE N 342 " --> pdb=" O ILE N 316 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE N 342 " --> pdb=" O GLY N 394 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLY N 394 " --> pdb=" O ILE N 342 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'N' and resid 319 through 321 Processing sheet with id= AQ, first strand: chain 'N' and resid 425 through 427 removed outlier: 3.710A pdb=" N ASN N 425 " --> pdb=" O THR N 493 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 482 through 486 removed outlier: 7.259A pdb=" N LEU N 501 " --> pdb=" O ILE N 512 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N TRP N 514 " --> pdb=" O ILE N 499 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE N 499 " --> pdb=" O TRP N 514 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG N 504 " --> pdb=" O VAL N 461 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL N 461 " --> pdb=" O ARG N 504 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR N 471 " --> pdb=" O VAL N 464 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG N 484 " --> pdb=" O VAL N 476 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'K' and resid 262 through 264 Processing sheet with id= AT, first strand: chain 'K' and resid 72 through 77 removed outlier: 6.629A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.965A pdb=" N ILE C 348 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 261 " --> pdb=" O PRO C 189 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'C' and resid 339 through 341 removed outlier: 3.636A pdb=" N ASP C 339 " --> pdb=" O SER C 273 " (cutoff:3.500A) 1111 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.50 Time building geometry restraints manager: 13.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6299 1.32 - 1.45: 9109 1.45 - 1.57: 21943 1.57 - 1.70: 5 1.70 - 1.83: 242 Bond restraints: 37598 Sorted by residual: bond pdb=" N ASN B 89 " pdb=" CA ASN B 89 " ideal model delta sigma weight residual 1.459 1.543 -0.085 1.28e-02 6.10e+03 4.37e+01 bond pdb=" O3P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.495 0.115 2.00e-02 2.50e+03 3.28e+01 bond pdb=" C ALA B 68 " pdb=" N GLY B 69 " ideal model delta sigma weight residual 1.334 1.254 0.080 1.42e-02 4.96e+03 3.21e+01 bond pdb=" O1P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.506 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" O2P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 37593 not shown) Histogram of bond angle deviations from ideal: 96.44 - 103.99: 483 103.99 - 111.55: 13726 111.55 - 119.10: 16842 119.10 - 126.65: 19489 126.65 - 134.21: 350 Bond angle restraints: 50890 Sorted by residual: angle pdb=" N ARG N 356 " pdb=" CA ARG N 356 " pdb=" C ARG N 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ARG M 356 " pdb=" CA ARG M 356 " pdb=" C ARG M 356 " ideal model delta sigma weight residual 112.35 121.39 -9.04 1.34e+00 5.57e-01 4.55e+01 angle pdb=" N ILE H 501 " pdb=" CA ILE H 501 " pdb=" C ILE H 501 " ideal model delta sigma weight residual 109.02 114.80 -5.78 9.30e-01 1.16e+00 3.86e+01 angle pdb=" CA LEU C 125 " pdb=" C LEU C 125 " pdb=" N GLN C 126 " ideal model delta sigma weight residual 119.56 116.25 3.31 5.80e-01 2.97e+00 3.25e+01 angle pdb=" N ILE A 207 " pdb=" CA ILE A 207 " pdb=" C ILE A 207 " ideal model delta sigma weight residual 108.46 116.34 -7.88 1.49e+00 4.50e-01 2.79e+01 ... (remaining 50885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 19287 16.66 - 33.32: 2680 33.32 - 49.98: 612 49.98 - 66.63: 334 66.63 - 83.29: 69 Dihedral angle restraints: 22982 sinusoidal: 9164 harmonic: 13818 Sorted by residual: dihedral pdb=" C GLN I 289 " pdb=" N GLN I 289 " pdb=" CA GLN I 289 " pdb=" CB GLN I 289 " ideal model delta harmonic sigma weight residual -122.60 -136.49 13.89 0 2.50e+00 1.60e-01 3.09e+01 dihedral pdb=" C LEU J 202 " pdb=" N LEU J 202 " pdb=" CA LEU J 202 " pdb=" CB LEU J 202 " ideal model delta harmonic sigma weight residual -122.60 -136.47 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLN J 289 " pdb=" N GLN J 289 " pdb=" CA GLN J 289 " pdb=" CB GLN J 289 " ideal model delta harmonic sigma weight residual -122.60 -136.24 13.64 0 2.50e+00 1.60e-01 2.98e+01 ... (remaining 22979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 5051 0.109 - 0.217: 800 0.217 - 0.326: 98 0.326 - 0.434: 15 0.434 - 0.543: 8 Chirality restraints: 5972 Sorted by residual: chirality pdb=" CA GLN I 289 " pdb=" N GLN I 289 " pdb=" C GLN I 289 " pdb=" CB GLN I 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CA GLN J 289 " pdb=" N GLN J 289 " pdb=" C GLN J 289 " pdb=" CB GLN J 289 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA ASN C 275 " pdb=" N ASN C 275 " pdb=" C ASN C 275 " pdb=" CB ASN C 275 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 ... (remaining 5969 not shown) Planarity restraints: 6496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU L 51 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LEU L 51 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU L 51 " 0.022 2.00e-02 2.50e+03 pdb=" N SEP L 52 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 249 " -0.016 2.00e-02 2.50e+03 2.35e-02 9.66e+00 pdb=" CG PHE C 249 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE C 249 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE C 249 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 249 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 249 " 0.036 2.00e-02 2.50e+03 pdb=" CZ PHE C 249 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 24 " 0.014 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C VAL K 24 " -0.052 2.00e-02 2.50e+03 pdb=" O VAL K 24 " 0.020 2.00e-02 2.50e+03 pdb=" N GLN K 25 " 0.018 2.00e-02 2.50e+03 ... (remaining 6493 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.60: 6 1.60 - 2.42: 17 2.42 - 3.25: 31767 3.25 - 4.07: 88855 4.07 - 4.90: 152385 Warning: very small nonbonded interaction distances. Nonbonded interactions: 273030 Sorted by model distance: nonbonded pdb=" NE2 GLN L 26 " pdb=" CB ALA L 32 " model vdw 0.775 3.540 nonbonded pdb=" NE2 GLN L 26 " pdb=" CA ALA L 32 " model vdw 0.867 3.550 nonbonded pdb=" CD GLN L 26 " pdb=" CA ALA L 32 " model vdw 1.219 3.700 nonbonded pdb=" ND2 ASN A 80 " pdb=" CD2 LEU A 94 " model vdw 1.552 3.540 nonbonded pdb=" ND2 ASN B 80 " pdb=" CG LEU B 94 " model vdw 1.572 3.550 ... (remaining 273025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 6.890 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 90.690 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 37598 Z= 0.589 Angle : 1.399 12.373 50890 Z= 0.896 Chirality : 0.083 0.543 5972 Planarity : 0.005 0.047 6496 Dihedral : 18.074 83.294 13990 Min Nonbonded Distance : 0.775 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 2.44 % Allowed : 9.97 % Favored : 87.59 % Rotamer: Outliers : 5.91 % Allowed : 12.82 % Favored : 81.27 % Cbeta Deviations : 0.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.10), residues: 4632 helix: -2.05 (0.10), residues: 1536 sheet: -0.65 (0.19), residues: 606 loop : -2.53 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 87 HIS 0.008 0.001 HIS H 475 PHE 0.042 0.003 PHE C 249 TYR 0.022 0.003 TYR G 469 ARG 0.018 0.001 ARG H 486 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1183 time to evaluate : 4.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 241 outliers final: 54 residues processed: 1337 average time/residue: 0.5140 time to fit residues: 1104.9823 Evaluate side-chains 748 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 694 time to evaluate : 4.443 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4319 time to fit residues: 46.5337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 195 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 238 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 365 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 271 optimal weight: 0.8980 chunk 423 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 ASN A 144 ASN A 164 GLN A 222 ASN B 62 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN D 10 HIS D 72 ASN D 221 ASN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 14 ASN E 59 GLN E 308 ASN E 309 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN G 280 HIS G 301 GLN G 384 GLN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN H 384 GLN ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 539 ASN H 546 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 HIS I 247 GLN I 296 GLN I 429 ASN J 247 GLN J 296 GLN J 371 ASN J 409 ASN L 103 GLN M 98 GLN M 108 HIS M 197 HIS M 286 GLN N 197 HIS N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 103 GLN K 243 GLN C 10 HIS C 61 ASN C 72 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 37598 Z= 0.245 Angle : 0.737 14.196 50890 Z= 0.384 Chirality : 0.048 0.418 5972 Planarity : 0.005 0.081 6496 Dihedral : 5.919 81.289 5048 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 1.06 % Allowed : 8.57 % Favored : 90.37 % Rotamer: Outliers : 0.39 % Allowed : 4.93 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.11), residues: 4632 helix: -0.17 (0.12), residues: 1548 sheet: -0.06 (0.20), residues: 598 loop : -2.42 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 346 HIS 0.013 0.001 HIS G 280 PHE 0.025 0.002 PHE B 236 TYR 0.039 0.002 TYR G 322 ARG 0.010 0.001 ARG F 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 881 time to evaluate : 4.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 2 residues processed: 892 average time/residue: 0.4691 time to fit residues: 689.6403 Evaluate side-chains 636 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 634 time to evaluate : 4.526 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3522 time to fit residues: 7.6479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 235 optimal weight: 3.9990 chunk 131 optimal weight: 0.0050 chunk 352 optimal weight: 6.9990 chunk 288 optimal weight: 0.7980 chunk 116 optimal weight: 0.0040 chunk 423 optimal weight: 30.0000 chunk 457 optimal weight: 0.8980 chunk 377 optimal weight: 8.9990 chunk 420 optimal weight: 9.9990 chunk 144 optimal weight: 10.0000 chunk 340 optimal weight: 30.0000 overall best weight: 1.1408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN G 514 GLN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN H 475 HIS I 56 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 ASN J 56 ASN J 247 GLN J 249 ASN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 415 GLN N 98 GLN K 25 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37598 Z= 0.212 Angle : 0.656 8.043 50890 Z= 0.338 Chirality : 0.046 0.328 5972 Planarity : 0.005 0.067 6496 Dihedral : 5.669 84.690 5048 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.97 % Allowed : 9.28 % Favored : 89.75 % Rotamer: Outliers : 0.12 % Allowed : 3.41 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.12), residues: 4632 helix: 0.43 (0.13), residues: 1544 sheet: -0.29 (0.19), residues: 696 loop : -2.26 (0.12), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 366 HIS 0.012 0.001 HIS C 183 PHE 0.030 0.002 PHE D 315 TYR 0.023 0.002 TYR J 318 ARG 0.016 0.001 ARG H 432 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 812 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 817 average time/residue: 0.5102 time to fit residues: 689.4369 Evaluate side-chains 621 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 620 time to evaluate : 4.247 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3865 time to fit residues: 6.6678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 418 optimal weight: 20.0000 chunk 318 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 284 optimal weight: 0.9980 chunk 425 optimal weight: 40.0000 chunk 450 optimal weight: 0.0030 chunk 222 optimal weight: 0.7980 chunk 403 optimal weight: 20.0000 chunk 121 optimal weight: 0.0970 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN D 368 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 ASN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN G 393 GLN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN H 480 ASN H 546 ASN I 56 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 241 HIS J 247 GLN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37598 Z= 0.197 Angle : 0.635 7.722 50890 Z= 0.325 Chirality : 0.046 0.271 5972 Planarity : 0.004 0.066 6496 Dihedral : 5.501 79.653 5048 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.91 % Allowed : 8.18 % Favored : 90.91 % Rotamer: Outliers : 0.05 % Allowed : 3.92 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4632 helix: 0.64 (0.13), residues: 1552 sheet: -0.09 (0.19), residues: 690 loop : -2.21 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 95 HIS 0.008 0.001 HIS A 129 PHE 0.023 0.002 PHE I 250 TYR 0.020 0.002 TYR J 318 ARG 0.009 0.000 ARG H 432 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 805 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 807 average time/residue: 0.4645 time to fit residues: 620.7033 Evaluate side-chains 624 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 624 time to evaluate : 4.254 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.9514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 375 optimal weight: 5.9990 chunk 255 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 335 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 384 optimal weight: 2.9990 chunk 311 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 230 optimal weight: 8.9990 chunk 404 optimal weight: 30.0000 chunk 113 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS G 301 GLN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 393 GLN G 415 HIS ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 539 ASN H 389 ASN H 416 ASN H 475 HIS ** H 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 249 ASN ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 429 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37598 Z= 0.244 Angle : 0.656 9.558 50890 Z= 0.337 Chirality : 0.047 0.242 5972 Planarity : 0.005 0.062 6496 Dihedral : 5.540 77.937 5048 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.69 % Allowed : 9.28 % Favored : 90.03 % Rotamer: Outliers : 0.07 % Allowed : 2.57 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.12), residues: 4632 helix: 0.55 (0.13), residues: 1572 sheet: -0.08 (0.19), residues: 670 loop : -2.23 (0.12), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 303 HIS 0.007 0.001 HIS B 129 PHE 0.023 0.002 PHE B 101 TYR 0.020 0.002 TYR B 228 ARG 0.009 0.001 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 755 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 758 average time/residue: 0.4752 time to fit residues: 596.6197 Evaluate side-chains 609 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 608 time to evaluate : 4.400 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3756 time to fit residues: 7.0521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 151 optimal weight: 0.0470 chunk 405 optimal weight: 20.0000 chunk 89 optimal weight: 0.8980 chunk 264 optimal weight: 0.9980 chunk 111 optimal weight: 0.4980 chunk 450 optimal weight: 0.7980 chunk 374 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 164 GLN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN G 480 ASN H 480 ASN I 56 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 324 ASN ** N 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37598 Z= 0.172 Angle : 0.621 9.609 50890 Z= 0.314 Chirality : 0.045 0.240 5972 Planarity : 0.004 0.077 6496 Dihedral : 5.321 77.944 5048 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.03 % Favored : 91.30 % Rotamer: Outliers : 0.02 % Allowed : 1.79 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.12), residues: 4632 helix: 0.87 (0.14), residues: 1522 sheet: -0.02 (0.20), residues: 654 loop : -2.15 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP J 95 HIS 0.008 0.001 HIS H 280 PHE 0.023 0.002 PHE A 119 TYR 0.022 0.001 TYR J 318 ARG 0.009 0.000 ARG D 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 773 time to evaluate : 4.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 774 average time/residue: 0.4713 time to fit residues: 608.2446 Evaluate side-chains 620 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 4.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.3746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 434 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 256 optimal weight: 1.9990 chunk 329 optimal weight: 0.2980 chunk 255 optimal weight: 0.9990 chunk 379 optimal weight: 50.0000 chunk 251 optimal weight: 7.9990 chunk 449 optimal weight: 0.1980 chunk 281 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 301 GLN H 480 ASN ** I 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 367 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 415 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37598 Z= 0.173 Angle : 0.618 9.017 50890 Z= 0.313 Chirality : 0.045 0.226 5972 Planarity : 0.005 0.167 6496 Dihedral : 5.225 76.692 5048 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.71 % Allowed : 8.25 % Favored : 91.04 % Rotamer: Outliers : 0.02 % Allowed : 1.13 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 4632 helix: 0.97 (0.14), residues: 1526 sheet: 0.03 (0.20), residues: 652 loop : -2.13 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 303 HIS 0.006 0.001 HIS D 236 PHE 0.023 0.001 PHE B 101 TYR 0.018 0.001 TYR J 318 ARG 0.015 0.000 ARG G 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 762 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 763 average time/residue: 0.4491 time to fit residues: 574.0139 Evaluate side-chains 628 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 627 time to evaluate : 3.171 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3062 time to fit residues: 5.0281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 277 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 268 optimal weight: 0.6980 chunk 135 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 285 optimal weight: 0.0970 chunk 306 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 353 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN G 301 GLN ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 301 GLN H 480 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37598 Z= 0.166 Angle : 0.616 10.551 50890 Z= 0.310 Chirality : 0.045 0.211 5972 Planarity : 0.004 0.062 6496 Dihedral : 5.129 75.484 5048 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.94 % Favored : 91.39 % Rotamer: Outliers : 0.05 % Allowed : 0.88 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.12), residues: 4632 helix: 1.06 (0.14), residues: 1526 sheet: 0.08 (0.20), residues: 648 loop : -2.11 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 303 HIS 0.009 0.001 HIS C 227 PHE 0.031 0.001 PHE D 315 TYR 0.020 0.001 TYR K 33 ARG 0.007 0.000 ARG K 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 765 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 765 average time/residue: 0.4410 time to fit residues: 563.0899 Evaluate side-chains 614 residues out of total 4206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 613 time to evaluate : 3.204 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2649 time to fit residues: 4.9123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 408 optimal weight: 30.0000 chunk 430 optimal weight: 8.9990 chunk 392 optimal weight: 20.0000 chunk 418 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 328 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 378 optimal weight: 0.0030 chunk 395 optimal weight: 20.0000 chunk 417 optimal weight: 10.0000 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 GLN ** D 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 ASN G 253 ASN G 280 HIS ** G 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 ASN ** G 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 530 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 376 ASN ** J 272 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 388 ASN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** M 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 376 ASN M 433 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.5764 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: