Starting phenix.real_space_refine on Sat Feb 24 11:46:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sm3_10241/02_2024/6sm3_10241_updated.pdb" } resolution = 3.3 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 21772 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 13982 2.51 5 N 3700 2.21 5 O 4276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 207": "OD1" <-> "OD2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "A TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 488": "OD1" <-> "OD2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 257": "OD1" <-> "OD2" Residue "B ASP 286": "OD1" <-> "OD2" Residue "B TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 304": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B GLU 357": "OE1" <-> "OE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 446": "OE1" <-> "OE2" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 516": "OD1" <-> "OD2" Residue "B ASP 532": "OD1" <-> "OD2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B GLU 549": "OE1" <-> "OE2" Residue "B TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 635": "OD1" <-> "OD2" Residue "B ASP 649": "OD1" <-> "OD2" Residue "B TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 817": "OE1" <-> "OE2" Residue "B ASP 822": "OD1" <-> "OD2" Residue "B ASP 837": "OD1" <-> "OD2" Residue "B ASP 857": "OD1" <-> "OD2" Residue "B ASP 882": "OD1" <-> "OD2" Residue "B PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 926": "OD1" <-> "OD2" Residue "B TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 77": "OD1" <-> "OD2" Residue "D ARG 97": "NH1" <-> "NH2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 207": "OD1" <-> "OD2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D PHE 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "D TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 488": "OD1" <-> "OD2" Residue "E GLU 165": "OE1" <-> "OE2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 257": "OD1" <-> "OD2" Residue "E ASP 286": "OD1" <-> "OD2" Residue "E TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 304": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 314": "OD1" <-> "OD2" Residue "E ASP 335": "OD1" <-> "OD2" Residue "E GLU 357": "OE1" <-> "OE2" Residue "E TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 516": "OD1" <-> "OD2" Residue "E ASP 532": "OD1" <-> "OD2" Residue "E GLU 533": "OE1" <-> "OE2" Residue "E GLU 549": "OE1" <-> "OE2" Residue "E TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 635": "OD1" <-> "OD2" Residue "E ASP 649": "OD1" <-> "OD2" Residue "E TYR 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 817": "OE1" <-> "OE2" Residue "E ASP 822": "OD1" <-> "OD2" Residue "E ASP 837": "OD1" <-> "OD2" Residue "E ASP 857": "OD1" <-> "OD2" Residue "E ASP 882": "OD1" <-> "OD2" Residue "E PHE 883": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 898": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 926": "OD1" <-> "OD2" Residue "E TYR 975": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 991": "OD1" <-> "OD2" Residue "E TYR 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22040 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "B" Number of atoms: 7064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 7056 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 871} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 903, 7056 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 871} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 7210 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 79 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, 'PLM:plan-1': 1, '5PL:plan-2': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3843 Classifications: {'peptide': 482} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 460} Chain: "E" Number of atoms: 7064 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 903, 7056 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 871} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 903, 7056 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 31, 'TRANS': 871} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 7210 Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 79 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "D" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'5PL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'5PL:plan-1': 1, 'PLM:plan-1': 1, '5PL:plan-2': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 18.49, per 1000 atoms: 0.84 Number of scatterers: 22040 At special positions: 0 Unit cell: (161.57, 101.65, 134.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 4276 8.00 N 3700 7.00 C 13982 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.96 Conformation dependent library (CDL) restraints added in 6.7 seconds 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 34 sheets defined 18.1% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.56 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 105 through 133 removed outlier: 3.604A pdb=" N TYR A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 167 removed outlier: 4.148A pdb=" N ARG A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 249 through 258 removed outlier: 3.622A pdb=" N LYS A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 381 through 394 Processing helix chain 'A' and resid 398 through 411 removed outlier: 3.802A pdb=" N TYR A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 431 Processing helix chain 'A' and resid 439 through 444 Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 189 through 194 removed outlier: 3.807A pdb=" N THR B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 254 through 257 Processing helix chain 'B' and resid 262 through 271 Processing helix chain 'B' and resid 281 through 287 removed outlier: 3.996A pdb=" N MET B 287 " --> pdb=" O LYS B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 895 through 897 No H-bonds generated for 'chain 'B' and resid 895 through 897' Processing helix chain 'B' and resid 960 through 962 No H-bonds generated for 'chain 'B' and resid 960 through 962' Processing helix chain 'D' and resid 38 through 53 Processing helix chain 'D' and resid 63 through 66 No H-bonds generated for 'chain 'D' and resid 63 through 66' Processing helix chain 'D' and resid 82 through 85 No H-bonds generated for 'chain 'D' and resid 82 through 85' Processing helix chain 'D' and resid 105 through 133 removed outlier: 3.604A pdb=" N TYR D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN D 114 " --> pdb=" O TYR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 167 removed outlier: 4.148A pdb=" N ARG D 166 " --> pdb=" O ARG D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 249 through 258 removed outlier: 3.622A pdb=" N LYS D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 381 through 394 Processing helix chain 'D' and resid 398 through 411 removed outlier: 3.802A pdb=" N TYR D 404 " --> pdb=" O THR D 400 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 405 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 189 through 194 removed outlier: 3.807A pdb=" N THR E 194 " --> pdb=" O ASP E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 199 No H-bonds generated for 'chain 'E' and resid 197 through 199' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 254 through 257 Processing helix chain 'E' and resid 262 through 271 Processing helix chain 'E' and resid 281 through 287 removed outlier: 3.996A pdb=" N MET E 287 " --> pdb=" O LYS E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 298 No H-bonds generated for 'chain 'E' and resid 296 through 298' Processing helix chain 'E' and resid 410 through 416 Processing helix chain 'E' and resid 446 through 452 Processing helix chain 'E' and resid 568 through 570 No H-bonds generated for 'chain 'E' and resid 568 through 570' Processing helix chain 'E' and resid 738 through 740 No H-bonds generated for 'chain 'E' and resid 738 through 740' Processing helix chain 'E' and resid 895 through 897 No H-bonds generated for 'chain 'E' and resid 895 through 897' Processing helix chain 'E' and resid 960 through 962 No H-bonds generated for 'chain 'E' and resid 960 through 962' Processing sheet with id= A, first strand: chain 'A' and resid 71 through 73 Processing sheet with id= B, first strand: chain 'A' and resid 97 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 308 through 311 Processing sheet with id= D, first strand: chain 'A' and resid 342 through 346 removed outlier: 6.079A pdb=" N GLY A 351 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 122 through 125 removed outlier: 7.182A pdb=" N GLN B 227 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET B 203 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE B 225 " --> pdb=" O MET B 203 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL B 205 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 223 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU B 179 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE B 226 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 181 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR B 228 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 149 through 152 Processing sheet with id= G, first strand: chain 'B' and resid 329 through 339 removed outlier: 3.823A pdb=" N GLY B1012 " --> pdb=" O TYR B 975 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 974 " --> pdb=" O TYR B 956 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA B 978 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 884 " --> pdb=" O ARG B 948 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP B 882 " --> pdb=" O LYS B 950 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU B 952 " --> pdb=" O ASP B 880 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP B 880 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 954 " --> pdb=" O SER B 878 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER B 878 " --> pdb=" O LEU B 954 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 864 " --> pdb=" O VAL B 887 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 775 " --> pdb=" O GLY B 763 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 758 " --> pdb=" O ASP B 721 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA B 718 " --> pdb=" O ALA B 709 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR B 628 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY B 660 " --> pdb=" O TRP B 626 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N TRP B 626 " --> pdb=" O GLY B 660 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 541 " --> pdb=" O ALA B 525 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY B 507 " --> pdb=" O GLY B 559 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER B 457 " --> pdb=" O ARG B 396 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG B 396 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN B 465 " --> pdb=" O ASN B 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY B 352 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 390 through 394 Processing sheet with id= I, first strand: chain 'B' and resid 673 through 675 Processing sheet with id= J, first strand: chain 'B' and resid 699 through 701 Processing sheet with id= K, first strand: chain 'B' and resid 731 through 735 Processing sheet with id= L, first strand: chain 'B' and resid 795 through 797 Processing sheet with id= M, first strand: chain 'B' and resid 813 through 816 removed outlier: 3.915A pdb=" N PHE B 813 " --> pdb=" O ILE B 856 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 890 through 892 Processing sheet with id= O, first strand: chain 'B' and resid 946 through 949 removed outlier: 4.526A pdb=" N LEU B 982 " --> pdb=" O LEU B 949 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 751 through 753 removed outlier: 5.921A pdb=" N LYS B 753 " --> pdb=" O ILE B 786 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE B 786 " --> pdb=" O LYS B 753 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 818 through 821 removed outlier: 6.917A pdb=" N LEU B 829 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 71 through 73 Processing sheet with id= S, first strand: chain 'D' and resid 97 through 99 Processing sheet with id= T, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= U, first strand: chain 'D' and resid 342 through 346 removed outlier: 6.079A pdb=" N GLY D 351 " --> pdb=" O VAL D 345 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 122 through 125 removed outlier: 7.182A pdb=" N GLN E 227 " --> pdb=" O GLU E 201 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET E 203 " --> pdb=" O PHE E 225 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N PHE E 225 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL E 205 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL E 223 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 179 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE E 226 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE E 181 " --> pdb=" O ILE E 226 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N THR E 228 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 149 through 152 Processing sheet with id= X, first strand: chain 'E' and resid 329 through 339 removed outlier: 3.823A pdb=" N GLY E1012 " --> pdb=" O TYR E 975 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL E 974 " --> pdb=" O TYR E 956 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 978 " --> pdb=" O LEU E 952 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA E 884 " --> pdb=" O ARG E 948 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP E 882 " --> pdb=" O LYS E 950 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU E 952 " --> pdb=" O ASP E 880 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP E 880 " --> pdb=" O LEU E 952 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU E 954 " --> pdb=" O SER E 878 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER E 878 " --> pdb=" O LEU E 954 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE E 864 " --> pdb=" O VAL E 887 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA E 775 " --> pdb=" O GLY E 763 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP E 758 " --> pdb=" O ASP E 721 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA E 718 " --> pdb=" O ALA E 709 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR E 628 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY E 660 " --> pdb=" O TRP E 626 " (cutoff:3.500A) removed outlier: 10.522A pdb=" N TRP E 626 " --> pdb=" O GLY E 660 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET E 541 " --> pdb=" O ALA E 525 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLY E 507 " --> pdb=" O GLY E 559 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER E 457 " --> pdb=" O ARG E 396 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ARG E 396 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASN E 465 " --> pdb=" O ASN E 388 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY E 352 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 390 through 394 Processing sheet with id= Z, first strand: chain 'E' and resid 673 through 675 Processing sheet with id= AA, first strand: chain 'E' and resid 699 through 701 Processing sheet with id= AB, first strand: chain 'E' and resid 731 through 735 Processing sheet with id= AC, first strand: chain 'E' and resid 795 through 797 Processing sheet with id= AD, first strand: chain 'E' and resid 813 through 816 removed outlier: 3.915A pdb=" N PHE E 813 " --> pdb=" O ILE E 856 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 890 through 892 Processing sheet with id= AF, first strand: chain 'E' and resid 946 through 949 removed outlier: 4.526A pdb=" N LEU E 982 " --> pdb=" O LEU E 949 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 751 through 753 removed outlier: 5.921A pdb=" N LYS E 753 " --> pdb=" O ILE E 786 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE E 786 " --> pdb=" O LYS E 753 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 818 through 821 removed outlier: 6.917A pdb=" N LEU E 829 " --> pdb=" O ALA E 819 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.97 Time building geometry restraints manager: 8.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3726 1.30 - 1.42: 6106 1.42 - 1.55: 12510 1.55 - 1.68: 38 1.68 - 1.80: 158 Bond restraints: 22538 Sorted by residual: bond pdb=" CA TYR B 405 " pdb=" CB TYR B 405 " ideal model delta sigma weight residual 1.526 1.473 0.053 1.76e-02 3.23e+03 9.07e+00 bond pdb=" CA TYR E 405 " pdb=" CB TYR E 405 " ideal model delta sigma weight residual 1.526 1.473 0.053 1.76e-02 3.23e+03 9.07e+00 bond pdb=" C GLY B 665 " pdb=" N ASN B 666 " ideal model delta sigma weight residual 1.333 1.289 0.044 1.55e-02 4.16e+03 7.98e+00 bond pdb=" C GLY E 665 " pdb=" N ASN E 666 " ideal model delta sigma weight residual 1.333 1.289 0.044 1.55e-02 4.16e+03 7.98e+00 bond pdb=" C ASN E 498 " pdb=" N ASN E 499 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.61e-02 3.86e+03 4.78e+00 ... (remaining 22533 not shown) Histogram of bond angle deviations from ideal: 96.89 - 104.44: 344 104.44 - 112.00: 10006 112.00 - 119.56: 8448 119.56 - 127.12: 11498 127.12 - 134.68: 218 Bond angle restraints: 30514 Sorted by residual: angle pdb=" CBR 5PL A 601 " pdb=" CBS 5PL A 601 " pdb=" CBT 5PL A 601 " ideal model delta sigma weight residual 131.61 109.95 21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" CBR 5PL D 601 " pdb=" CBS 5PL D 601 " pdb=" CBT 5PL D 601 " ideal model delta sigma weight residual 131.61 109.95 21.66 3.00e+00 1.11e-01 5.21e+01 angle pdb=" N GLU D 422 " pdb=" CA GLU D 422 " pdb=" C GLU D 422 " ideal model delta sigma weight residual 114.04 107.41 6.63 1.24e+00 6.50e-01 2.86e+01 angle pdb=" N GLU A 422 " pdb=" CA GLU A 422 " pdb=" C GLU A 422 " ideal model delta sigma weight residual 114.04 107.41 6.63 1.24e+00 6.50e-01 2.86e+01 angle pdb=" C PHE E 712 " pdb=" N ASN E 713 " pdb=" CA ASN E 713 " ideal model delta sigma weight residual 121.54 131.57 -10.03 1.91e+00 2.74e-01 2.76e+01 ... (remaining 30509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 11958 17.79 - 35.58: 1164 35.58 - 53.37: 200 53.37 - 71.16: 26 71.16 - 88.95: 8 Dihedral angle restraints: 13356 sinusoidal: 5256 harmonic: 8100 Sorted by residual: dihedral pdb=" CA ASN E 713 " pdb=" C ASN E 713 " pdb=" N ASN E 714 " pdb=" CA ASN E 714 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ASN B 713 " pdb=" C ASN B 713 " pdb=" N ASN B 714 " pdb=" CA ASN B 714 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 dihedral pdb=" CA ALA B 292 " pdb=" C ALA B 292 " pdb=" N GLU B 293 " pdb=" CA GLU B 293 " ideal model delta harmonic sigma weight residual 180.00 150.95 29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 13353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2456 0.062 - 0.125: 664 0.125 - 0.187: 102 0.187 - 0.250: 14 0.250 - 0.312: 8 Chirality restraints: 3244 Sorted by residual: chirality pdb=" CA PHE B 790 " pdb=" N PHE B 790 " pdb=" C PHE B 790 " pdb=" CB PHE B 790 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA PHE E 790 " pdb=" N PHE E 790 " pdb=" C PHE E 790 " pdb=" CB PHE E 790 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CG LEU B 506 " pdb=" CB LEU B 506 " pdb=" CD1 LEU B 506 " pdb=" CD2 LEU B 506 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3241 not shown) Planarity restraints: 3996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 82 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO D 83 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO D 83 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 83 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 82 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 83 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 254 " -0.046 5.00e-02 4.00e+02 6.83e-02 7.46e+00 pdb=" N PRO E 255 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 255 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 255 " -0.039 5.00e-02 4.00e+02 ... (remaining 3993 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2732 2.74 - 3.28: 18141 3.28 - 3.82: 34792 3.82 - 4.36: 42214 4.36 - 4.90: 78802 Nonbonded interactions: 176681 Sorted by model distance: nonbonded pdb=" OG SER B 377 " pdb=" OH TYR E 347 " model vdw 2.206 2.440 nonbonded pdb=" OH TYR B 347 " pdb=" OG SER E 377 " model vdw 2.206 2.440 nonbonded pdb=" O SER A 437 " pdb=" OG SER A 437 " model vdw 2.294 2.440 nonbonded pdb=" O SER D 437 " pdb=" OG SER D 437 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR E 405 " pdb=" OD1 ASP E 895 " model vdw 2.298 2.440 ... (remaining 176676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 115 through 721 or resid 723 through 1017)) selection = (chain 'E' and (resid 115 through 721 or resid 723 through 1017)) } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.020 Extract box with map and model: 3.400 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 69.260 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 0.082 22538 Z= 0.600 Angle : 0.961 21.659 30514 Z= 0.519 Chirality : 0.059 0.312 3244 Planarity : 0.006 0.071 3996 Dihedral : 14.107 88.945 8212 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.26 % Allowed : 9.12 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.64 (0.13), residues: 2786 helix: -2.81 (0.15), residues: 580 sheet: -1.45 (0.17), residues: 836 loop : -2.86 (0.13), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 874 HIS 0.009 0.002 HIS A 451 PHE 0.034 0.003 PHE E1017 TYR 0.019 0.003 TYR E 587 ARG 0.005 0.001 ARG E 617 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 331 time to evaluate : 2.717 Fit side-chains REVERT: A 22 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8039 (pp) REVERT: A 164 MET cc_start: 0.8088 (mmm) cc_final: 0.7718 (mmm) REVERT: A 181 LYS cc_start: 0.8903 (tttt) cc_final: 0.8606 (tttm) REVERT: A 251 LYS cc_start: 0.8392 (mttt) cc_final: 0.7902 (mtmm) REVERT: A 255 ASP cc_start: 0.7678 (m-30) cc_final: 0.7298 (m-30) REVERT: A 410 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8724 (ttpt) REVERT: A 494 GLN cc_start: 0.8690 (tt0) cc_final: 0.8488 (tt0) REVERT: B 271 LYS cc_start: 0.8346 (mttp) cc_final: 0.8043 (mtmt) REVERT: B 353 TYR cc_start: 0.8260 (p90) cc_final: 0.6813 (p90) REVERT: B 564 LYS cc_start: 0.8572 (mptt) cc_final: 0.8343 (mmmt) REVERT: B 604 MET cc_start: 0.8225 (ttt) cc_final: 0.8025 (ttp) REVERT: B 822 ASP cc_start: 0.7993 (t0) cc_final: 0.7665 (t0) REVERT: D 22 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8091 (pp) REVERT: D 100 GLU cc_start: 0.7106 (mt-10) cc_final: 0.6827 (mt-10) REVERT: D 137 LYS cc_start: 0.8499 (mmtt) cc_final: 0.7975 (mtpt) REVERT: D 223 ASN cc_start: 0.8907 (m-40) cc_final: 0.8641 (m-40) REVERT: D 251 LYS cc_start: 0.8149 (mttt) cc_final: 0.7541 (mttm) REVERT: D 255 ASP cc_start: 0.7768 (m-30) cc_final: 0.7452 (m-30) REVERT: D 410 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8657 (ttpt) REVERT: E 308 LYS cc_start: 0.8631 (ttmm) cc_final: 0.8286 (ttpp) REVERT: E 353 TYR cc_start: 0.8003 (p90) cc_final: 0.7387 (p90) REVERT: E 404 LYS cc_start: 0.8361 (mppt) cc_final: 0.8062 (mptt) REVERT: E 564 LYS cc_start: 0.8099 (mptt) cc_final: 0.7804 (mmtt) REVERT: E 890 TRP cc_start: 0.8760 (m100) cc_final: 0.8479 (m100) outliers start: 6 outliers final: 3 residues processed: 335 average time/residue: 0.3505 time to fit residues: 181.5546 Evaluate side-chains 265 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 260 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain E residue 659 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 234 optimal weight: 2.9990 chunk 210 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 162 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 133 ASN A 449 ASN B 137 ASN B 252 ASN B 278 ASN B 279 GLN B 298 ASN B 316 ASN B 374 ASN B 427 ASN B 463 ASN B 748 ASN B 847 GLN D 133 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN E 252 ASN E 278 ASN E 279 GLN E 298 ASN E 316 ASN E 374 ASN E 427 ASN E 463 ASN E 748 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22538 Z= 0.181 Angle : 0.551 8.544 30514 Z= 0.291 Chirality : 0.043 0.179 3244 Planarity : 0.004 0.045 3996 Dihedral : 6.473 66.821 3129 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.89 % Allowed : 11.23 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 2786 helix: -1.01 (0.21), residues: 558 sheet: -0.97 (0.17), residues: 834 loop : -2.37 (0.14), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 161 HIS 0.003 0.001 HIS D 451 PHE 0.012 0.001 PHE B 791 TYR 0.015 0.001 TYR E1003 ARG 0.004 0.000 ARG E 490 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 320 time to evaluate : 2.439 Fit side-chains REVERT: A 164 MET cc_start: 0.7846 (mmm) cc_final: 0.7566 (mmm) REVERT: A 251 LYS cc_start: 0.8256 (mttt) cc_final: 0.7935 (mttm) REVERT: A 255 ASP cc_start: 0.7603 (m-30) cc_final: 0.7342 (m-30) REVERT: A 410 LYS cc_start: 0.8955 (ttpp) cc_final: 0.8744 (ttpt) REVERT: B 353 TYR cc_start: 0.8414 (p90) cc_final: 0.7040 (p90) REVERT: B 376 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: B 551 ASP cc_start: 0.7552 (t70) cc_final: 0.7351 (t70) REVERT: B 761 LEU cc_start: 0.8824 (pp) cc_final: 0.8622 (pp) REVERT: B 984 VAL cc_start: 0.8611 (OUTLIER) cc_final: 0.8378 (t) REVERT: D 251 LYS cc_start: 0.8097 (mttt) cc_final: 0.7773 (mttm) REVERT: D 335 ASP cc_start: 0.8145 (t0) cc_final: 0.7942 (t70) REVERT: D 410 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8672 (ttpt) REVERT: E 152 MET cc_start: 0.8498 (mtp) cc_final: 0.8277 (tpp) REVERT: E 308 LYS cc_start: 0.8610 (ttmm) cc_final: 0.8265 (ttpp) REVERT: E 353 TYR cc_start: 0.8352 (p90) cc_final: 0.7042 (p90) outliers start: 44 outliers final: 26 residues processed: 339 average time/residue: 0.3532 time to fit residues: 189.2535 Evaluate side-chains 298 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 270 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 847 GLN Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 210 optimal weight: 7.9990 chunk 171 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 225 optimal weight: 2.9990 chunk 250 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN A 449 ASN B 252 ASN B 427 ASN B 778 ASN B 847 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22538 Z= 0.261 Angle : 0.584 10.252 30514 Z= 0.307 Chirality : 0.044 0.201 3244 Planarity : 0.004 0.041 3996 Dihedral : 6.339 70.255 3127 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.80 % Allowed : 13.21 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.15), residues: 2786 helix: -0.38 (0.22), residues: 556 sheet: -0.78 (0.17), residues: 840 loop : -2.15 (0.14), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 161 HIS 0.004 0.001 HIS A 451 PHE 0.016 0.001 PHE B 990 TYR 0.020 0.001 TYR E1003 ARG 0.006 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 286 time to evaluate : 2.769 Fit side-chains REVERT: A 22 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8125 (pp) REVERT: A 164 MET cc_start: 0.8001 (mmm) cc_final: 0.7604 (mmm) REVERT: A 251 LYS cc_start: 0.8276 (mttt) cc_final: 0.7907 (mttm) REVERT: A 255 ASP cc_start: 0.7728 (m-30) cc_final: 0.7432 (m-30) REVERT: B 353 TYR cc_start: 0.8547 (p90) cc_final: 0.7078 (p90) REVERT: B 376 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: B 551 ASP cc_start: 0.7683 (t70) cc_final: 0.7338 (t70) REVERT: B 568 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8661 (mp) REVERT: D 251 LYS cc_start: 0.8241 (mttt) cc_final: 0.7984 (mttm) REVERT: D 410 LYS cc_start: 0.8931 (ttpp) cc_final: 0.8699 (ttpt) REVERT: E 308 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8339 (ttpp) REVERT: E 353 TYR cc_start: 0.8498 (p90) cc_final: 0.7163 (p90) REVERT: E 388 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.8072 (p0) REVERT: E 568 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8643 (mp) outliers start: 65 outliers final: 48 residues processed: 320 average time/residue: 0.3179 time to fit residues: 162.0622 Evaluate side-chains 325 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 249 optimal weight: 4.9990 chunk 190 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 169 optimal weight: 0.9990 chunk 253 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN B 252 ASN B 427 ASN D 449 ASN E 778 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22538 Z= 0.249 Angle : 0.562 11.369 30514 Z= 0.295 Chirality : 0.044 0.177 3244 Planarity : 0.003 0.037 3996 Dihedral : 6.150 72.020 3127 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.14 % Allowed : 13.81 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 2786 helix: -0.12 (0.23), residues: 558 sheet: -0.68 (0.17), residues: 836 loop : -1.99 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 161 HIS 0.004 0.001 HIS B 535 PHE 0.012 0.001 PHE B 990 TYR 0.017 0.001 TYR B1003 ARG 0.005 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 286 time to evaluate : 2.622 Fit side-chains REVERT: A 22 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8196 (pp) REVERT: A 164 MET cc_start: 0.7949 (mmm) cc_final: 0.7536 (mmm) REVERT: A 251 LYS cc_start: 0.8273 (mttt) cc_final: 0.7956 (mttm) REVERT: A 255 ASP cc_start: 0.7746 (m-30) cc_final: 0.7444 (m-30) REVERT: B 353 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7136 (p90) REVERT: B 376 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7345 (tp30) REVERT: B 388 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8014 (p0) REVERT: B 543 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.8109 (t-90) REVERT: B 551 ASP cc_start: 0.7441 (t70) cc_final: 0.7036 (t70) REVERT: B 568 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8647 (mp) REVERT: D 22 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8139 (pp) REVERT: D 251 LYS cc_start: 0.8268 (mttt) cc_final: 0.8015 (mttm) REVERT: E 308 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8381 (ttpp) REVERT: E 353 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7077 (p90) REVERT: E 388 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8094 (p0) REVERT: E 543 HIS cc_start: 0.8728 (OUTLIER) cc_final: 0.8053 (t-90) REVERT: E 568 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8619 (mp) REVERT: E 653 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8237 (mttt) outliers start: 73 outliers final: 52 residues processed: 323 average time/residue: 0.3219 time to fit residues: 166.6858 Evaluate side-chains 341 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 277 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 400 ASP Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 223 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 ASN D 40 GLN D 449 ASN E 523 ASN E 778 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 22538 Z= 0.379 Angle : 0.622 11.747 30514 Z= 0.326 Chirality : 0.046 0.192 3244 Planarity : 0.004 0.044 3996 Dihedral : 6.454 72.840 3127 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.74 % Allowed : 14.07 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.15), residues: 2786 helix: -0.14 (0.23), residues: 558 sheet: -0.73 (0.18), residues: 812 loop : -1.95 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.004 0.001 HIS D 451 PHE 0.015 0.002 PHE E1017 TYR 0.022 0.002 TYR B1003 ARG 0.006 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 272 time to evaluate : 2.558 Fit side-chains REVERT: A 22 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8284 (pp) REVERT: A 164 MET cc_start: 0.8049 (mmm) cc_final: 0.7551 (mmm) REVERT: A 251 LYS cc_start: 0.8379 (mttt) cc_final: 0.8087 (mttm) REVERT: A 255 ASP cc_start: 0.7788 (m-30) cc_final: 0.7546 (m-30) REVERT: B 152 MET cc_start: 0.8779 (tpp) cc_final: 0.8525 (tpp) REVERT: B 353 TYR cc_start: 0.8746 (OUTLIER) cc_final: 0.7228 (p90) REVERT: B 376 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: B 543 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8194 (t-90) REVERT: B 551 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7084 (t70) REVERT: B 568 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8670 (mp) REVERT: B 715 ARG cc_start: 0.7413 (mtm180) cc_final: 0.7156 (mtp-110) REVERT: D 22 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8193 (pp) REVERT: D 251 LYS cc_start: 0.8293 (mttt) cc_final: 0.8075 (mttm) REVERT: E 152 MET cc_start: 0.8826 (tpp) cc_final: 0.8593 (tpp) REVERT: E 308 LYS cc_start: 0.8910 (ttmm) cc_final: 0.8437 (ttpp) REVERT: E 353 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7244 (p90) REVERT: E 543 HIS cc_start: 0.8824 (OUTLIER) cc_final: 0.8230 (t-90) REVERT: E 568 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8641 (mp) outliers start: 87 outliers final: 67 residues processed: 321 average time/residue: 0.3137 time to fit residues: 160.4367 Evaluate side-chains 340 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 263 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 90 optimal weight: 9.9990 chunk 241 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 268 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN E 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22538 Z= 0.393 Angle : 0.628 12.595 30514 Z= 0.329 Chirality : 0.046 0.177 3244 Planarity : 0.004 0.042 3996 Dihedral : 6.539 73.322 3127 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 3.92 % Allowed : 14.85 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.15), residues: 2786 helix: -0.14 (0.22), residues: 558 sheet: -0.72 (0.18), residues: 810 loop : -1.92 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.004 0.001 HIS D 451 PHE 0.015 0.002 PHE E1017 TYR 0.021 0.002 TYR B1003 ARG 0.006 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 262 time to evaluate : 2.865 Fit side-chains REVERT: A 22 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8189 (pp) REVERT: A 164 MET cc_start: 0.8046 (mmm) cc_final: 0.7566 (mmm) REVERT: A 251 LYS cc_start: 0.8381 (mttt) cc_final: 0.8079 (mttm) REVERT: A 255 ASP cc_start: 0.7798 (m-30) cc_final: 0.7534 (m-30) REVERT: B 152 MET cc_start: 0.8798 (tpp) cc_final: 0.8516 (tpp) REVERT: B 353 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.7226 (p90) REVERT: B 376 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: B 543 HIS cc_start: 0.8834 (OUTLIER) cc_final: 0.8189 (t-90) REVERT: B 551 ASP cc_start: 0.7401 (t70) cc_final: 0.7009 (t70) REVERT: B 568 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8662 (mp) REVERT: B 715 ARG cc_start: 0.7363 (mtm180) cc_final: 0.7142 (mtp-110) REVERT: D 22 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8138 (pp) REVERT: D 164 MET cc_start: 0.8024 (mtp) cc_final: 0.7729 (mtp) REVERT: E 152 MET cc_start: 0.8798 (tpp) cc_final: 0.8520 (tpp) REVERT: E 308 LYS cc_start: 0.8961 (ttmm) cc_final: 0.8401 (ttpp) REVERT: E 353 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7231 (p90) REVERT: E 543 HIS cc_start: 0.8821 (OUTLIER) cc_final: 0.8156 (t-90) REVERT: E 568 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8597 (mp) outliers start: 91 outliers final: 69 residues processed: 314 average time/residue: 0.3106 time to fit residues: 156.3029 Evaluate side-chains 335 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 257 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 487 THR Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 20.0000 chunk 30 optimal weight: 0.7980 chunk 153 optimal weight: 0.9990 chunk 196 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 150 optimal weight: 10.0000 chunk 267 optimal weight: 0.5980 chunk 167 optimal weight: 3.9990 chunk 163 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 449 ASN E 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22538 Z= 0.196 Angle : 0.536 11.986 30514 Z= 0.282 Chirality : 0.043 0.166 3244 Planarity : 0.003 0.037 3996 Dihedral : 5.977 70.472 3127 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.61 % Allowed : 15.58 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.15), residues: 2786 helix: 0.29 (0.23), residues: 546 sheet: -0.55 (0.18), residues: 810 loop : -1.86 (0.15), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 161 HIS 0.004 0.001 HIS D 451 PHE 0.010 0.001 PHE E 790 TYR 0.015 0.001 TYR B 215 ARG 0.003 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 287 time to evaluate : 2.679 Fit side-chains REVERT: A 22 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8256 (pp) REVERT: A 164 MET cc_start: 0.7886 (mmm) cc_final: 0.7499 (mmm) REVERT: A 251 LYS cc_start: 0.8255 (mttt) cc_final: 0.7963 (mttm) REVERT: A 255 ASP cc_start: 0.7710 (m-30) cc_final: 0.7439 (m-30) REVERT: B 152 MET cc_start: 0.8741 (tpp) cc_final: 0.8475 (tpp) REVERT: B 353 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7212 (p90) REVERT: B 376 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7376 (tp30) REVERT: B 388 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8285 (p0) REVERT: B 551 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7040 (t70) REVERT: B 568 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8654 (mp) REVERT: D 22 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8136 (pp) REVERT: D 212 ARG cc_start: 0.8173 (mmp-170) cc_final: 0.7888 (mmp-170) REVERT: E 152 MET cc_start: 0.8773 (tpp) cc_final: 0.8506 (tpp) REVERT: E 308 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8520 (ttpp) REVERT: E 353 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7079 (p90) REVERT: E 543 HIS cc_start: 0.8719 (OUTLIER) cc_final: 0.8071 (t-90) REVERT: E 568 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8624 (mp) outliers start: 84 outliers final: 58 residues processed: 330 average time/residue: 0.3198 time to fit residues: 169.2323 Evaluate side-chains 348 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 280 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 165 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 52 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 182 optimal weight: 0.4980 chunk 132 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 ASN D 118 GLN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 22538 Z= 0.312 Angle : 0.590 12.307 30514 Z= 0.309 Chirality : 0.045 0.174 3244 Planarity : 0.004 0.039 3996 Dihedral : 6.165 72.981 3127 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.70 % Allowed : 15.62 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 2786 helix: 0.27 (0.23), residues: 546 sheet: -0.65 (0.18), residues: 820 loop : -1.86 (0.15), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 161 HIS 0.004 0.001 HIS D 451 PHE 0.013 0.001 PHE B 990 TYR 0.019 0.002 TYR B1003 ARG 0.005 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 275 time to evaluate : 2.557 Fit side-chains REVERT: A 22 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8286 (pp) REVERT: A 164 MET cc_start: 0.7976 (mmm) cc_final: 0.7540 (mmm) REVERT: A 251 LYS cc_start: 0.8284 (mttt) cc_final: 0.7987 (mttm) REVERT: A 255 ASP cc_start: 0.7733 (m-30) cc_final: 0.7463 (m-30) REVERT: B 152 MET cc_start: 0.8776 (tpp) cc_final: 0.8491 (tpp) REVERT: B 353 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.7197 (p90) REVERT: B 376 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: B 543 HIS cc_start: 0.8827 (OUTLIER) cc_final: 0.8212 (t-90) REVERT: B 551 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7044 (t70) REVERT: B 568 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8664 (mp) REVERT: D 22 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8171 (pp) REVERT: D 212 ARG cc_start: 0.8197 (mmp-170) cc_final: 0.7907 (mmp-170) REVERT: E 152 MET cc_start: 0.8789 (tpp) cc_final: 0.8500 (tpp) REVERT: E 308 LYS cc_start: 0.8946 (ttmm) cc_final: 0.8492 (ttpp) REVERT: E 353 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7230 (p90) REVERT: E 543 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8123 (t-90) REVERT: E 568 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8630 (mp) outliers start: 86 outliers final: 70 residues processed: 321 average time/residue: 0.3199 time to fit residues: 165.1286 Evaluate side-chains 355 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 275 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 267 ASP Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 243 optimal weight: 0.8980 chunk 256 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 196 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 236 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22538 Z= 0.221 Angle : 0.548 12.347 30514 Z= 0.287 Chirality : 0.043 0.167 3244 Planarity : 0.003 0.037 3996 Dihedral : 5.923 71.758 3127 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.57 % Allowed : 16.01 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 2786 helix: 0.39 (0.23), residues: 548 sheet: -0.52 (0.18), residues: 810 loop : -1.82 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 161 HIS 0.004 0.001 HIS D 451 PHE 0.011 0.001 PHE E 990 TYR 0.018 0.001 TYR B 215 ARG 0.004 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 285 time to evaluate : 2.415 Fit side-chains REVERT: A 22 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8261 (pp) REVERT: A 164 MET cc_start: 0.7937 (mmm) cc_final: 0.7522 (mmm) REVERT: A 251 LYS cc_start: 0.8248 (mttt) cc_final: 0.7969 (mttm) REVERT: B 152 MET cc_start: 0.8741 (tpp) cc_final: 0.8466 (tpp) REVERT: B 353 TYR cc_start: 0.8693 (OUTLIER) cc_final: 0.7161 (p90) REVERT: B 376 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: B 388 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7947 (p0) REVERT: B 543 HIS cc_start: 0.8747 (OUTLIER) cc_final: 0.8171 (t-90) REVERT: B 551 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7002 (t70) REVERT: B 568 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8649 (mp) REVERT: D 22 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8139 (pp) REVERT: D 162 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8865 (tpp-160) REVERT: D 212 ARG cc_start: 0.8173 (mmp-170) cc_final: 0.7883 (mmp-170) REVERT: E 152 MET cc_start: 0.8759 (tpp) cc_final: 0.8472 (tpp) REVERT: E 308 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8530 (ttpp) REVERT: E 353 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7015 (p90) REVERT: E 543 HIS cc_start: 0.8745 (OUTLIER) cc_final: 0.8136 (t-90) REVERT: E 568 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8633 (mp) outliers start: 83 outliers final: 67 residues processed: 331 average time/residue: 0.3229 time to fit residues: 172.1571 Evaluate side-chains 357 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 278 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 163 optimal weight: 8.9990 chunk 264 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 220 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22538 Z= 0.262 Angle : 0.567 12.459 30514 Z= 0.297 Chirality : 0.044 0.169 3244 Planarity : 0.003 0.052 3996 Dihedral : 5.979 72.846 3127 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.61 % Allowed : 15.96 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 2786 helix: 0.41 (0.23), residues: 546 sheet: -0.56 (0.18), residues: 816 loop : -1.79 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 161 HIS 0.004 0.001 HIS D 451 PHE 0.011 0.001 PHE B 779 TYR 0.019 0.001 TYR B 215 ARG 0.004 0.000 ARG B 490 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5572 Ramachandran restraints generated. 2786 Oldfield, 0 Emsley, 2786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 278 time to evaluate : 2.442 Fit side-chains REVERT: A 22 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8304 (pp) REVERT: A 164 MET cc_start: 0.7958 (mmm) cc_final: 0.7521 (mmm) REVERT: A 251 LYS cc_start: 0.8227 (mttt) cc_final: 0.8017 (mttm) REVERT: B 152 MET cc_start: 0.8750 (tpp) cc_final: 0.8461 (tpp) REVERT: B 353 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.7191 (p90) REVERT: B 376 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: B 388 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 543 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8185 (t-90) REVERT: B 551 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7016 (t70) REVERT: B 568 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8666 (mp) REVERT: D 22 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8162 (pp) REVERT: D 162 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8855 (tpp-160) REVERT: D 212 ARG cc_start: 0.8194 (mmp-170) cc_final: 0.7896 (mmp-170) REVERT: E 152 MET cc_start: 0.8763 (tpp) cc_final: 0.8470 (tpp) REVERT: E 308 LYS cc_start: 0.8931 (ttmm) cc_final: 0.8539 (ttpp) REVERT: E 353 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.7137 (p90) REVERT: E 543 HIS cc_start: 0.8750 (OUTLIER) cc_final: 0.8161 (t-90) REVERT: E 568 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8667 (mp) outliers start: 84 outliers final: 68 residues processed: 325 average time/residue: 0.3104 time to fit residues: 161.5083 Evaluate side-chains 357 residues out of total 2328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 277 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 162 ARG Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 349 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 382 TRP Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 543 HIS Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 553 ILE Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 629 SER Chi-restraints excluded: chain B residue 653 LYS Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 721 ASP Chi-restraints excluded: chain B residue 765 ILE Chi-restraints excluded: chain B residue 776 SER Chi-restraints excluded: chain B residue 887 VAL Chi-restraints excluded: chain B residue 916 ASN Chi-restraints excluded: chain B residue 927 VAL Chi-restraints excluded: chain B residue 957 VAL Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 998 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 138 ASN Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 475 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 353 TYR Chi-restraints excluded: chain E residue 382 TRP Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 389 LEU Chi-restraints excluded: chain E residue 414 VAL Chi-restraints excluded: chain E residue 429 ASP Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 522 THR Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 543 HIS Chi-restraints excluded: chain E residue 553 ILE Chi-restraints excluded: chain E residue 568 LEU Chi-restraints excluded: chain E residue 607 ASP Chi-restraints excluded: chain E residue 609 SER Chi-restraints excluded: chain E residue 610 VAL Chi-restraints excluded: chain E residue 613 ASP Chi-restraints excluded: chain E residue 629 SER Chi-restraints excluded: chain E residue 653 LYS Chi-restraints excluded: chain E residue 659 THR Chi-restraints excluded: chain E residue 721 ASP Chi-restraints excluded: chain E residue 761 LEU Chi-restraints excluded: chain E residue 765 ILE Chi-restraints excluded: chain E residue 776 SER Chi-restraints excluded: chain E residue 869 SER Chi-restraints excluded: chain E residue 887 VAL Chi-restraints excluded: chain E residue 913 MET Chi-restraints excluded: chain E residue 916 ASN Chi-restraints excluded: chain E residue 927 VAL Chi-restraints excluded: chain E residue 957 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 9 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 175 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 chunk 67 optimal weight: 0.0970 chunk 203 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 ASN ** D 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 778 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.114788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.092465 restraints weight = 35268.797| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.25 r_work: 0.2678 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22538 Z= 0.222 Angle : 0.546 12.467 30514 Z= 0.286 Chirality : 0.043 0.165 3244 Planarity : 0.003 0.060 3996 Dihedral : 5.857 72.127 3127 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.53 % Allowed : 16.22 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.15), residues: 2786 helix: 0.48 (0.24), residues: 546 sheet: -0.50 (0.18), residues: 814 loop : -1.76 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 161 HIS 0.004 0.001 HIS D 451 PHE 0.011 0.001 PHE E 990 TYR 0.019 0.001 TYR B 215 ARG 0.004 0.000 ARG B 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4650.09 seconds wall clock time: 85 minutes 41.38 seconds (5141.38 seconds total)