Starting phenix.real_space_refine on Tue Mar 19 10:50:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/03_2024/7jzx_22583.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/03_2024/7jzx_22583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/03_2024/7jzx_22583.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/03_2024/7jzx_22583.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/03_2024/7jzx_22583.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jzx_22583/03_2024/7jzx_22583.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 60 5.49 5 S 26 5.16 5 C 14832 2.51 5 N 4354 2.21 5 O 4676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 12": "OD1" <-> "OD2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ARG 151": "NH1" <-> "NH2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 174": "NH1" <-> "NH2" Residue "B ARG 175": "NH1" <-> "NH2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B ASP 272": "OD1" <-> "OD2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "E ASP 147": "OD1" <-> "OD2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ASP 208": "OD1" <-> "OD2" Residue "E PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 253": "OD1" <-> "OD2" Residue "E ASP 270": "OD1" <-> "OD2" Residue "E ASP 292": "OD1" <-> "OD2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D ASP 130": "OD1" <-> "OD2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D ASP 196": "OD1" <-> "OD2" Residue "D PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D ASP 294": "OD1" <-> "OD2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D ASP 334": "OD1" <-> "OD2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ASP 80": "OD1" <-> "OD2" Residue "F ASP 82": "OD1" <-> "OD2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F ASP 204": "OD1" <-> "OD2" Residue "F GLU 216": "OE1" <-> "OE2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "F ASP 292": "OD1" <-> "OD2" Residue "F ASP 334": "OD1" <-> "OD2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "G ASP 208": "OD1" <-> "OD2" Residue "G GLU 216": "OE1" <-> "OE2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G ASP 294": "OD1" <-> "OD2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "G GLU 335": "OE1" <-> "OE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 34": "OE1" <-> "OE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H ASP 82": "OD1" <-> "OD2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "H GLU 188": "OE1" <-> "OE2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H ASP 294": "OD1" <-> "OD2" Residue "H GLU 302": "OE1" <-> "OE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "I GLU 65": "OE1" <-> "OE2" Residue "I ASP 80": "OD1" <-> "OD2" Residue "I ASP 87": "OD1" <-> "OD2" Residue "I ASP 147": "OD1" <-> "OD2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I ASP 208": "OD1" <-> "OD2" Residue "I GLU 249": "OE1" <-> "OE2" Residue "I ASP 253": "OD1" <-> "OD2" Residue "I TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 292": "OD1" <-> "OD2" Residue "I GLU 302": "OE1" <-> "OE2" Residue "I ASP 322": "OD1" <-> "OD2" Residue "I GLU 335": "OE1" <-> "OE2" Residue "I GLU 357": "OE1" <-> "OE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 432": "OE1" <-> "OE2" Residue "J GLU 63": "OE1" <-> "OE2" Residue "J GLU 82": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23948 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 1448 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 187, 1445 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 171} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 1480 Chain: "B" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2411 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 24, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2307 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 10, 'TRANS': 287} Chain breaks: 2 Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "G" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "H" Number of atoms: 2554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2554 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 1 Chain: "I" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2592 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain: "A" Number of atoms: 3079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3079 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 24, 'TRANS': 402} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 366 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 306 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 9, 'ASP:plan': 11, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 240 Chain: "M" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1273 Classifications: {'DNA': 1, 'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 17, 'rna3p_pyr': 14} Link IDs: {'rna2p': 28, 'rna3p': 32} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 11 Chain: "J" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 508 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Time building chain proxies: 13.74, per 1000 atoms: 0.57 Number of scatterers: 23948 At special positions: 0 Unit cell: (133.35, 157.5, 148.05, 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 26 16.00 P 60 15.00 O 4676 8.00 N 4354 7.00 C 14832 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: 9.89 Conformation dependent library (CDL) restraints added in 5.1 seconds 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5496 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 52 sheets defined 32.6% alpha, 21.8% beta 6 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 10.80 Creating SS restraints... Processing helix chain 'C' and resid 16 through 36 Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.628A pdb=" N LEU C 76 " --> pdb=" O ARG C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.700A pdb=" N LEU C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 132 through 136 removed outlier: 3.583A pdb=" N VAL C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA C 136 " --> pdb=" O ASP C 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 132 through 136' Processing helix chain 'B' and resid 33 through 48 removed outlier: 4.011A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 135 Processing helix chain 'B' and resid 165 through 178 Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.866A pdb=" N LEU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 291 through 295 removed outlier: 3.938A pdb=" N VAL B 295 " --> pdb=" O PRO B 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 55 removed outlier: 3.608A pdb=" N SER E 55 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 92 removed outlier: 3.705A pdb=" N SER E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 148 Processing helix chain 'E' and resid 151 through 163 Processing helix chain 'E' and resid 209 through 223 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.568A pdb=" N ILE E 279 " --> pdb=" O HIS E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 297 removed outlier: 3.855A pdb=" N LEU E 296 " --> pdb=" O GLU E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 338 through 352 Processing helix chain 'D' and resid 130 through 148 Processing helix chain 'D' and resid 152 through 163 Processing helix chain 'D' and resid 208 through 223 removed outlier: 3.605A pdb=" N ASP D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 338 through 352 Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.671A pdb=" N SER F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 148 Processing helix chain 'F' and resid 151 through 163 Processing helix chain 'F' and resid 209 through 223 Processing helix chain 'F' and resid 275 through 284 Processing helix chain 'F' and resid 322 through 332 Processing helix chain 'F' and resid 338 through 352 Processing helix chain 'G' and resid 51 through 55 Processing helix chain 'G' and resid 82 through 92 removed outlier: 3.648A pdb=" N SER G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 148 Processing helix chain 'G' and resid 151 through 163 Processing helix chain 'G' and resid 208 through 223 Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 322 through 332 removed outlier: 3.599A pdb=" N LEU G 326 " --> pdb=" O ASP G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 352 Processing helix chain 'H' and resid 82 through 92 Processing helix chain 'H' and resid 130 through 148 Processing helix chain 'H' and resid 151 through 163 Processing helix chain 'H' and resid 208 through 223 Processing helix chain 'H' and resid 275 through 284 Processing helix chain 'H' and resid 322 through 331 Processing helix chain 'H' and resid 338 through 352 Processing helix chain 'I' and resid 51 through 55 removed outlier: 3.531A pdb=" N SER I 55 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 130 through 148 Processing helix chain 'I' and resid 152 through 163 Processing helix chain 'I' and resid 208 through 224 Processing helix chain 'I' and resid 275 through 284 Processing helix chain 'I' and resid 322 through 332 Processing helix chain 'I' and resid 338 through 352 Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.650A pdb=" N LEU A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.172A pdb=" N THR A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 60 removed outlier: 3.533A pdb=" N ALA A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.010A pdb=" N PHE A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 removed outlier: 3.753A pdb=" N GLU A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 196 through 212 Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.909A pdb=" N ALA A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.582A pdb=" N ASN A 250 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 251' Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.013A pdb=" N GLU A 257 " --> pdb=" O GLN A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 294 through 306 removed outlier: 3.618A pdb=" N THR A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 344 removed outlier: 4.517A pdb=" N ALA A 317 " --> pdb=" O HIS A 313 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 Processing helix chain 'A' and resid 376 through 381 removed outlier: 3.967A pdb=" N GLY A 381 " --> pdb=" O ARG A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 399 removed outlier: 3.739A pdb=" N ARG A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TRP A 394 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 395 " --> pdb=" O PHE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 409 through 431 removed outlier: 4.040A pdb=" N ASP A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 52 Processing helix chain 'J' and resid 59 through 70 removed outlier: 4.306A pdb=" N GLU J 63 " --> pdb=" O ALA J 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.335A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 65 through 68 removed outlier: 5.335A pdb=" N LEU B 105 " --> pdb=" O GLN B 18 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLN B 18 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL B 107 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N SER B 16 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 109 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ARG B 14 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 111 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 12 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 113 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU B 10 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA B 157 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 5.953A pdb=" N TRP B 29 " --> pdb=" O SER A 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 188 removed outlier: 7.545A pdb=" N PHE B 279 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 257 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP B 247 " --> pdb=" O TRP B 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AB3, first strand: chain 'B' and resid 304 through 306 Processing sheet with id=AB4, first strand: chain 'E' and resid 127 through 128 Processing sheet with id=AB5, first strand: chain 'E' and resid 38 through 39 removed outlier: 4.325A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 189 through 192 removed outlier: 6.790A pdb=" N HIS E 183 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA E 192 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE E 181 " --> pdb=" O ALA E 192 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 229 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL E 228 " --> pdb=" O VAL E 118 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 64 through 70 removed outlier: 3.579A pdb=" N ASN E 94 " --> pdb=" O GLY E 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 248 through 249 removed outlier: 4.399A pdb=" N THR E 264 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 285 through 287 Processing sheet with id=AC1, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AC2, first strand: chain 'D' and resid 38 through 39 removed outlier: 4.163A pdb=" N VAL D 228 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 191 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AC4, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AC5, first strand: chain 'D' and resid 248 through 249 removed outlier: 4.541A pdb=" N THR D 264 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 285 through 287 Processing sheet with id=AC7, first strand: chain 'D' and resid 306 through 307 Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 33 Processing sheet with id=AC9, first strand: chain 'F' and resid 38 through 39 removed outlier: 4.074A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 189 through 192 removed outlier: 6.808A pdb=" N HIS F 183 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ALA F 192 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE F 181 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 229 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL F 228 " --> pdb=" O VAL F 118 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 64 through 70 removed outlier: 3.511A pdb=" N GLY F 70 " --> pdb=" O ASN F 94 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN F 94 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA F 101 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 306 through 307 Processing sheet with id=AD4, first strand: chain 'G' and resid 127 through 128 removed outlier: 3.534A pdb=" N ALA G 127 " --> pdb=" O ALA G 32 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 38 through 39 removed outlier: 4.126A pdb=" N VAL G 228 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU G 229 " --> pdb=" O ILE G 184 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL G 177 " --> pdb=" O ASP G 196 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP G 196 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 179 " --> pdb=" O ARG G 194 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 194 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE G 181 " --> pdb=" O ALA G 192 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ALA G 192 " --> pdb=" O ILE G 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS G 183 " --> pdb=" O ALA G 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AD7, first strand: chain 'G' and resid 64 through 70 removed outlier: 4.395A pdb=" N ALA G 101 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 306 through 307 Processing sheet with id=AD9, first strand: chain 'H' and resid 127 through 128 Processing sheet with id=AE1, first strand: chain 'H' and resid 38 through 39 removed outlier: 4.068A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 189 through 192 removed outlier: 6.712A pdb=" N HIS H 183 " --> pdb=" O ALA H 190 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA H 192 " --> pdb=" O ILE H 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE H 181 " --> pdb=" O ALA H 192 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 229 " --> pdb=" O ILE H 184 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N VAL H 228 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 64 through 70 removed outlier: 3.754A pdb=" N ASN H 94 " --> pdb=" O GLY H 70 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA H 101 " --> pdb=" O VAL H 244 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 248 through 249 removed outlier: 4.662A pdb=" N THR H 264 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 306 through 307 removed outlier: 3.670A pdb=" N LYS H 312 " --> pdb=" O VAL H 307 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 127 through 128 Processing sheet with id=AE7, first strand: chain 'I' and resid 38 through 39 removed outlier: 4.429A pdb=" N LEU I 229 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG I 191 " --> pdb=" O HIS I 183 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AE9, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.641A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA I 101 " --> pdb=" O VAL I 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 63 through 70 removed outlier: 3.641A pdb=" N ASN I 94 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LYS I 261 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N THR I 97 " --> pdb=" O LYS I 261 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS I 263 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 285 through 287 Processing sheet with id=AF3, first strand: chain 'I' and resid 306 through 307 removed outlier: 3.561A pdb=" N LYS I 312 " --> pdb=" O VAL I 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AF5, first strand: chain 'A' and resid 68 through 69 Processing sheet with id=AF6, first strand: chain 'A' and resid 180 through 181 Processing sheet with id=AF7, first strand: chain 'J' and resid 20 through 25 removed outlier: 4.206A pdb=" N PHE J 35 " --> pdb=" O VAL J 79 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 28 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 11.28 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5557 1.33 - 1.45: 5414 1.45 - 1.57: 13418 1.57 - 1.69: 120 1.69 - 1.81: 40 Bond restraints: 24549 Sorted by residual: bond pdb=" O3' A M 36 " pdb=" P C M 37 " ideal model delta sigma weight residual 1.607 1.672 -0.065 1.50e-02 4.44e+03 1.89e+01 bond pdb=" C LEU B 181 " pdb=" N PRO B 182 " ideal model delta sigma weight residual 1.337 1.379 -0.042 9.80e-03 1.04e+04 1.83e+01 bond pdb=" N ARG H 185 " pdb=" CA ARG H 185 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.92e+00 bond pdb=" N LEU B 301 " pdb=" CA LEU B 301 " ideal model delta sigma weight residual 1.462 1.500 -0.039 1.48e-02 4.57e+03 6.82e+00 bond pdb=" N ASP I 135 " pdb=" CA ASP I 135 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.28e+00 ... (remaining 24544 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.14: 837 106.14 - 113.13: 13378 113.13 - 120.11: 8696 120.11 - 127.10: 10278 127.10 - 134.09: 441 Bond angle restraints: 33630 Sorted by residual: angle pdb=" C GLN A 124 " pdb=" N TYR A 125 " pdb=" CA TYR A 125 " ideal model delta sigma weight residual 120.79 128.74 -7.95 1.39e+00 5.18e-01 3.27e+01 angle pdb=" C LYS G 77 " pdb=" N THR G 78 " pdb=" CA THR G 78 " ideal model delta sigma weight residual 121.54 132.33 -10.79 1.91e+00 2.74e-01 3.19e+01 angle pdb=" C LYS E 77 " pdb=" N THR E 78 " pdb=" CA THR E 78 " ideal model delta sigma weight residual 121.54 130.74 -9.20 1.91e+00 2.74e-01 2.32e+01 angle pdb=" C ARG I 185 " pdb=" N GLN I 186 " pdb=" CA GLN I 186 " ideal model delta sigma weight residual 120.82 128.04 -7.22 1.50e+00 4.44e-01 2.32e+01 angle pdb=" C LYS H 77 " pdb=" N THR H 78 " pdb=" CA THR H 78 " ideal model delta sigma weight residual 121.54 129.95 -8.41 1.91e+00 2.74e-01 1.94e+01 ... (remaining 33625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 14349 35.96 - 71.92: 423 71.92 - 107.88: 43 107.88 - 143.84: 2 143.84 - 179.80: 5 Dihedral angle restraints: 14822 sinusoidal: 6316 harmonic: 8506 Sorted by residual: dihedral pdb=" O4' U M 33 " pdb=" C1' U M 33 " pdb=" N1 U M 33 " pdb=" C2 U M 33 " ideal model delta sinusoidal sigma weight residual 200.00 56.03 143.97 1 1.50e+01 4.44e-03 7.72e+01 dihedral pdb=" O4' U M 21 " pdb=" C1' U M 21 " pdb=" N1 U M 21 " pdb=" C2 U M 21 " ideal model delta sinusoidal sigma weight residual 200.00 70.81 129.19 1 1.50e+01 4.44e-03 6.96e+01 dihedral pdb=" O4' C M 20 " pdb=" C1' C M 20 " pdb=" N1 C M 20 " pdb=" C2 C M 20 " ideal model delta sinusoidal sigma weight residual -128.00 51.80 -179.80 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 14819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2631 0.048 - 0.096: 893 0.096 - 0.144: 228 0.144 - 0.192: 42 0.192 - 0.241: 4 Chirality restraints: 3798 Sorted by residual: chirality pdb=" C1' U M 33 " pdb=" O4' U M 33 " pdb=" C2' U M 33 " pdb=" N1 U M 33 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA LEU B 181 " pdb=" N LEU B 181 " pdb=" C LEU B 181 " pdb=" CB LEU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE J 23 " pdb=" CA ILE J 23 " pdb=" CG1 ILE J 23 " pdb=" CG2 ILE J 23 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3795 not shown) Planarity restraints: 4221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 71 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO A 72 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 291 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 292 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 292 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 292 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 25 " -0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 26 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 26 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 26 " -0.037 5.00e-02 4.00e+02 ... (remaining 4218 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5107 2.77 - 3.30: 21176 3.30 - 3.84: 41098 3.84 - 4.37: 49237 4.37 - 4.90: 84009 Nonbonded interactions: 200627 Sorted by model distance: nonbonded pdb=" OH TYR G 324 " pdb=" O SER H 73 " model vdw 2.239 2.440 nonbonded pdb=" OG SER E 29 " pdb=" OD1 ASN E 129 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR H 324 " pdb=" O SER I 73 " model vdw 2.266 2.440 nonbonded pdb=" O ARG I 69 " pdb=" O2' C M 13 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR F 324 " pdb=" O SER G 73 " model vdw 2.285 2.440 ... (remaining 200622 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 'D' selection = (chain 'E' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'F' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'G' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'H' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) selection = (chain 'I' and (resid 24 through 68 or resid 96 through 250 or resid 261 through \ 358)) } 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=0.37 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.040 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 78.540 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.140 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: 0.020 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 0.076 24549 Z= 0.572 Angle : 0.916 10.795 33630 Z= 0.514 Chirality : 0.051 0.241 3798 Planarity : 0.006 0.072 4221 Dihedral : 17.055 179.805 9326 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.40 % Allowed : 7.51 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -3.94 (0.12), residues: 2927 helix: -2.81 (0.11), residues: 905 sheet: -1.73 (0.21), residues: 495 loop : -2.82 (0.13), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 49 HIS 0.007 0.002 HIS B 42 PHE 0.022 0.003 PHE G 166 TYR 0.017 0.003 TYR E 304 ARG 0.014 0.001 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 184 time to evaluate : 2.853 Fit side-chains REVERT: C 19 GLN cc_start: 0.7841 (tt0) cc_final: 0.7565 (mt0) REVERT: C 110 GLU cc_start: 0.7623 (mp0) cc_final: 0.7184 (pm20) REVERT: B 244 LYS cc_start: 0.8488 (mtmt) cc_final: 0.8231 (mtmm) REVERT: I 257 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7637 (tptt) REVERT: A 228 TRP cc_start: 0.8689 (t-100) cc_final: 0.8469 (t-100) REVERT: A 299 ARG cc_start: 0.8001 (tmm160) cc_final: 0.7788 (tmm160) REVERT: J 44 ASP cc_start: 0.8331 (t0) cc_final: 0.8046 (t0) outliers start: 9 outliers final: 0 residues processed: 190 average time/residue: 0.5171 time to fit residues: 140.5213 Evaluate side-chains 136 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN C 84 GLN C 165 GLN E 159 HIS E 348 ASN D 102 ASN D 348 ASN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 129 ASN G 51 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 183 HIS I 342 GLN ** A 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN A 335 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 24549 Z= 0.285 Angle : 0.568 12.787 33630 Z= 0.300 Chirality : 0.040 0.186 3798 Planarity : 0.004 0.060 4221 Dihedral : 15.408 179.824 4162 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.19 % Allowed : 11.25 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.14), residues: 2927 helix: -0.63 (0.15), residues: 927 sheet: -1.02 (0.23), residues: 433 loop : -2.41 (0.14), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 49 HIS 0.007 0.001 HIS B 305 PHE 0.013 0.001 PHE E 166 TYR 0.017 0.002 TYR I 304 ARG 0.007 0.000 ARG H 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 2.683 Fit side-chains REVERT: C 19 GLN cc_start: 0.7934 (tt0) cc_final: 0.7560 (tt0) REVERT: C 35 GLN cc_start: 0.8365 (tp40) cc_final: 0.7891 (tp40) REVERT: B 244 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8115 (mtmm) REVERT: B 311 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8066 (ttpp) REVERT: D 318 LYS cc_start: 0.8770 (tttm) cc_final: 0.8542 (tttp) REVERT: F 307 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8768 (m) REVERT: I 216 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7071 (mt-10) REVERT: I 257 LYS cc_start: 0.7812 (mmmt) cc_final: 0.7577 (tptt) REVERT: A 228 TRP cc_start: 0.8652 (t-100) cc_final: 0.8431 (t-100) REVERT: J 44 ASP cc_start: 0.8159 (t0) cc_final: 0.7696 (t0) REVERT: J 61 VAL cc_start: 0.8419 (t) cc_final: 0.8217 (t) outliers start: 27 outliers final: 11 residues processed: 172 average time/residue: 0.4609 time to fit residues: 118.4136 Evaluate side-chains 155 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 58 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 269 optimal weight: 20.0000 chunk 290 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS E 91 GLN F 96 GLN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS A 335 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24549 Z= 0.252 Angle : 0.532 10.899 33630 Z= 0.278 Chirality : 0.039 0.173 3798 Planarity : 0.004 0.060 4221 Dihedral : 15.253 178.925 4162 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.76 % Allowed : 12.74 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.61 (0.15), residues: 2927 helix: 0.47 (0.17), residues: 920 sheet: -0.79 (0.23), residues: 466 loop : -2.21 (0.14), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 394 HIS 0.005 0.001 HIS B 305 PHE 0.011 0.001 PHE I 114 TYR 0.014 0.001 TYR H 290 ARG 0.005 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 150 time to evaluate : 2.805 Fit side-chains REVERT: C 19 GLN cc_start: 0.7802 (tt0) cc_final: 0.7396 (mt0) REVERT: C 35 GLN cc_start: 0.8416 (tp40) cc_final: 0.7882 (tp40) REVERT: C 110 GLU cc_start: 0.7540 (mp0) cc_final: 0.7070 (pm20) REVERT: F 307 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8742 (m) REVERT: G 307 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7958 (m) REVERT: I 216 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7064 (mt-10) REVERT: A 107 ASP cc_start: 0.7468 (m-30) cc_final: 0.7251 (m-30) REVERT: A 228 TRP cc_start: 0.8603 (t-100) cc_final: 0.8372 (t-100) REVERT: J 34 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7503 (mt-10) REVERT: J 36 TYR cc_start: 0.8427 (m-80) cc_final: 0.7994 (m-80) REVERT: J 44 ASP cc_start: 0.8227 (t0) cc_final: 0.7741 (t0) REVERT: J 61 VAL cc_start: 0.8443 (t) cc_final: 0.8200 (t) outliers start: 40 outliers final: 22 residues processed: 177 average time/residue: 0.4048 time to fit residues: 109.5513 Evaluate side-chains 169 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 154 HIS B 19 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN E 148 GLN D 102 ASN D 146 ASN F 159 HIS F 183 HIS H 51 GLN ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 227 HIS H 281 ASN I 148 GLN I 159 HIS A 74 HIS A 124 GLN A 157 GLN A 172 HIS J 65 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.085 24549 Z= 0.685 Angle : 0.727 12.930 33630 Z= 0.371 Chirality : 0.047 0.193 3798 Planarity : 0.005 0.072 4221 Dihedral : 15.307 179.862 4162 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.46 % Allowed : 14.19 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % 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: -1.63 (0.15), residues: 2927 helix: 0.52 (0.17), residues: 920 sheet: -0.72 (0.23), residues: 463 loop : -2.29 (0.14), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 49 HIS 0.007 0.002 HIS B 42 PHE 0.022 0.002 PHE H 114 TYR 0.018 0.002 TYR B 314 ARG 0.006 0.001 ARG I 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 138 time to evaluate : 2.879 Fit side-chains REVERT: C 19 GLN cc_start: 0.7809 (tt0) cc_final: 0.7379 (mt0) REVERT: C 35 GLN cc_start: 0.8503 (tp40) cc_final: 0.7959 (tp40) REVERT: B 137 MET cc_start: 0.9061 (mtp) cc_final: 0.8857 (mtp) REVERT: B 311 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8322 (tttm) REVERT: E 318 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8244 (mmmt) REVERT: H 251 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8527 (mp) REVERT: I 216 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: J 38 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: J 44 ASP cc_start: 0.8287 (t0) cc_final: 0.7783 (t0) outliers start: 56 outliers final: 35 residues processed: 182 average time/residue: 0.3803 time to fit residues: 106.9222 Evaluate side-chains 173 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 135 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain E residue 146 ASN Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 270 ASP Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 251 ILE Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 38 GLU Chi-restraints excluded: chain J residue 41 GLN Chi-restraints excluded: chain J residue 58 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS J 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24549 Z= 0.175 Angle : 0.504 9.508 33630 Z= 0.264 Chirality : 0.039 0.164 3798 Planarity : 0.003 0.064 4221 Dihedral : 15.168 179.215 4162 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.58 % Allowed : 15.91 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.15), residues: 2927 helix: 1.15 (0.17), residues: 924 sheet: -0.59 (0.24), residues: 456 loop : -2.04 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 228 HIS 0.005 0.001 HIS B 293 PHE 0.011 0.001 PHE E 166 TYR 0.015 0.001 TYR I 304 ARG 0.004 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 2.716 Fit side-chains REVERT: C 19 GLN cc_start: 0.7756 (tt0) cc_final: 0.7321 (mt0) REVERT: C 35 GLN cc_start: 0.8429 (tp40) cc_final: 0.8096 (tp40) REVERT: C 110 GLU cc_start: 0.7488 (mp0) cc_final: 0.6984 (pm20) REVERT: B 244 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8021 (ttmm) REVERT: B 311 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8334 (ttpp) REVERT: E 354 VAL cc_start: 0.8859 (OUTLIER) cc_final: 0.8552 (p) REVERT: G 307 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7961 (m) REVERT: J 36 TYR cc_start: 0.8477 (m-80) cc_final: 0.8228 (m-80) REVERT: J 44 ASP cc_start: 0.8270 (t0) cc_final: 0.7737 (t0) outliers start: 36 outliers final: 18 residues processed: 168 average time/residue: 0.4067 time to fit residues: 104.5587 Evaluate side-chains 159 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 2.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 250 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 58 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.9980 chunk 257 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 286 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 348 ASN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 24549 Z= 0.314 Angle : 0.547 10.458 33630 Z= 0.283 Chirality : 0.040 0.167 3798 Planarity : 0.004 0.067 4221 Dihedral : 15.125 179.935 4162 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.28 % Allowed : 15.82 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 2927 helix: 1.25 (0.17), residues: 925 sheet: -0.48 (0.24), residues: 464 loop : -2.02 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 49 HIS 0.005 0.001 HIS B 293 PHE 0.014 0.001 PHE H 114 TYR 0.013 0.002 TYR H 290 ARG 0.004 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 2.855 Fit side-chains REVERT: C 1 MET cc_start: 0.5987 (mtp) cc_final: 0.5297 (mpp) REVERT: C 35 GLN cc_start: 0.8434 (tp40) cc_final: 0.8082 (tp40) REVERT: C 110 GLU cc_start: 0.7515 (mp0) cc_final: 0.7011 (pm20) REVERT: B 181 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7723 (tp) REVERT: B 244 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8186 (ttmm) REVERT: B 311 LYS cc_start: 0.8674 (ttpp) cc_final: 0.8321 (tttm) REVERT: E 354 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8589 (p) REVERT: I 216 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: A 107 ASP cc_start: 0.7233 (m-30) cc_final: 0.6998 (m-30) REVERT: J 44 ASP cc_start: 0.8284 (t0) cc_final: 0.7751 (t0) outliers start: 52 outliers final: 35 residues processed: 181 average time/residue: 0.4096 time to fit residues: 114.0131 Evaluate side-chains 175 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 322 ASP Chi-restraints excluded: chain I residue 170 ASN Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 277 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 30.0000 chunk 32 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 285 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN A 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24549 Z= 0.165 Angle : 0.492 9.334 33630 Z= 0.256 Chirality : 0.038 0.157 3798 Planarity : 0.003 0.063 4221 Dihedral : 15.013 179.732 4162 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.89 % Allowed : 16.61 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.16), residues: 2927 helix: 1.54 (0.18), residues: 925 sheet: -0.41 (0.23), residues: 481 loop : -1.93 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 49 HIS 0.005 0.001 HIS B 293 PHE 0.010 0.001 PHE B 152 TYR 0.012 0.001 TYR I 304 ARG 0.003 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 142 time to evaluate : 2.670 Fit side-chains REVERT: C 1 MET cc_start: 0.5750 (mtp) cc_final: 0.5255 (mpp) REVERT: C 35 GLN cc_start: 0.8359 (tp40) cc_final: 0.8120 (tt0) REVERT: B 244 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8028 (ttmm) REVERT: B 311 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8351 (ttpp) REVERT: B 314 TYR cc_start: 0.8135 (m-80) cc_final: 0.7657 (m-80) REVERT: E 318 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7836 (mmtt) REVERT: J 44 ASP cc_start: 0.8281 (t0) cc_final: 0.7752 (t0) outliers start: 43 outliers final: 37 residues processed: 174 average time/residue: 0.4027 time to fit residues: 106.5848 Evaluate side-chains 174 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 24549 Z= 0.429 Angle : 0.593 14.735 33630 Z= 0.304 Chirality : 0.042 0.173 3798 Planarity : 0.004 0.070 4221 Dihedral : 15.091 179.551 4162 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.20 % Allowed : 16.87 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2927 helix: 1.30 (0.17), residues: 930 sheet: -0.40 (0.24), residues: 464 loop : -1.99 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 49 HIS 0.005 0.001 HIS B 42 PHE 0.016 0.002 PHE H 114 TYR 0.014 0.002 TYR H 290 ARG 0.005 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 132 time to evaluate : 2.744 Fit side-chains REVERT: C 35 GLN cc_start: 0.8443 (tp40) cc_final: 0.8193 (tt0) REVERT: B 152 PHE cc_start: 0.6164 (m-80) cc_final: 0.5945 (m-10) REVERT: B 181 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7698 (tp) REVERT: B 244 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8187 (ttmm) REVERT: B 311 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8311 (tttm) REVERT: I 216 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: J 44 ASP cc_start: 0.8303 (t0) cc_final: 0.7768 (t0) outliers start: 50 outliers final: 42 residues processed: 170 average time/residue: 0.3936 time to fit residues: 102.9159 Evaluate side-chains 177 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 132 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain I residue 44 MET Chi-restraints excluded: chain I residue 170 ASN Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 2.9990 chunk 273 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 265 optimal weight: 0.3980 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 240 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 24549 Z= 0.307 Angle : 0.547 14.495 33630 Z= 0.282 Chirality : 0.040 0.170 3798 Planarity : 0.003 0.066 4221 Dihedral : 15.032 179.823 4162 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.15 % Allowed : 17.18 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.16), residues: 2927 helix: 1.42 (0.17), residues: 925 sheet: -0.36 (0.24), residues: 464 loop : -1.96 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 49 HIS 0.005 0.001 HIS B 42 PHE 0.013 0.001 PHE H 114 TYR 0.013 0.002 TYR H 290 ARG 0.004 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 137 time to evaluate : 2.751 Fit side-chains revert: symmetry clash REVERT: C 35 GLN cc_start: 0.8396 (tp40) cc_final: 0.8153 (tt0) REVERT: C 110 GLU cc_start: 0.7502 (mp0) cc_final: 0.6928 (pm20) REVERT: B 152 PHE cc_start: 0.6105 (m-80) cc_final: 0.5888 (m-80) REVERT: B 181 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7727 (tp) REVERT: B 244 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8270 (ttmm) REVERT: B 311 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8317 (tttm) REVERT: I 216 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7186 (mt-10) REVERT: J 44 ASP cc_start: 0.8303 (t0) cc_final: 0.7752 (t0) outliers start: 49 outliers final: 41 residues processed: 172 average time/residue: 0.3965 time to fit residues: 104.0697 Evaluate side-chains 179 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 135 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain I residue 170 ASN Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 22 SER Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 6.9990 chunk 281 optimal weight: 30.0000 chunk 171 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 195 optimal weight: 0.7980 chunk 294 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24549 Z= 0.237 Angle : 0.522 13.763 33630 Z= 0.268 Chirality : 0.039 0.166 3798 Planarity : 0.003 0.066 4221 Dihedral : 14.992 179.266 4162 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.11 % Allowed : 17.09 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.16), residues: 2927 helix: 1.58 (0.18), residues: 925 sheet: -0.28 (0.24), residues: 464 loop : -1.91 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 155 HIS 0.005 0.001 HIS B 42 PHE 0.011 0.001 PHE I 114 TYR 0.013 0.001 TYR H 290 ARG 0.003 0.000 ARG G 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5854 Ramachandran restraints generated. 2927 Oldfield, 0 Emsley, 2927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 138 time to evaluate : 2.896 Fit side-chains revert: symmetry clash REVERT: C 35 GLN cc_start: 0.8370 (tp40) cc_final: 0.8156 (tt0) REVERT: C 166 VAL cc_start: 0.8694 (t) cc_final: 0.8493 (p) REVERT: B 181 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7731 (tp) REVERT: B 244 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8192 (ttmm) REVERT: B 311 LYS cc_start: 0.8637 (ttpp) cc_final: 0.8309 (tttm) REVERT: I 216 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: J 44 ASP cc_start: 0.8304 (t0) cc_final: 0.7761 (t0) outliers start: 48 outliers final: 41 residues processed: 173 average time/residue: 0.4067 time to fit residues: 107.4494 Evaluate side-chains 180 residues out of total 2385 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 86 ASN Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 244 LYS Chi-restraints excluded: chain B residue 300 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 251 ILE Chi-restraints excluded: chain E residue 348 ASN Chi-restraints excluded: chain E residue 354 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 304 TYR Chi-restraints excluded: chain D residue 348 ASN Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain F residue 304 TYR Chi-restraints excluded: chain G residue 147 ASP Chi-restraints excluded: chain G residue 264 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 340 GLU Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain I residue 170 ASN Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain J residue 25 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 41 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 241 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.051311 restraints weight = 84265.724| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.78 r_work: 0.2695 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 24549 Z= 0.353 Angle : 0.566 14.145 33630 Z= 0.290 Chirality : 0.041 0.170 3798 Planarity : 0.004 0.068 4221 Dihedral : 15.014 179.684 4162 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.24 % Allowed : 17.09 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2927 helix: 1.47 (0.17), residues: 925 sheet: -0.31 (0.24), residues: 464 loop : -1.96 (0.15), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 49 HIS 0.006 0.001 HIS A 200 PHE 0.014 0.001 PHE H 114 TYR 0.015 0.002 TYR J 36 ARG 0.004 0.000 ARG G 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4133.53 seconds wall clock time: 76 minutes 15.55 seconds (4575.55 seconds total)