Starting phenix.real_space_refine on Sat Feb 24 15:44:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baa_7073/02_2024/6baa_7073_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baa_7073/02_2024/6baa_7073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baa_7073/02_2024/6baa_7073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baa_7073/02_2024/6baa_7073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baa_7073/02_2024/6baa_7073_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6baa_7073/02_2024/6baa_7073_updated.pdb" } resolution = 3.63 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= 0.167 sd= 1.369 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 188 5.16 5 Cl 4 4.86 5 C 28728 2.51 5 N 7884 2.21 5 O 8036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 702": "NH1" <-> "NH2" Residue "E PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 702": "NH1" <-> "NH2" Residue "F PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 702": "NH1" <-> "NH2" Residue "G PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 702": "NH1" <-> "NH2" Residue "H PHE 1560": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44852 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2507 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 306} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2507 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 306} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2507 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 306} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2507 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 306} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 8642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 8642 Classifications: {'peptide': 1317} Incomplete info: {'truncation_to_alanine': 531} Link IDs: {'PTRANS': 41, 'TRANS': 1275} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1814 Unresolved non-hydrogen angles: 2312 Unresolved non-hydrogen dihedrals: 1455 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 31, 'HIS:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 6, 'ASP:plan': 33, 'PHE:plan': 26, 'GLU:plan': 30, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 882 Chain: "F" Number of atoms: 8642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 8642 Classifications: {'peptide': 1317} Incomplete info: {'truncation_to_alanine': 531} Link IDs: {'PTRANS': 41, 'TRANS': 1275} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1814 Unresolved non-hydrogen angles: 2312 Unresolved non-hydrogen dihedrals: 1455 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 31, 'HIS:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 6, 'ASP:plan': 33, 'PHE:plan': 26, 'GLU:plan': 30, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 882 Chain: "G" Number of atoms: 8642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 8642 Classifications: {'peptide': 1317} Incomplete info: {'truncation_to_alanine': 531} Link IDs: {'PTRANS': 41, 'TRANS': 1275} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1814 Unresolved non-hydrogen angles: 2312 Unresolved non-hydrogen dihedrals: 1455 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 31, 'HIS:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 6, 'ASP:plan': 33, 'PHE:plan': 26, 'GLU:plan': 30, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 882 Chain: "H" Number of atoms: 8642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 8642 Classifications: {'peptide': 1317} Incomplete info: {'truncation_to_alanine': 531} Link IDs: {'PTRANS': 41, 'TRANS': 1275} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1814 Unresolved non-hydrogen angles: 2312 Unresolved non-hydrogen dihedrals: 1455 Unresolved non-hydrogen chiralities: 225 Planarities with less than four sites: {'GLN:plan1': 31, 'HIS:plan': 13, 'TYR:plan': 6, 'ASN:plan1': 19, 'TRP:plan': 6, 'ASP:plan': 33, 'PHE:plan': 26, 'GLU:plan': 30, 'ARG:plan': 33} Unresolved non-hydrogen planarities: 882 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GBM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 22.16, per 1000 atoms: 0.49 Number of scatterers: 44852 At special positions: 0 Unit cell: (233.415, 233.415, 141.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 188 16.00 P 12 15.00 O 8036 8.00 N 7884 7.00 C 28728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.02 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.02 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.02 Simple disulfide: pdb=" SG CYS E 6 " - pdb=" SG CYS E 26 " distance=2.04 Simple disulfide: pdb=" SG CYS F 6 " - pdb=" SG CYS F 26 " distance=2.04 Simple disulfide: pdb=" SG CYS G 6 " - pdb=" SG CYS G 26 " distance=2.04 Simple disulfide: pdb=" SG CYS H 6 " - pdb=" SG CYS H 26 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.39 Conformation dependent library (CDL) restraints added in 10.1 seconds 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 256 helices and 36 sheets defined 60.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.72 Creating SS restraints... Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 68 through 97 removed outlier: 3.635A pdb=" N VAL A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 102 No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 170 Processing helix chain 'A' and resid 174 through 180 Processing helix chain 'A' and resid 274 through 277 No H-bonds generated for 'chain 'A' and resid 274 through 277' Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 54 through 57 No H-bonds generated for 'chain 'B' and resid 54 through 57' Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 68 through 97 removed outlier: 3.635A pdb=" N VAL B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 143 through 170 Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 274 through 277 No H-bonds generated for 'chain 'B' and resid 274 through 277' Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 330 through 332 No H-bonds generated for 'chain 'B' and resid 330 through 332' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 68 through 97 removed outlier: 3.635A pdb=" N VAL C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 170 Processing helix chain 'C' and resid 174 through 180 Processing helix chain 'C' and resid 274 through 277 No H-bonds generated for 'chain 'C' and resid 274 through 277' Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 330 through 332 No H-bonds generated for 'chain 'C' and resid 330 through 332' Processing helix chain 'C' and resid 346 through 351 Processing helix chain 'D' and resid 54 through 57 No H-bonds generated for 'chain 'D' and resid 54 through 57' Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 68 through 97 removed outlier: 3.635A pdb=" N VAL D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 102 No H-bonds generated for 'chain 'D' and resid 99 through 102' Processing helix chain 'D' and resid 117 through 128 Processing helix chain 'D' and resid 143 through 170 Processing helix chain 'D' and resid 174 through 180 Processing helix chain 'D' and resid 274 through 277 No H-bonds generated for 'chain 'D' and resid 274 through 277' Processing helix chain 'D' and resid 306 through 308 No H-bonds generated for 'chain 'D' and resid 306 through 308' Processing helix chain 'D' and resid 330 through 332 No H-bonds generated for 'chain 'D' and resid 330 through 332' Processing helix chain 'D' and resid 346 through 351 Processing helix chain 'E' and resid 14 through 17 No H-bonds generated for 'chain 'E' and resid 14 through 17' Processing helix chain 'E' and resid 27 through 56 removed outlier: 3.506A pdb=" N VAL E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Proline residue: E 35 - end of helix Proline residue: E 45 - end of helix Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 72 through 98 removed outlier: 4.507A pdb=" N VAL E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 106 No H-bonds generated for 'chain 'E' and resid 104 through 106' Processing helix chain 'E' and resid 108 through 129 removed outlier: 3.915A pdb=" N TYR E 124 " --> pdb=" O SER E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 167 through 193 removed outlier: 3.601A pdb=" N GLU E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 213 removed outlier: 3.710A pdb=" N ASP E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU E 213 " --> pdb=" O ASP E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 220 No H-bonds generated for 'chain 'E' and resid 218 through 220' Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 231 through 242 removed outlier: 4.115A pdb=" N ALA E 235 " --> pdb=" O TRP E 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE E 236 " --> pdb=" O TRP E 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 238 " --> pdb=" O ASN E 234 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA E 240 " --> pdb=" O PHE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 271 Processing helix chain 'E' and resid 287 through 326 removed outlier: 5.775A pdb=" N ARG E 297 " --> pdb=" O HIS E 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY E 316 " --> pdb=" O LEU E 312 " (cutoff:3.500A) Proline residue: E 317 - end of helix Processing helix chain 'E' and resid 356 through 400 Processing helix chain 'E' and resid 415 through 504 removed outlier: 3.657A pdb=" N THR E 425 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Proline residue: E 436 - end of helix removed outlier: 4.933A pdb=" N TRP E 439 " --> pdb=" O CYS E 435 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 440 " --> pdb=" O PRO E 436 " (cutoff:3.500A) Proline residue: E 442 - end of helix removed outlier: 8.865A pdb=" N VAL E 458 " --> pdb=" O TYR E 454 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER E 459 " --> pdb=" O ILE E 455 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU E 461 " --> pdb=" O GLY E 457 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY E 463 " --> pdb=" O SER E 459 " (cutoff:3.500A) Proline residue: E 472 - end of helix Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 515 through 565 Proline residue: E 551 - end of helix removed outlier: 3.574A pdb=" N VAL E 555 " --> pdb=" O PRO E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 614 removed outlier: 3.805A pdb=" N ALA E 578 " --> pdb=" O SER E 574 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL E 587 " --> pdb=" O PHE E 583 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR E 588 " --> pdb=" O HIS E 584 " (cutoff:3.500A) Proline residue: E 589 - end of helix removed outlier: 4.299A pdb=" N SER E 595 " --> pdb=" O PHE E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 719 through 726 Processing helix chain 'E' and resid 784 through 789 Processing helix chain 'E' and resid 796 through 805 Processing helix chain 'E' and resid 808 through 813 Processing helix chain 'E' and resid 818 through 820 No H-bonds generated for 'chain 'E' and resid 818 through 820' Processing helix chain 'E' and resid 832 through 846 Processing helix chain 'E' and resid 862 through 873 Processing helix chain 'E' and resid 894 through 896 No H-bonds generated for 'chain 'E' and resid 894 through 896' Processing helix chain 'E' and resid 914 through 919 Processing helix chain 'E' and resid 923 through 927 Processing helix chain 'E' and resid 1001 through 1008 Processing helix chain 'E' and resid 1010 through 1038 Processing helix chain 'E' and resid 1065 through 1077 removed outlier: 3.971A pdb=" N VAL E1077 " --> pdb=" O SER E1073 " (cutoff:3.500A) Processing helix chain 'E' and resid 1081 through 1107 Processing helix chain 'E' and resid 1110 through 1115 Processing helix chain 'E' and resid 1118 through 1134 removed outlier: 3.970A pdb=" N ARG E1124 " --> pdb=" O SER E1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1136 through 1160 Processing helix chain 'E' and resid 1162 through 1209 removed outlier: 3.652A pdb=" N LEU E1165 " --> pdb=" O PRO E1162 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E1166 " --> pdb=" O VAL E1163 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU E1169 " --> pdb=" O VAL E1166 " (cutoff:3.500A) Proline residue: E1170 - end of helix removed outlier: 3.588A pdb=" N ILE E1178 " --> pdb=" O CYS E1175 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E1189 " --> pdb=" O SER E1186 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN E1190 " --> pdb=" O ARG E1187 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN E1197 " --> pdb=" O ASP E1194 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E1198 " --> pdb=" O THR E1195 " (cutoff:3.500A) Proline residue: E1199 - end of helix removed outlier: 3.517A pdb=" N GLU E1206 " --> pdb=" O HIS E1203 " (cutoff:3.500A) Processing helix chain 'E' and resid 1211 through 1217 Processing helix chain 'E' and resid 1220 through 1271 Processing helix chain 'E' and resid 1278 through 1316 removed outlier: 4.408A pdb=" N SER E1292 " --> pdb=" O ALA E1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN E1293 " --> pdb=" O LEU E1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY E1310 " --> pdb=" O GLU E1306 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA E1311 " --> pdb=" O ILE E1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1385 through 1392 Processing helix chain 'E' and resid 1410 through 1412 No H-bonds generated for 'chain 'E' and resid 1410 through 1412' Processing helix chain 'E' and resid 1415 through 1421 removed outlier: 3.678A pdb=" N SER E1420 " --> pdb=" O HIS E1416 " (cutoff:3.500A) Processing helix chain 'E' and resid 1436 through 1439 No H-bonds generated for 'chain 'E' and resid 1436 through 1439' Processing helix chain 'E' and resid 1448 through 1457 Processing helix chain 'E' and resid 1461 through 1466 Processing helix chain 'E' and resid 1470 through 1472 No H-bonds generated for 'chain 'E' and resid 1470 through 1472' Processing helix chain 'E' and resid 1476 through 1478 No H-bonds generated for 'chain 'E' and resid 1476 through 1478' Processing helix chain 'E' and resid 1484 through 1498 Processing helix chain 'E' and resid 1514 through 1528 Processing helix chain 'E' and resid 1543 through 1545 No H-bonds generated for 'chain 'E' and resid 1543 through 1545' Processing helix chain 'E' and resid 1566 through 1569 No H-bonds generated for 'chain 'E' and resid 1566 through 1569' Processing helix chain 'E' and resid 1572 through 1576 Processing helix chain 'F' and resid 14 through 17 No H-bonds generated for 'chain 'F' and resid 14 through 17' Processing helix chain 'F' and resid 27 through 56 removed outlier: 3.506A pdb=" N VAL F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Proline residue: F 35 - end of helix Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 61 through 63 No H-bonds generated for 'chain 'F' and resid 61 through 63' Processing helix chain 'F' and resid 72 through 98 removed outlier: 4.507A pdb=" N VAL F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 108 through 129 removed outlier: 3.915A pdb=" N TYR F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 167 through 193 removed outlier: 3.601A pdb=" N GLU F 186 " --> pdb=" O LEU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 213 removed outlier: 3.710A pdb=" N ASP F 212 " --> pdb=" O GLU F 208 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N LEU F 213 " --> pdb=" O ASP F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 231 through 242 removed outlier: 4.115A pdb=" N ALA F 235 " --> pdb=" O TRP F 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE F 236 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 238 " --> pdb=" O ASN F 234 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 240 " --> pdb=" O PHE F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 271 Processing helix chain 'F' and resid 287 through 326 removed outlier: 5.775A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 301 " --> pdb=" O ARG F 297 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY F 316 " --> pdb=" O LEU F 312 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 356 through 400 Processing helix chain 'F' and resid 415 through 504 removed outlier: 3.657A pdb=" N THR F 425 " --> pdb=" O VAL F 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Proline residue: F 436 - end of helix removed outlier: 4.933A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 440 " --> pdb=" O PRO F 436 " (cutoff:3.500A) Proline residue: F 442 - end of helix removed outlier: 8.865A pdb=" N VAL F 458 " --> pdb=" O TYR F 454 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY F 463 " --> pdb=" O SER F 459 " (cutoff:3.500A) Proline residue: F 472 - end of helix Processing helix chain 'F' and resid 506 through 512 Processing helix chain 'F' and resid 515 through 565 Proline residue: F 551 - end of helix removed outlier: 3.574A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 614 removed outlier: 3.805A pdb=" N ALA F 578 " --> pdb=" O SER F 574 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL F 587 " --> pdb=" O PHE F 583 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR F 588 " --> pdb=" O HIS F 584 " (cutoff:3.500A) Proline residue: F 589 - end of helix removed outlier: 4.299A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 726 Processing helix chain 'F' and resid 784 through 789 Processing helix chain 'F' and resid 796 through 805 Processing helix chain 'F' and resid 808 through 813 Processing helix chain 'F' and resid 818 through 820 No H-bonds generated for 'chain 'F' and resid 818 through 820' Processing helix chain 'F' and resid 832 through 846 Processing helix chain 'F' and resid 862 through 873 Processing helix chain 'F' and resid 894 through 896 No H-bonds generated for 'chain 'F' and resid 894 through 896' Processing helix chain 'F' and resid 914 through 919 Processing helix chain 'F' and resid 923 through 927 Processing helix chain 'F' and resid 1001 through 1008 Processing helix chain 'F' and resid 1010 through 1038 Processing helix chain 'F' and resid 1065 through 1077 removed outlier: 3.971A pdb=" N VAL F1077 " --> pdb=" O SER F1073 " (cutoff:3.500A) Processing helix chain 'F' and resid 1081 through 1107 Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1134 removed outlier: 3.970A pdb=" N ARG F1124 " --> pdb=" O SER F1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS F1129 " --> pdb=" O PHE F1125 " (cutoff:3.500A) Processing helix chain 'F' and resid 1136 through 1160 Processing helix chain 'F' and resid 1162 through 1209 removed outlier: 3.652A pdb=" N LEU F1165 " --> pdb=" O PRO F1162 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL F1166 " --> pdb=" O VAL F1163 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU F1169 " --> pdb=" O VAL F1166 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.588A pdb=" N ILE F1178 " --> pdb=" O CYS F1175 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F1189 " --> pdb=" O SER F1186 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN F1190 " --> pdb=" O ARG F1187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN F1197 " --> pdb=" O ASP F1194 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU F1198 " --> pdb=" O THR F1195 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.517A pdb=" N GLU F1206 " --> pdb=" O HIS F1203 " (cutoff:3.500A) Processing helix chain 'F' and resid 1211 through 1217 Processing helix chain 'F' and resid 1220 through 1271 Processing helix chain 'F' and resid 1278 through 1316 removed outlier: 4.408A pdb=" N SER F1292 " --> pdb=" O ALA F1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN F1293 " --> pdb=" O LEU F1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN F1296 " --> pdb=" O SER F1292 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY F1310 " --> pdb=" O GLU F1306 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA F1311 " --> pdb=" O ILE F1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL F1312 " --> pdb=" O GLN F1308 " (cutoff:3.500A) Processing helix chain 'F' and resid 1385 through 1392 Processing helix chain 'F' and resid 1410 through 1412 No H-bonds generated for 'chain 'F' and resid 1410 through 1412' Processing helix chain 'F' and resid 1415 through 1421 removed outlier: 3.678A pdb=" N SER F1420 " --> pdb=" O HIS F1416 " (cutoff:3.500A) Processing helix chain 'F' and resid 1436 through 1439 No H-bonds generated for 'chain 'F' and resid 1436 through 1439' Processing helix chain 'F' and resid 1448 through 1457 Processing helix chain 'F' and resid 1461 through 1466 Processing helix chain 'F' and resid 1470 through 1472 No H-bonds generated for 'chain 'F' and resid 1470 through 1472' Processing helix chain 'F' and resid 1476 through 1478 No H-bonds generated for 'chain 'F' and resid 1476 through 1478' Processing helix chain 'F' and resid 1484 through 1498 Processing helix chain 'F' and resid 1514 through 1528 Processing helix chain 'F' and resid 1543 through 1545 No H-bonds generated for 'chain 'F' and resid 1543 through 1545' Processing helix chain 'F' and resid 1566 through 1569 No H-bonds generated for 'chain 'F' and resid 1566 through 1569' Processing helix chain 'F' and resid 1572 through 1576 Processing helix chain 'G' and resid 14 through 17 No H-bonds generated for 'chain 'G' and resid 14 through 17' Processing helix chain 'G' and resid 27 through 56 removed outlier: 3.506A pdb=" N VAL G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) Proline residue: G 35 - end of helix Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 61 through 63 No H-bonds generated for 'chain 'G' and resid 61 through 63' Processing helix chain 'G' and resid 72 through 98 removed outlier: 4.508A pdb=" N VAL G 98 " --> pdb=" O LEU G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 108 through 129 removed outlier: 3.915A pdb=" N TYR G 124 " --> pdb=" O SER G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 167 through 193 removed outlier: 3.601A pdb=" N GLU G 186 " --> pdb=" O LEU G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 213 removed outlier: 3.710A pdb=" N ASP G 212 " --> pdb=" O GLU G 208 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 224 through 229 Processing helix chain 'G' and resid 231 through 242 removed outlier: 4.115A pdb=" N ALA G 235 " --> pdb=" O TRP G 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE G 236 " --> pdb=" O TRP G 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS G 238 " --> pdb=" O ASN G 234 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR G 239 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA G 240 " --> pdb=" O PHE G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 271 Processing helix chain 'G' and resid 287 through 326 removed outlier: 5.775A pdb=" N ARG G 297 " --> pdb=" O HIS G 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER G 302 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY G 316 " --> pdb=" O LEU G 312 " (cutoff:3.500A) Proline residue: G 317 - end of helix Processing helix chain 'G' and resid 356 through 400 Processing helix chain 'G' and resid 415 through 504 removed outlier: 3.657A pdb=" N THR G 425 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN G 426 " --> pdb=" O ALA G 422 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 4.933A pdb=" N TRP G 439 " --> pdb=" O CYS G 435 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR G 440 " --> pdb=" O PRO G 436 " (cutoff:3.500A) Proline residue: G 442 - end of helix removed outlier: 8.865A pdb=" N VAL G 458 " --> pdb=" O TYR G 454 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER G 459 " --> pdb=" O ILE G 455 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ALA G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU G 461 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE G 462 " --> pdb=" O VAL G 458 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY G 463 " --> pdb=" O SER G 459 " (cutoff:3.500A) Proline residue: G 472 - end of helix Processing helix chain 'G' and resid 506 through 512 Processing helix chain 'G' and resid 515 through 565 Proline residue: G 551 - end of helix removed outlier: 3.574A pdb=" N VAL G 555 " --> pdb=" O PRO G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 614 removed outlier: 3.806A pdb=" N ALA G 578 " --> pdb=" O SER G 574 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL G 587 " --> pdb=" O PHE G 583 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR G 588 " --> pdb=" O HIS G 584 " (cutoff:3.500A) Proline residue: G 589 - end of helix removed outlier: 4.299A pdb=" N SER G 595 " --> pdb=" O PHE G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 719 through 726 Processing helix chain 'G' and resid 784 through 789 Processing helix chain 'G' and resid 796 through 805 Processing helix chain 'G' and resid 808 through 813 Processing helix chain 'G' and resid 818 through 820 No H-bonds generated for 'chain 'G' and resid 818 through 820' Processing helix chain 'G' and resid 832 through 846 Processing helix chain 'G' and resid 862 through 873 Processing helix chain 'G' and resid 894 through 896 No H-bonds generated for 'chain 'G' and resid 894 through 896' Processing helix chain 'G' and resid 914 through 919 Processing helix chain 'G' and resid 923 through 927 Processing helix chain 'G' and resid 1001 through 1008 Processing helix chain 'G' and resid 1010 through 1038 Processing helix chain 'G' and resid 1065 through 1077 removed outlier: 3.971A pdb=" N VAL G1077 " --> pdb=" O SER G1073 " (cutoff:3.500A) Processing helix chain 'G' and resid 1081 through 1107 Processing helix chain 'G' and resid 1110 through 1115 Processing helix chain 'G' and resid 1118 through 1134 removed outlier: 3.970A pdb=" N ARG G1124 " --> pdb=" O SER G1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS G1129 " --> pdb=" O PHE G1125 " (cutoff:3.500A) Processing helix chain 'G' and resid 1136 through 1160 Processing helix chain 'G' and resid 1162 through 1209 removed outlier: 3.652A pdb=" N LEU G1165 " --> pdb=" O PRO G1162 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL G1166 " --> pdb=" O VAL G1163 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU G1169 " --> pdb=" O VAL G1166 " (cutoff:3.500A) Proline residue: G1170 - end of helix removed outlier: 3.588A pdb=" N ILE G1178 " --> pdb=" O CYS G1175 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G1189 " --> pdb=" O SER G1186 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN G1190 " --> pdb=" O ARG G1187 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN G1197 " --> pdb=" O ASP G1194 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU G1198 " --> pdb=" O THR G1195 " (cutoff:3.500A) Proline residue: G1199 - end of helix removed outlier: 3.517A pdb=" N GLU G1206 " --> pdb=" O HIS G1203 " (cutoff:3.500A) Processing helix chain 'G' and resid 1211 through 1217 Processing helix chain 'G' and resid 1220 through 1271 Processing helix chain 'G' and resid 1278 through 1316 removed outlier: 4.408A pdb=" N SER G1292 " --> pdb=" O ALA G1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN G1293 " --> pdb=" O LEU G1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN G1296 " --> pdb=" O SER G1292 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY G1310 " --> pdb=" O GLU G1306 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA G1311 " --> pdb=" O ILE G1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G1312 " --> pdb=" O GLN G1308 " (cutoff:3.500A) Processing helix chain 'G' and resid 1385 through 1392 Processing helix chain 'G' and resid 1410 through 1412 No H-bonds generated for 'chain 'G' and resid 1410 through 1412' Processing helix chain 'G' and resid 1415 through 1421 removed outlier: 3.678A pdb=" N SER G1420 " --> pdb=" O HIS G1416 " (cutoff:3.500A) Processing helix chain 'G' and resid 1436 through 1439 No H-bonds generated for 'chain 'G' and resid 1436 through 1439' Processing helix chain 'G' and resid 1448 through 1457 Processing helix chain 'G' and resid 1461 through 1466 Processing helix chain 'G' and resid 1470 through 1472 No H-bonds generated for 'chain 'G' and resid 1470 through 1472' Processing helix chain 'G' and resid 1476 through 1478 No H-bonds generated for 'chain 'G' and resid 1476 through 1478' Processing helix chain 'G' and resid 1484 through 1498 Processing helix chain 'G' and resid 1514 through 1528 Processing helix chain 'G' and resid 1543 through 1545 No H-bonds generated for 'chain 'G' and resid 1543 through 1545' Processing helix chain 'G' and resid 1566 through 1569 No H-bonds generated for 'chain 'G' and resid 1566 through 1569' Processing helix chain 'G' and resid 1572 through 1576 Processing helix chain 'H' and resid 14 through 17 No H-bonds generated for 'chain 'H' and resid 14 through 17' Processing helix chain 'H' and resid 27 through 56 removed outlier: 3.505A pdb=" N VAL H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Proline residue: H 35 - end of helix Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 61 through 63 No H-bonds generated for 'chain 'H' and resid 61 through 63' Processing helix chain 'H' and resid 72 through 98 removed outlier: 4.508A pdb=" N VAL H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 106 No H-bonds generated for 'chain 'H' and resid 104 through 106' Processing helix chain 'H' and resid 108 through 129 removed outlier: 3.915A pdb=" N TYR H 124 " --> pdb=" O SER H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 167 through 193 removed outlier: 3.602A pdb=" N GLU H 186 " --> pdb=" O LEU H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 213 removed outlier: 3.711A pdb=" N ASP H 212 " --> pdb=" O GLU H 208 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N LEU H 213 " --> pdb=" O ASP H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 220 No H-bonds generated for 'chain 'H' and resid 218 through 220' Processing helix chain 'H' and resid 224 through 229 Processing helix chain 'H' and resid 231 through 242 removed outlier: 4.115A pdb=" N ALA H 235 " --> pdb=" O TRP H 231 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE H 236 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS H 238 " --> pdb=" O ASN H 234 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA H 240 " --> pdb=" O PHE H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 271 Processing helix chain 'H' and resid 287 through 326 removed outlier: 5.775A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU H 301 " --> pdb=" O ARG H 297 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER H 302 " --> pdb=" O ARG H 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY H 316 " --> pdb=" O LEU H 312 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 356 through 400 Processing helix chain 'H' and resid 415 through 504 removed outlier: 3.658A pdb=" N THR H 425 " --> pdb=" O VAL H 421 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASN H 426 " --> pdb=" O ALA H 422 " (cutoff:3.500A) Proline residue: H 436 - end of helix removed outlier: 4.933A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR H 440 " --> pdb=" O PRO H 436 " (cutoff:3.500A) Proline residue: H 442 - end of helix removed outlier: 8.865A pdb=" N VAL H 458 " --> pdb=" O TYR H 454 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N SER H 459 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ALA H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY H 463 " --> pdb=" O SER H 459 " (cutoff:3.500A) Proline residue: H 472 - end of helix Processing helix chain 'H' and resid 506 through 512 Processing helix chain 'H' and resid 515 through 565 Proline residue: H 551 - end of helix removed outlier: 3.574A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 614 removed outlier: 3.805A pdb=" N ALA H 578 " --> pdb=" O SER H 574 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL H 587 " --> pdb=" O PHE H 583 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N THR H 588 " --> pdb=" O HIS H 584 " (cutoff:3.500A) Proline residue: H 589 - end of helix removed outlier: 4.298A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 726 Processing helix chain 'H' and resid 784 through 789 Processing helix chain 'H' and resid 796 through 805 Processing helix chain 'H' and resid 808 through 813 Processing helix chain 'H' and resid 818 through 820 No H-bonds generated for 'chain 'H' and resid 818 through 820' Processing helix chain 'H' and resid 832 through 846 Processing helix chain 'H' and resid 862 through 873 Processing helix chain 'H' and resid 894 through 896 No H-bonds generated for 'chain 'H' and resid 894 through 896' Processing helix chain 'H' and resid 914 through 919 Processing helix chain 'H' and resid 923 through 927 Processing helix chain 'H' and resid 1001 through 1008 Processing helix chain 'H' and resid 1010 through 1038 Processing helix chain 'H' and resid 1065 through 1077 removed outlier: 3.971A pdb=" N VAL H1077 " --> pdb=" O SER H1073 " (cutoff:3.500A) Processing helix chain 'H' and resid 1081 through 1107 Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1134 removed outlier: 3.970A pdb=" N ARG H1124 " --> pdb=" O SER H1120 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS H1129 " --> pdb=" O PHE H1125 " (cutoff:3.500A) Processing helix chain 'H' and resid 1136 through 1160 Processing helix chain 'H' and resid 1162 through 1209 removed outlier: 3.652A pdb=" N LEU H1165 " --> pdb=" O PRO H1162 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL H1166 " --> pdb=" O VAL H1163 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU H1169 " --> pdb=" O VAL H1166 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.588A pdb=" N ILE H1178 " --> pdb=" O CYS H1175 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU H1189 " --> pdb=" O SER H1186 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN H1190 " --> pdb=" O ARG H1187 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN H1197 " --> pdb=" O ASP H1194 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H1198 " --> pdb=" O THR H1195 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.517A pdb=" N GLU H1206 " --> pdb=" O HIS H1203 " (cutoff:3.500A) Processing helix chain 'H' and resid 1211 through 1217 Processing helix chain 'H' and resid 1220 through 1271 Processing helix chain 'H' and resid 1278 through 1316 removed outlier: 4.407A pdb=" N SER H1292 " --> pdb=" O ALA H1288 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASN H1293 " --> pdb=" O LEU H1289 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN H1296 " --> pdb=" O SER H1292 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY H1310 " --> pdb=" O GLU H1306 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA H1311 " --> pdb=" O ILE H1307 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL H1312 " --> pdb=" O GLN H1308 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1392 Processing helix chain 'H' and resid 1410 through 1412 No H-bonds generated for 'chain 'H' and resid 1410 through 1412' Processing helix chain 'H' and resid 1415 through 1421 removed outlier: 3.678A pdb=" N SER H1420 " --> pdb=" O HIS H1416 " (cutoff:3.500A) Processing helix chain 'H' and resid 1436 through 1439 No H-bonds generated for 'chain 'H' and resid 1436 through 1439' Processing helix chain 'H' and resid 1448 through 1457 Processing helix chain 'H' and resid 1461 through 1466 Processing helix chain 'H' and resid 1470 through 1472 No H-bonds generated for 'chain 'H' and resid 1470 through 1472' Processing helix chain 'H' and resid 1476 through 1478 No H-bonds generated for 'chain 'H' and resid 1476 through 1478' Processing helix chain 'H' and resid 1484 through 1498 Processing helix chain 'H' and resid 1514 through 1528 Processing helix chain 'H' and resid 1543 through 1545 No H-bonds generated for 'chain 'H' and resid 1543 through 1545' Processing helix chain 'H' and resid 1566 through 1569 No H-bonds generated for 'chain 'H' and resid 1566 through 1569' Processing helix chain 'H' and resid 1572 through 1576 Processing sheet with id= A, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= B, first strand: chain 'A' and resid 309 through 311 removed outlier: 6.676A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.250A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 319 through 321 Processing sheet with id= F, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= G, first strand: chain 'B' and resid 309 through 311 removed outlier: 6.676A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.250A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 313 through 315 Processing sheet with id= J, first strand: chain 'B' and resid 319 through 321 Processing sheet with id= K, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= L, first strand: chain 'C' and resid 309 through 311 removed outlier: 6.676A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.250A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= O, first strand: chain 'C' and resid 319 through 321 Processing sheet with id= P, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= Q, first strand: chain 'D' and resid 309 through 311 removed outlier: 6.676A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.250A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'D' and resid 319 through 321 Processing sheet with id= U, first strand: chain 'E' and resid 701 through 703 Processing sheet with id= V, first strand: chain 'E' and resid 907 through 912 removed outlier: 7.020A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL E 884 " --> pdb=" O THR E 709 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE E 711 " --> pdb=" O VAL E 884 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU E 886 " --> pdb=" O ILE E 711 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N GLY E 713 " --> pdb=" O LEU E 886 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASP E 854 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA E 773 " --> pdb=" O ASP E 854 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 1556 through 1561 removed outlier: 7.013A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL E1533 " --> pdb=" O ILE E1375 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE E1377 " --> pdb=" O VAL E1533 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR E1535 " --> pdb=" O ILE E1377 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 1345 through 1350 removed outlier: 5.134A pdb=" N VAL E1365 " --> pdb=" O ASN E1349 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 701 through 703 Processing sheet with id= Z, first strand: chain 'F' and resid 907 through 912 removed outlier: 7.020A pdb=" N ALA F 902 " --> pdb=" O GLN F 909 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU F 911 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE F 900 " --> pdb=" O GLU F 911 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL F 884 " --> pdb=" O THR F 709 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE F 711 " --> pdb=" O VAL F 884 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU F 886 " --> pdb=" O ILE F 711 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N GLY F 713 " --> pdb=" O LEU F 886 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 1556 through 1561 removed outlier: 7.013A pdb=" N VAL F1551 " --> pdb=" O LEU F1558 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE F1560 " --> pdb=" O VAL F1549 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL F1549 " --> pdb=" O PHE F1560 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL F1533 " --> pdb=" O ILE F1375 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE F1377 " --> pdb=" O VAL F1533 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR F1535 " --> pdb=" O ILE F1377 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 1345 through 1350 removed outlier: 5.134A pdb=" N VAL F1365 " --> pdb=" O ASN F1349 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 701 through 703 Processing sheet with id= AD, first strand: chain 'G' and resid 907 through 912 removed outlier: 7.020A pdb=" N ALA G 902 " --> pdb=" O GLN G 909 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU G 911 " --> pdb=" O ILE G 900 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE G 900 " --> pdb=" O GLU G 911 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL G 884 " --> pdb=" O THR G 709 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE G 711 " --> pdb=" O VAL G 884 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU G 886 " --> pdb=" O ILE G 711 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N GLY G 713 " --> pdb=" O LEU G 886 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA G 771 " --> pdb=" O PHE G 852 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASP G 854 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA G 773 " --> pdb=" O ASP G 854 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 1556 through 1561 removed outlier: 7.013A pdb=" N VAL G1551 " --> pdb=" O LEU G1558 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE G1560 " --> pdb=" O VAL G1549 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G1549 " --> pdb=" O PHE G1560 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL G1533 " --> pdb=" O ILE G1375 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE G1377 " --> pdb=" O VAL G1533 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR G1535 " --> pdb=" O ILE G1377 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 1345 through 1350 removed outlier: 5.133A pdb=" N VAL G1365 " --> pdb=" O ASN G1349 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 701 through 703 Processing sheet with id= AH, first strand: chain 'H' and resid 907 through 912 removed outlier: 7.020A pdb=" N ALA H 902 " --> pdb=" O GLN H 909 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU H 911 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE H 900 " --> pdb=" O GLU H 911 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL H 884 " --> pdb=" O THR H 709 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N ILE H 711 " --> pdb=" O VAL H 884 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU H 886 " --> pdb=" O ILE H 711 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N GLY H 713 " --> pdb=" O LEU H 886 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 1556 through 1561 removed outlier: 7.013A pdb=" N VAL H1551 " --> pdb=" O LEU H1558 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE H1560 " --> pdb=" O VAL H1549 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL H1549 " --> pdb=" O PHE H1560 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL H1533 " --> pdb=" O ILE H1375 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE H1377 " --> pdb=" O VAL H1533 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR H1535 " --> pdb=" O ILE H1377 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 1345 through 1350 removed outlier: 5.133A pdb=" N VAL H1365 " --> pdb=" O ASN H1349 " (cutoff:3.500A) 2992 hydrogen bonds defined for protein. 8352 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: 18.82 Time building geometry restraints manager: 19.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7328 1.31 - 1.44: 12027 1.44 - 1.57: 26061 1.57 - 1.69: 28 1.69 - 1.82: 292 Bond restraints: 45736 Sorted by residual: bond pdb=" O5 GBM E2001 " pdb=" S2 GBM E2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O5 GBM F2001 " pdb=" S2 GBM F2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O5 GBM G2001 " pdb=" S2 GBM G2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O5 GBM H2001 " pdb=" S2 GBM H2001 " ideal model delta sigma weight residual 1.448 1.650 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" O4 GBM E2001 " pdb=" S2 GBM E2001 " ideal model delta sigma weight residual 1.453 1.650 -0.197 2.00e-02 2.50e+03 9.70e+01 ... (remaining 45731 not shown) Histogram of bond angle deviations from ideal: 93.71 - 102.98: 417 102.98 - 112.25: 24089 112.25 - 121.52: 27423 121.52 - 130.78: 10531 130.78 - 140.05: 264 Bond angle restraints: 62724 Sorted by residual: angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 115.07 24.80 1.00e+00 1.00e+00 6.15e+02 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 115.07 24.80 1.00e+00 1.00e+00 6.15e+02 angle pdb=" PB ATP D 401 " pdb=" O3B ATP D 401 " pdb=" PG ATP D 401 " ideal model delta sigma weight residual 139.87 115.08 24.79 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 115.08 24.79 1.00e+00 1.00e+00 6.14e+02 angle pdb=" PA ATP B 401 " pdb=" O3A ATP B 401 " pdb=" PB ATP B 401 " ideal model delta sigma weight residual 136.83 114.29 22.54 1.00e+00 1.00e+00 5.08e+02 ... (remaining 62719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 25895 21.72 - 43.44: 709 43.44 - 65.16: 156 65.16 - 86.87: 32 86.87 - 108.59: 8 Dihedral angle restraints: 26800 sinusoidal: 7772 harmonic: 19028 Sorted by residual: dihedral pdb=" CA PHE H 197 " pdb=" C PHE H 197 " pdb=" N PHE H 198 " pdb=" CA PHE H 198 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE F 197 " pdb=" C PHE F 197 " pdb=" N PHE F 198 " pdb=" CA PHE F 198 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PHE G 197 " pdb=" C PHE G 197 " pdb=" N PHE G 198 " pdb=" CA PHE G 198 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 26797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 6486 0.094 - 0.187: 1017 0.187 - 0.281: 124 0.281 - 0.374: 25 0.374 - 0.468: 20 Chirality restraints: 7672 Sorted by residual: chirality pdb=" CA LEU D 100 " pdb=" N LEU D 100 " pdb=" C LEU D 100 " pdb=" CB LEU D 100 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA LEU C 100 " pdb=" N LEU C 100 " pdb=" C LEU C 100 " pdb=" CB LEU C 100 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA LEU A 100 " pdb=" N LEU A 100 " pdb=" C LEU A 100 " pdb=" CB LEU A 100 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 7669 not shown) Planarity restraints: 8064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL H 33 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL H 33 " -0.089 2.00e-02 2.50e+03 pdb=" O VAL H 33 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL H 34 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 33 " 0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL E 33 " -0.089 2.00e-02 2.50e+03 pdb=" O VAL E 33 " 0.034 2.00e-02 2.50e+03 pdb=" N VAL E 34 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 33 " -0.025 2.00e-02 2.50e+03 5.14e-02 2.64e+01 pdb=" C VAL G 33 " 0.089 2.00e-02 2.50e+03 pdb=" O VAL G 33 " -0.034 2.00e-02 2.50e+03 pdb=" N VAL G 34 " -0.030 2.00e-02 2.50e+03 ... (remaining 8061 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8551 2.77 - 3.30: 47703 3.30 - 3.83: 76478 3.83 - 4.37: 84032 4.37 - 4.90: 139150 Nonbonded interactions: 355914 Sorted by model distance: nonbonded pdb=" O LEU F1192 " pdb=" OG1 THR F1196 " model vdw 2.235 2.440 nonbonded pdb=" O LEU E1192 " pdb=" OG1 THR E1196 " model vdw 2.235 2.440 nonbonded pdb=" O LEU H1192 " pdb=" OG1 THR H1196 " model vdw 2.235 2.440 nonbonded pdb=" O LEU G1192 " pdb=" OG1 THR G1196 " model vdw 2.235 2.440 nonbonded pdb=" O HIS E1203 " pdb=" OG1 THR E1207 " model vdw 2.244 2.440 ... (remaining 355909 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.530 Check model and map are aligned: 0.580 Set scattering table: 0.360 Process input model: 118.840 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 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 : 0.008 0.202 45736 Z= 0.528 Angle : 1.289 24.805 62724 Z= 0.847 Chirality : 0.073 0.468 7672 Planarity : 0.009 0.105 8064 Dihedral : 11.985 108.592 14392 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.01 % Allowed : 4.60 % Favored : 94.39 % 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: -1.13 (0.10), residues: 6464 helix: -0.32 (0.07), residues: 3904 sheet: -1.04 (0.20), residues: 552 loop : -1.24 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP H 688 HIS 0.011 0.002 HIS G 105 PHE 0.032 0.003 PHE D 75 TYR 0.033 0.004 TYR H 179 ARG 0.009 0.001 ARG H 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1620 time to evaluate : 5.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.5842 (p0) cc_final: 0.5626 (p0) REVERT: B 262 ASP cc_start: 0.5863 (p0) cc_final: 0.5592 (p0) REVERT: C 262 ASP cc_start: 0.5820 (p0) cc_final: 0.5543 (p0) REVERT: D 262 ASP cc_start: 0.5868 (p0) cc_final: 0.5615 (p0) REVERT: E 42 ILE cc_start: 0.8296 (tt) cc_final: 0.7957 (tt) REVERT: E 91 GLU cc_start: 0.8238 (tt0) cc_final: 0.7931 (tt0) REVERT: E 166 GLN cc_start: 0.5802 (tt0) cc_final: 0.4916 (tt0) REVERT: E 232 TRP cc_start: 0.9029 (p-90) cc_final: 0.8804 (p-90) REVERT: E 247 LEU cc_start: 0.8654 (tt) cc_final: 0.8262 (mm) REVERT: E 297 ARG cc_start: 0.7861 (mmt180) cc_final: 0.7650 (ttm110) REVERT: E 298 ARG cc_start: 0.8311 (tpt170) cc_final: 0.7771 (mmm-85) REVERT: E 400 MET cc_start: 0.8101 (mmp) cc_final: 0.7816 (mmp) REVERT: E 483 GLN cc_start: 0.8370 (tp40) cc_final: 0.8132 (mt0) REVERT: E 574 SER cc_start: 0.8281 (p) cc_final: 0.7968 (p) REVERT: E 598 ARG cc_start: 0.8829 (ttp-170) cc_final: 0.8612 (mmm-85) REVERT: E 772 TYR cc_start: 0.6923 (t80) cc_final: 0.6404 (t80) REVERT: E 1120 SER cc_start: 0.8800 (t) cc_final: 0.8369 (p) REVERT: E 1125 PHE cc_start: 0.7545 (t80) cc_final: 0.7059 (t80) REVERT: E 1176 TYR cc_start: 0.8462 (t80) cc_final: 0.7955 (t80) REVERT: E 1196 THR cc_start: 0.8124 (m) cc_final: 0.7587 (m) REVERT: E 1197 GLN cc_start: 0.8377 (pp30) cc_final: 0.8161 (tm-30) REVERT: E 1222 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.8232 (ttm-80) REVERT: E 1229 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8447 (mt-10) REVERT: E 1230 TYR cc_start: 0.9069 (m-10) cc_final: 0.8672 (m-80) REVERT: E 1304 ASP cc_start: 0.8978 (t70) cc_final: 0.8665 (t70) REVERT: E 1496 PHE cc_start: 0.6029 (t80) cc_final: 0.5598 (t80) REVERT: F 42 ILE cc_start: 0.8263 (tt) cc_final: 0.7922 (tt) REVERT: F 91 GLU cc_start: 0.8250 (tt0) cc_final: 0.7932 (tt0) REVERT: F 166 GLN cc_start: 0.5808 (tt0) cc_final: 0.4918 (tt0) REVERT: F 232 TRP cc_start: 0.9035 (p-90) cc_final: 0.8817 (p-90) REVERT: F 247 LEU cc_start: 0.8660 (tt) cc_final: 0.8274 (mm) REVERT: F 297 ARG cc_start: 0.7833 (mmt180) cc_final: 0.7632 (ttm110) REVERT: F 298 ARG cc_start: 0.8319 (tpt170) cc_final: 0.7776 (mmm-85) REVERT: F 400 MET cc_start: 0.8081 (mmp) cc_final: 0.7786 (mmp) REVERT: F 483 GLN cc_start: 0.8351 (tp40) cc_final: 0.8120 (mt0) REVERT: F 574 SER cc_start: 0.8278 (p) cc_final: 0.7958 (p) REVERT: F 598 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8618 (mmm-85) REVERT: F 772 TYR cc_start: 0.6926 (t80) cc_final: 0.6404 (t80) REVERT: F 1120 SER cc_start: 0.8817 (t) cc_final: 0.8374 (p) REVERT: F 1125 PHE cc_start: 0.7542 (t80) cc_final: 0.7052 (t80) REVERT: F 1176 TYR cc_start: 0.8454 (t80) cc_final: 0.7946 (t80) REVERT: F 1196 THR cc_start: 0.8113 (m) cc_final: 0.7576 (m) REVERT: F 1197 GLN cc_start: 0.8388 (pp30) cc_final: 0.8164 (tm-30) REVERT: F 1206 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8440 (mt-10) REVERT: F 1222 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.8250 (ttm-80) REVERT: F 1229 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8451 (mt-10) REVERT: F 1230 TYR cc_start: 0.9068 (m-10) cc_final: 0.8677 (m-80) REVERT: F 1304 ASP cc_start: 0.8954 (t70) cc_final: 0.8646 (t70) REVERT: F 1496 PHE cc_start: 0.6038 (t80) cc_final: 0.5609 (t80) REVERT: G 42 ILE cc_start: 0.8282 (tt) cc_final: 0.7944 (tt) REVERT: G 91 GLU cc_start: 0.8254 (tt0) cc_final: 0.7926 (tt0) REVERT: G 145 LEU cc_start: 0.8394 (tt) cc_final: 0.8153 (tp) REVERT: G 166 GLN cc_start: 0.5821 (tt0) cc_final: 0.4891 (tt0) REVERT: G 232 TRP cc_start: 0.9046 (p-90) cc_final: 0.8786 (p-90) REVERT: G 247 LEU cc_start: 0.8676 (tt) cc_final: 0.8299 (mm) REVERT: G 297 ARG cc_start: 0.7821 (mmt180) cc_final: 0.7616 (ttm110) REVERT: G 298 ARG cc_start: 0.8327 (tpt170) cc_final: 0.7784 (mmm-85) REVERT: G 370 ARG cc_start: 0.8389 (mmt-90) cc_final: 0.7968 (mpt-90) REVERT: G 400 MET cc_start: 0.8043 (mmp) cc_final: 0.7739 (mmp) REVERT: G 574 SER cc_start: 0.8300 (p) cc_final: 0.7981 (p) REVERT: G 598 ARG cc_start: 0.8820 (ttp-170) cc_final: 0.8612 (mmm-85) REVERT: G 772 TYR cc_start: 0.6936 (t80) cc_final: 0.6417 (t80) REVERT: G 1120 SER cc_start: 0.8815 (t) cc_final: 0.8368 (p) REVERT: G 1125 PHE cc_start: 0.7465 (t80) cc_final: 0.6971 (t80) REVERT: G 1176 TYR cc_start: 0.8464 (t80) cc_final: 0.7977 (t80) REVERT: G 1193 ASP cc_start: 0.8161 (t70) cc_final: 0.7922 (t70) REVERT: G 1222 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8240 (ttm-80) REVERT: G 1229 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8449 (mt-10) REVERT: G 1230 TYR cc_start: 0.9072 (m-10) cc_final: 0.8678 (m-80) REVERT: G 1304 ASP cc_start: 0.8954 (t70) cc_final: 0.8648 (t70) REVERT: G 1496 PHE cc_start: 0.6004 (t80) cc_final: 0.5579 (t80) REVERT: H 42 ILE cc_start: 0.8283 (tt) cc_final: 0.7950 (tt) REVERT: H 91 GLU cc_start: 0.8241 (tt0) cc_final: 0.7928 (tt0) REVERT: H 166 GLN cc_start: 0.5807 (tt0) cc_final: 0.4901 (tt0) REVERT: H 232 TRP cc_start: 0.9038 (p-90) cc_final: 0.8771 (p-90) REVERT: H 247 LEU cc_start: 0.8675 (tt) cc_final: 0.8287 (mm) REVERT: H 298 ARG cc_start: 0.8335 (tpt170) cc_final: 0.7808 (mmm-85) REVERT: H 400 MET cc_start: 0.8079 (mmp) cc_final: 0.7776 (mmp) REVERT: H 483 GLN cc_start: 0.8372 (tp40) cc_final: 0.8136 (mt0) REVERT: H 574 SER cc_start: 0.8280 (p) cc_final: 0.7957 (p) REVERT: H 598 ARG cc_start: 0.8836 (ttp-170) cc_final: 0.8618 (mmm-85) REVERT: H 772 TYR cc_start: 0.6945 (t80) cc_final: 0.6417 (t80) REVERT: H 1120 SER cc_start: 0.8806 (t) cc_final: 0.8369 (p) REVERT: H 1125 PHE cc_start: 0.7485 (t80) cc_final: 0.6981 (t80) REVERT: H 1176 TYR cc_start: 0.8460 (t80) cc_final: 0.7975 (t80) REVERT: H 1196 THR cc_start: 0.8115 (m) cc_final: 0.7599 (m) REVERT: H 1197 GLN cc_start: 0.8372 (pp30) cc_final: 0.8159 (tm-30) REVERT: H 1222 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8239 (ttm-80) REVERT: H 1229 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8452 (mt-10) REVERT: H 1230 TYR cc_start: 0.9056 (m-10) cc_final: 0.8675 (m-80) REVERT: H 1304 ASP cc_start: 0.8977 (t70) cc_final: 0.8659 (t70) REVERT: H 1496 PHE cc_start: 0.5990 (t80) cc_final: 0.5562 (t80) outliers start: 36 outliers final: 20 residues processed: 1644 average time/residue: 0.5476 time to fit residues: 1501.9068 Evaluate side-chains 1094 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1074 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 604 LEU Chi-restraints excluded: chain E residue 1248 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 604 LEU Chi-restraints excluded: chain F residue 1248 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 604 LEU Chi-restraints excluded: chain G residue 1248 LEU Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 604 LEU Chi-restraints excluded: chain H residue 1248 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 550 optimal weight: 6.9990 chunk 494 optimal weight: 9.9990 chunk 274 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 333 optimal weight: 40.0000 chunk 264 optimal weight: 0.3980 chunk 511 optimal weight: 50.0000 chunk 197 optimal weight: 30.0000 chunk 310 optimal weight: 40.0000 chunk 380 optimal weight: 40.0000 chunk 592 optimal weight: 20.0000 overall best weight: 7.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN B 235 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 GLN D 43 ASN D 235 GLN E 131 ASN E 326 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1224 GLN E1301 ASN F 131 ASN F 326 HIS ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1224 GLN F1301 ASN G 131 ASN G 326 HIS ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1197 GLN G1301 ASN H 131 ASN H 326 HIS ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1224 GLN H1301 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 45736 Z= 0.433 Angle : 0.791 12.976 62724 Z= 0.410 Chirality : 0.048 0.172 7672 Planarity : 0.006 0.056 8064 Dihedral : 8.834 87.668 7084 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.64 % Allowed : 15.18 % Favored : 79.18 % 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: 0.47 (0.10), residues: 6464 helix: 1.05 (0.08), residues: 3872 sheet: -0.82 (0.21), residues: 516 loop : -0.65 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP H 688 HIS 0.008 0.002 HIS E 103 PHE 0.024 0.002 PHE F 433 TYR 0.034 0.002 TYR H 179 ARG 0.010 0.001 ARG H1187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1129 time to evaluate : 4.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASN cc_start: 0.7154 (OUTLIER) cc_final: 0.6630 (p0) REVERT: E 91 GLU cc_start: 0.8194 (tt0) cc_final: 0.7972 (tt0) REVERT: E 264 GLN cc_start: 0.8676 (tp-100) cc_final: 0.8301 (tm-30) REVERT: E 298 ARG cc_start: 0.8318 (tpt170) cc_final: 0.7916 (mmm-85) REVERT: E 402 MET cc_start: 0.5249 (tmm) cc_final: 0.3628 (tmm) REVERT: E 432 PHE cc_start: 0.8881 (m-80) cc_final: 0.8527 (t80) REVERT: E 574 SER cc_start: 0.8108 (p) cc_final: 0.7762 (p) REVERT: E 817 HIS cc_start: 0.9132 (m-70) cc_final: 0.8892 (m90) REVERT: E 1125 PHE cc_start: 0.7591 (t80) cc_final: 0.7174 (t80) REVERT: E 1149 LEU cc_start: 0.8630 (mt) cc_final: 0.8374 (mp) REVERT: E 1186 SER cc_start: 0.8979 (t) cc_final: 0.8507 (p) REVERT: E 1222 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.8087 (ttp-110) REVERT: E 1225 GLN cc_start: 0.8908 (mm-40) cc_final: 0.8509 (mm-40) REVERT: E 1229 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8540 (mt-10) REVERT: E 1230 TYR cc_start: 0.9055 (m-10) cc_final: 0.8521 (m-80) REVERT: F 42 ILE cc_start: 0.8144 (tt) cc_final: 0.7918 (tt) REVERT: F 91 GLU cc_start: 0.8193 (tt0) cc_final: 0.7966 (tt0) REVERT: F 264 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8303 (tm-30) REVERT: F 298 ARG cc_start: 0.8329 (tpt170) cc_final: 0.7915 (mmm-85) REVERT: F 402 MET cc_start: 0.5255 (tmm) cc_final: 0.3621 (tmm) REVERT: F 432 PHE cc_start: 0.8890 (m-80) cc_final: 0.8525 (t80) REVERT: F 574 SER cc_start: 0.8148 (p) cc_final: 0.7797 (p) REVERT: F 817 HIS cc_start: 0.9132 (m-70) cc_final: 0.8910 (m90) REVERT: F 1125 PHE cc_start: 0.7591 (t80) cc_final: 0.7166 (t80) REVERT: F 1149 LEU cc_start: 0.8628 (mt) cc_final: 0.8376 (mp) REVERT: F 1186 SER cc_start: 0.8979 (t) cc_final: 0.8558 (p) REVERT: F 1222 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8104 (ttp-110) REVERT: F 1229 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8544 (mt-10) REVERT: F 1230 TYR cc_start: 0.9063 (m-10) cc_final: 0.8513 (m-80) REVERT: G 42 ILE cc_start: 0.8152 (tt) cc_final: 0.7938 (tt) REVERT: G 91 GLU cc_start: 0.8224 (tt0) cc_final: 0.7992 (tt0) REVERT: G 264 GLN cc_start: 0.8679 (tp-100) cc_final: 0.8297 (tm-30) REVERT: G 298 ARG cc_start: 0.8330 (tpt170) cc_final: 0.7916 (mmm-85) REVERT: G 402 MET cc_start: 0.5225 (tmm) cc_final: 0.4958 (tmm) REVERT: G 432 PHE cc_start: 0.8869 (m-80) cc_final: 0.8489 (t80) REVERT: G 574 SER cc_start: 0.8161 (p) cc_final: 0.7818 (p) REVERT: G 817 HIS cc_start: 0.9135 (m-70) cc_final: 0.8896 (m90) REVERT: G 1125 PHE cc_start: 0.7601 (t80) cc_final: 0.7160 (t80) REVERT: G 1149 LEU cc_start: 0.8643 (mt) cc_final: 0.8399 (mp) REVERT: G 1186 SER cc_start: 0.8984 (t) cc_final: 0.8564 (p) REVERT: G 1222 ARG cc_start: 0.8516 (mtt-85) cc_final: 0.8110 (ttp-110) REVERT: G 1225 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8489 (mm-40) REVERT: G 1229 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8544 (mt-10) REVERT: G 1230 TYR cc_start: 0.9056 (m-10) cc_final: 0.8506 (m-80) REVERT: G 1249 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8576 (tm-30) REVERT: G 1294 TYR cc_start: 0.8665 (m-10) cc_final: 0.8447 (m-10) REVERT: H 42 ILE cc_start: 0.8152 (tt) cc_final: 0.7939 (tt) REVERT: H 91 GLU cc_start: 0.8193 (tt0) cc_final: 0.7976 (tt0) REVERT: H 264 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8305 (tm-30) REVERT: H 298 ARG cc_start: 0.8381 (tpt170) cc_final: 0.7904 (mmm-85) REVERT: H 402 MET cc_start: 0.5189 (tmm) cc_final: 0.3561 (tmm) REVERT: H 432 PHE cc_start: 0.8877 (m-80) cc_final: 0.8518 (t80) REVERT: H 574 SER cc_start: 0.8114 (p) cc_final: 0.7770 (p) REVERT: H 817 HIS cc_start: 0.9139 (m-70) cc_final: 0.8892 (m90) REVERT: H 1125 PHE cc_start: 0.7589 (t80) cc_final: 0.7156 (t80) REVERT: H 1149 LEU cc_start: 0.8594 (mt) cc_final: 0.8349 (mp) REVERT: H 1186 SER cc_start: 0.8978 (t) cc_final: 0.8510 (p) REVERT: H 1222 ARG cc_start: 0.8514 (mtt-85) cc_final: 0.8084 (ttp-110) REVERT: H 1225 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8502 (mm-40) REVERT: H 1229 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8548 (mt-10) REVERT: H 1230 TYR cc_start: 0.9059 (m-10) cc_final: 0.8517 (m-80) outliers start: 201 outliers final: 128 residues processed: 1234 average time/residue: 0.5198 time to fit residues: 1085.1992 Evaluate side-chains 1066 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 937 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1248 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 226 SER Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 391 ILE Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1248 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1248 LEU Chi-restraints excluded: chain G residue 1250 VAL Chi-restraints excluded: chain G residue 1267 SER Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1248 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 329 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 492 optimal weight: 5.9990 chunk 403 optimal weight: 0.9980 chunk 163 optimal weight: 5.9990 chunk 593 optimal weight: 30.0000 chunk 640 optimal weight: 40.0000 chunk 528 optimal weight: 2.9990 chunk 588 optimal weight: 0.0270 chunk 202 optimal weight: 40.0000 chunk 475 optimal weight: 40.0000 overall best weight: 3.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 GLN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1224 GLN ** G1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1197 GLN G1224 GLN ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 45736 Z= 0.243 Angle : 0.628 10.299 62724 Z= 0.319 Chirality : 0.043 0.151 7672 Planarity : 0.004 0.044 8064 Dihedral : 8.219 87.736 7068 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.72 % Allowed : 18.74 % Favored : 75.53 % 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: 1.18 (0.11), residues: 6464 helix: 1.66 (0.08), residues: 3908 sheet: -0.68 (0.22), residues: 516 loop : -0.45 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 688 HIS 0.005 0.001 HIS G 36 PHE 0.029 0.002 PHE H 363 TYR 0.018 0.001 TYR E 123 ARG 0.006 0.001 ARG G 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1041 time to evaluate : 5.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASN cc_start: 0.7162 (OUTLIER) cc_final: 0.6813 (p0) REVERT: E 76 ILE cc_start: 0.9250 (pp) cc_final: 0.8991 (tp) REVERT: E 128 GLU cc_start: 0.8437 (tt0) cc_final: 0.7549 (tt0) REVERT: E 150 LYS cc_start: 0.9224 (tppt) cc_final: 0.8986 (tppt) REVERT: E 223 ASN cc_start: 0.6803 (p0) cc_final: 0.6535 (p0) REVERT: E 233 MET cc_start: 0.9286 (mmm) cc_final: 0.9072 (mmm) REVERT: E 264 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8277 (tm-30) REVERT: E 298 ARG cc_start: 0.8244 (tpt170) cc_final: 0.7761 (mmm-85) REVERT: E 319 CYS cc_start: 0.9008 (m) cc_final: 0.8520 (m) REVERT: E 402 MET cc_start: 0.5043 (tmm) cc_final: 0.4823 (tmm) REVERT: E 432 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8402 (t80) REVERT: E 483 GLN cc_start: 0.7662 (mt0) cc_final: 0.7425 (mt0) REVERT: E 574 SER cc_start: 0.7860 (p) cc_final: 0.7493 (p) REVERT: E 1125 PHE cc_start: 0.7661 (t80) cc_final: 0.7290 (t80) REVERT: E 1186 SER cc_start: 0.8737 (t) cc_final: 0.8336 (p) REVERT: E 1206 GLU cc_start: 0.8647 (mt-10) cc_final: 0.7788 (tp30) REVERT: E 1225 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8613 (mm-40) REVERT: E 1230 TYR cc_start: 0.9068 (m-10) cc_final: 0.8596 (m-80) REVERT: F 76 ILE cc_start: 0.9253 (pp) cc_final: 0.8992 (tp) REVERT: F 128 GLU cc_start: 0.8470 (tt0) cc_final: 0.7563 (tt0) REVERT: F 150 LYS cc_start: 0.9238 (tppt) cc_final: 0.9007 (tppt) REVERT: F 223 ASN cc_start: 0.6772 (p0) cc_final: 0.6504 (p0) REVERT: F 233 MET cc_start: 0.9303 (mmm) cc_final: 0.9088 (mmm) REVERT: F 264 GLN cc_start: 0.8629 (tp-100) cc_final: 0.8287 (tm-30) REVERT: F 298 ARG cc_start: 0.8251 (tpt170) cc_final: 0.7761 (mmm-85) REVERT: F 319 CYS cc_start: 0.8996 (m) cc_final: 0.8537 (m) REVERT: F 402 MET cc_start: 0.5023 (tmm) cc_final: 0.3480 (tmm) REVERT: F 432 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8410 (t80) REVERT: F 483 GLN cc_start: 0.7653 (mt0) cc_final: 0.7411 (mt0) REVERT: F 574 SER cc_start: 0.7858 (p) cc_final: 0.7496 (p) REVERT: F 1125 PHE cc_start: 0.7682 (t80) cc_final: 0.7297 (t80) REVERT: F 1145 ARG cc_start: 0.8181 (ttp80) cc_final: 0.7908 (ttp80) REVERT: F 1186 SER cc_start: 0.8823 (t) cc_final: 0.8388 (p) REVERT: F 1206 GLU cc_start: 0.8629 (mt-10) cc_final: 0.7837 (tp30) REVERT: F 1229 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8550 (mt-10) REVERT: F 1230 TYR cc_start: 0.9075 (m-10) cc_final: 0.8595 (m-80) REVERT: G 76 ILE cc_start: 0.9251 (pp) cc_final: 0.8996 (tp) REVERT: G 128 GLU cc_start: 0.8559 (tt0) cc_final: 0.7560 (tt0) REVERT: G 223 ASN cc_start: 0.6865 (p0) cc_final: 0.6598 (p0) REVERT: G 233 MET cc_start: 0.9308 (mmm) cc_final: 0.9093 (mmm) REVERT: G 264 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8274 (tm-30) REVERT: G 298 ARG cc_start: 0.8230 (tpt170) cc_final: 0.7730 (mmm-85) REVERT: G 319 CYS cc_start: 0.9005 (m) cc_final: 0.8555 (m) REVERT: G 402 MET cc_start: 0.4918 (tmm) cc_final: 0.3390 (tmm) REVERT: G 432 PHE cc_start: 0.8825 (OUTLIER) cc_final: 0.8401 (t80) REVERT: G 574 SER cc_start: 0.7903 (p) cc_final: 0.7539 (p) REVERT: G 1125 PHE cc_start: 0.7683 (t80) cc_final: 0.7291 (t80) REVERT: G 1186 SER cc_start: 0.8827 (t) cc_final: 0.8393 (p) REVERT: G 1225 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8498 (mm-40) REVERT: G 1229 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8543 (mt-10) REVERT: G 1230 TYR cc_start: 0.9072 (m-10) cc_final: 0.8620 (m-80) REVERT: G 1292 SER cc_start: 0.8441 (m) cc_final: 0.8036 (p) REVERT: H 76 ILE cc_start: 0.9247 (pp) cc_final: 0.8988 (tp) REVERT: H 128 GLU cc_start: 0.8428 (tt0) cc_final: 0.7520 (tt0) REVERT: H 150 LYS cc_start: 0.9225 (tppt) cc_final: 0.8991 (tppt) REVERT: H 223 ASN cc_start: 0.6795 (p0) cc_final: 0.6528 (p0) REVERT: H 233 MET cc_start: 0.9297 (mmm) cc_final: 0.9082 (mmm) REVERT: H 264 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8286 (tm-30) REVERT: H 298 ARG cc_start: 0.8295 (tpt170) cc_final: 0.7876 (mmm-85) REVERT: H 319 CYS cc_start: 0.9010 (m) cc_final: 0.8528 (m) REVERT: H 402 MET cc_start: 0.4890 (tmm) cc_final: 0.4632 (tmm) REVERT: H 432 PHE cc_start: 0.8813 (OUTLIER) cc_final: 0.8397 (t80) REVERT: H 483 GLN cc_start: 0.7657 (mt0) cc_final: 0.7413 (mt0) REVERT: H 574 SER cc_start: 0.7871 (p) cc_final: 0.7506 (p) REVERT: H 1125 PHE cc_start: 0.7639 (t80) cc_final: 0.7252 (t80) REVERT: H 1145 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7506 (tmm160) REVERT: H 1186 SER cc_start: 0.8729 (t) cc_final: 0.8330 (p) REVERT: H 1225 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8507 (mm-40) REVERT: H 1229 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8552 (mt-10) REVERT: H 1230 TYR cc_start: 0.9066 (m-10) cc_final: 0.8623 (m-80) REVERT: H 1292 SER cc_start: 0.8578 (m) cc_final: 0.7853 (p) outliers start: 204 outliers final: 142 residues processed: 1150 average time/residue: 0.5184 time to fit residues: 1021.9030 Evaluate side-chains 1071 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 924 time to evaluate : 4.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 97 HIS Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1157 ILE Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1255 ILE Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1136 ILE Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1157 ILE Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1255 ILE Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 440 THR Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1136 ILE Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1157 ILE Chi-restraints excluded: chain G residue 1173 VAL Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1250 VAL Chi-restraints excluded: chain G residue 1255 ILE Chi-restraints excluded: chain G residue 1267 SER Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1136 ILE Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1267 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 586 optimal weight: 8.9990 chunk 445 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 283 optimal weight: 7.9990 chunk 398 optimal weight: 5.9990 chunk 595 optimal weight: 50.0000 chunk 630 optimal weight: 6.9990 chunk 311 optimal weight: 9.9990 chunk 564 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 GLN C 48 ASN C 313 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1270 ASN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN ** G1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 GLN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 45736 Z= 0.356 Angle : 0.686 10.260 62724 Z= 0.350 Chirality : 0.046 0.172 7672 Planarity : 0.004 0.034 8064 Dihedral : 8.034 87.400 7060 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 8.08 % Allowed : 18.13 % Favored : 73.79 % 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: 1.01 (0.11), residues: 6464 helix: 1.57 (0.08), residues: 3996 sheet: -0.88 (0.21), residues: 556 loop : -0.70 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 688 HIS 0.006 0.001 HIS E 103 PHE 0.035 0.002 PHE G 169 TYR 0.017 0.002 TYR A 330 ARG 0.006 0.001 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 958 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASN cc_start: 0.7649 (p0) cc_final: 0.7230 (p0) REVERT: E 128 GLU cc_start: 0.8648 (tt0) cc_final: 0.7656 (tt0) REVERT: E 159 ASP cc_start: 0.8600 (t0) cc_final: 0.8255 (t70) REVERT: E 264 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8333 (tm-30) REVERT: E 298 ARG cc_start: 0.8274 (tpt170) cc_final: 0.7860 (mmm-85) REVERT: E 402 MET cc_start: 0.5077 (tmm) cc_final: 0.4035 (tmm) REVERT: E 432 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8448 (t80) REVERT: E 483 GLN cc_start: 0.7707 (mt0) cc_final: 0.7455 (mt0) REVERT: E 574 SER cc_start: 0.7963 (p) cc_final: 0.7665 (m) REVERT: E 1125 PHE cc_start: 0.7559 (t80) cc_final: 0.7219 (t80) REVERT: E 1186 SER cc_start: 0.8769 (t) cc_final: 0.8368 (p) REVERT: E 1188 ASP cc_start: 0.8506 (m-30) cc_final: 0.8261 (m-30) REVERT: E 1222 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8202 (ttp-110) REVERT: E 1225 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8430 (mm-40) REVERT: E 1226 LYS cc_start: 0.8971 (mttt) cc_final: 0.8678 (mttp) REVERT: E 1230 TYR cc_start: 0.9052 (m-10) cc_final: 0.8493 (m-80) REVERT: F 128 GLU cc_start: 0.8691 (tt0) cc_final: 0.7697 (tt0) REVERT: F 159 ASP cc_start: 0.8604 (t0) cc_final: 0.8257 (t70) REVERT: F 264 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8343 (tm-30) REVERT: F 298 ARG cc_start: 0.8282 (tpt170) cc_final: 0.7865 (mmm-85) REVERT: F 402 MET cc_start: 0.5026 (tmm) cc_final: 0.3940 (tmm) REVERT: F 432 PHE cc_start: 0.8896 (OUTLIER) cc_final: 0.8426 (t80) REVERT: F 483 GLN cc_start: 0.7698 (mt0) cc_final: 0.7447 (mt0) REVERT: F 574 SER cc_start: 0.7970 (p) cc_final: 0.7664 (m) REVERT: F 1125 PHE cc_start: 0.7572 (t80) cc_final: 0.7237 (t80) REVERT: F 1145 ARG cc_start: 0.8232 (ttp80) cc_final: 0.8028 (ttp80) REVERT: F 1186 SER cc_start: 0.8923 (t) cc_final: 0.8487 (p) REVERT: F 1222 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8113 (ttp-110) REVERT: F 1226 LYS cc_start: 0.9014 (mttt) cc_final: 0.8309 (mttp) REVERT: F 1229 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8479 (mt-10) REVERT: F 1230 TYR cc_start: 0.9068 (m-10) cc_final: 0.8482 (m-80) REVERT: G 264 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8335 (tm-30) REVERT: G 298 ARG cc_start: 0.8285 (tpt170) cc_final: 0.7864 (mmm-85) REVERT: G 402 MET cc_start: 0.5018 (tmm) cc_final: 0.3924 (tmm) REVERT: G 432 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8422 (t80) REVERT: G 574 SER cc_start: 0.7994 (p) cc_final: 0.7712 (m) REVERT: G 1125 PHE cc_start: 0.7576 (t80) cc_final: 0.7234 (t80) REVERT: G 1145 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7535 (tmm160) REVERT: G 1186 SER cc_start: 0.8915 (t) cc_final: 0.8478 (p) REVERT: G 1222 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8193 (ttp-110) REVERT: G 1226 LYS cc_start: 0.9034 (mttt) cc_final: 0.8663 (mttp) REVERT: G 1230 TYR cc_start: 0.9072 (m-10) cc_final: 0.8489 (m-80) REVERT: G 1292 SER cc_start: 0.8222 (m) cc_final: 0.7825 (p) REVERT: G 1294 TYR cc_start: 0.8607 (m-10) cc_final: 0.8276 (m-10) REVERT: H 159 ASP cc_start: 0.8599 (t0) cc_final: 0.8250 (t70) REVERT: H 264 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8340 (tm-30) REVERT: H 298 ARG cc_start: 0.8325 (tpt170) cc_final: 0.7886 (mmm-85) REVERT: H 402 MET cc_start: 0.4936 (tmm) cc_final: 0.3786 (tmm) REVERT: H 432 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8428 (t80) REVERT: H 483 GLN cc_start: 0.7703 (mt0) cc_final: 0.7448 (mt0) REVERT: H 574 SER cc_start: 0.8016 (p) cc_final: 0.7719 (m) REVERT: H 1125 PHE cc_start: 0.7562 (t80) cc_final: 0.7230 (t80) REVERT: H 1145 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7988 (ttp80) REVERT: H 1186 SER cc_start: 0.8768 (t) cc_final: 0.8365 (p) REVERT: H 1188 ASP cc_start: 0.8564 (m-30) cc_final: 0.8314 (m-30) REVERT: H 1222 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8201 (ttp-110) REVERT: H 1226 LYS cc_start: 0.9047 (mttt) cc_final: 0.8675 (mttp) REVERT: H 1230 TYR cc_start: 0.9056 (m-10) cc_final: 0.8485 (m-80) REVERT: H 1292 SER cc_start: 0.8390 (m) cc_final: 0.7794 (p) outliers start: 288 outliers final: 210 residues processed: 1138 average time/residue: 0.5472 time to fit residues: 1078.9370 Evaluate side-chains 1086 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 872 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 440 THR Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 474 GLN Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1146 SER Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1233 SER Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 474 GLN Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 600 THR Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1204 PHE Chi-restraints excluded: chain F residue 1211 LEU Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1233 SER Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 440 THR Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1146 SER Chi-restraints excluded: chain G residue 1155 THR Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1211 LEU Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1233 SER Chi-restraints excluded: chain G residue 1267 SER Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1283 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 366 LEU Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 440 THR Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1146 SER Chi-restraints excluded: chain H residue 1157 ILE Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1211 LEU Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1233 SER Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 524 optimal weight: 0.9990 chunk 357 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 469 optimal weight: 30.0000 chunk 260 optimal weight: 30.0000 chunk 537 optimal weight: 1.9990 chunk 435 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 321 optimal weight: 30.0000 chunk 565 optimal weight: 7.9990 chunk 159 optimal weight: 10.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 HIS ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 264 ASN B 277 HIS B 313 GLN C 264 ASN C 277 HIS C 313 GLN ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN D 277 HIS ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1270 ASN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 474 GLN ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN G1179 GLN G1270 ASN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 474 GLN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1270 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.5360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 45736 Z= 0.257 Angle : 0.613 9.132 62724 Z= 0.312 Chirality : 0.044 0.158 7672 Planarity : 0.004 0.035 8064 Dihedral : 7.789 87.861 7052 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.56 % Allowed : 21.32 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.11), residues: 6464 helix: 1.85 (0.08), residues: 3980 sheet: -0.64 (0.22), residues: 512 loop : -0.73 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 688 HIS 0.004 0.001 HIS A 70 PHE 0.028 0.002 PHE H 169 TYR 0.014 0.001 TYR F 107 ARG 0.005 0.001 ARG G 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 950 time to evaluate : 4.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 ASN cc_start: 0.7620 (p0) cc_final: 0.7115 (p0) REVERT: E 102 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7664 (mmp80) REVERT: E 182 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8148 (tt) REVERT: E 264 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8323 (tm-30) REVERT: E 298 ARG cc_start: 0.8203 (tpt170) cc_final: 0.7752 (mmm-85) REVERT: E 402 MET cc_start: 0.4961 (tmm) cc_final: 0.3930 (tmm) REVERT: E 432 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8433 (t80) REVERT: E 483 GLN cc_start: 0.7685 (mt0) cc_final: 0.7417 (mt0) REVERT: E 739 TRP cc_start: 0.6922 (OUTLIER) cc_final: 0.6013 (t60) REVERT: E 1125 PHE cc_start: 0.7519 (t80) cc_final: 0.7219 (t80) REVERT: E 1145 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7379 (tmm160) REVERT: E 1186 SER cc_start: 0.8726 (t) cc_final: 0.8322 (p) REVERT: E 1188 ASP cc_start: 0.8486 (m-30) cc_final: 0.8162 (m-30) REVERT: E 1225 GLN cc_start: 0.8719 (mm-40) cc_final: 0.7871 (mm-40) REVERT: E 1226 LYS cc_start: 0.9038 (mttt) cc_final: 0.8419 (mttp) REVERT: E 1229 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8213 (mp0) REVERT: E 1230 TYR cc_start: 0.9054 (m-10) cc_final: 0.8389 (m-80) REVERT: E 1298 MET cc_start: 0.8442 (tmm) cc_final: 0.8200 (tmm) REVERT: F 96 ASP cc_start: 0.8738 (t70) cc_final: 0.8167 (t0) REVERT: F 102 ARG cc_start: 0.8283 (mmt180) cc_final: 0.7611 (mmp80) REVERT: F 182 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8129 (tt) REVERT: F 264 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8328 (tm-30) REVERT: F 298 ARG cc_start: 0.8175 (tpt170) cc_final: 0.7706 (mmm-85) REVERT: F 402 MET cc_start: 0.4943 (tmm) cc_final: 0.3903 (tmm) REVERT: F 432 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8449 (t80) REVERT: F 483 GLN cc_start: 0.7678 (mt0) cc_final: 0.7409 (mt0) REVERT: F 739 TRP cc_start: 0.6914 (OUTLIER) cc_final: 0.5982 (t60) REVERT: F 1125 PHE cc_start: 0.7556 (t80) cc_final: 0.7249 (t80) REVERT: F 1186 SER cc_start: 0.8892 (t) cc_final: 0.8440 (p) REVERT: F 1226 LYS cc_start: 0.8985 (mttt) cc_final: 0.8673 (mttp) REVERT: F 1230 TYR cc_start: 0.9098 (m-10) cc_final: 0.8561 (m-80) REVERT: G 182 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8138 (tt) REVERT: G 264 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8333 (tm-30) REVERT: G 298 ARG cc_start: 0.8191 (tpt170) cc_final: 0.7744 (mmm-85) REVERT: G 402 MET cc_start: 0.4938 (tmm) cc_final: 0.3906 (tmm) REVERT: G 432 PHE cc_start: 0.8900 (OUTLIER) cc_final: 0.8448 (t80) REVERT: G 739 TRP cc_start: 0.6920 (OUTLIER) cc_final: 0.6006 (t60) REVERT: G 1125 PHE cc_start: 0.7557 (t80) cc_final: 0.7249 (t80) REVERT: G 1145 ARG cc_start: 0.8317 (ttp80) cc_final: 0.8099 (ttp80) REVERT: G 1186 SER cc_start: 0.8860 (t) cc_final: 0.8424 (p) REVERT: G 1206 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8475 (mt-10) REVERT: G 1222 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.8119 (ttp-110) REVERT: G 1226 LYS cc_start: 0.8992 (mttt) cc_final: 0.8676 (mttp) REVERT: G 1230 TYR cc_start: 0.9102 (m-10) cc_final: 0.8578 (m-80) REVERT: H 102 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7678 (mmp80) REVERT: H 128 GLU cc_start: 0.8706 (tt0) cc_final: 0.7686 (tt0) REVERT: H 182 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8115 (tt) REVERT: H 264 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8329 (tm-30) REVERT: H 298 ARG cc_start: 0.8254 (tpt170) cc_final: 0.7838 (mmm-85) REVERT: H 402 MET cc_start: 0.4982 (tmm) cc_final: 0.3869 (tmm) REVERT: H 432 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.8432 (t80) REVERT: H 483 GLN cc_start: 0.7683 (mt0) cc_final: 0.7413 (mt0) REVERT: H 739 TRP cc_start: 0.6937 (OUTLIER) cc_final: 0.6012 (t60) REVERT: H 1125 PHE cc_start: 0.7566 (t80) cc_final: 0.7232 (t80) REVERT: H 1186 SER cc_start: 0.8697 (t) cc_final: 0.8282 (p) REVERT: H 1206 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8481 (mt-10) REVERT: H 1222 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8105 (ttp-110) REVERT: H 1226 LYS cc_start: 0.9010 (mttt) cc_final: 0.8698 (mttp) REVERT: H 1230 TYR cc_start: 0.9088 (m-10) cc_final: 0.8571 (m-80) REVERT: H 1298 MET cc_start: 0.8467 (tmm) cc_final: 0.8208 (tmm) outliers start: 198 outliers final: 159 residues processed: 1069 average time/residue: 0.5062 time to fit residues: 934.7982 Evaluate side-chains 1055 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 884 time to evaluate : 4.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 351 GLU Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 581 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1204 PHE Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1204 PHE Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1146 SER Chi-restraints excluded: chain G residue 1155 THR Chi-restraints excluded: chain G residue 1157 ILE Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1179 GLN Chi-restraints excluded: chain G residue 1211 LEU Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1267 SER Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1283 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 474 GLN Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1146 SER Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 212 optimal weight: 20.0000 chunk 567 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 370 optimal weight: 50.0000 chunk 155 optimal weight: 9.9990 chunk 630 optimal weight: 20.0000 chunk 523 optimal weight: 9.9990 chunk 292 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 208 optimal weight: 10.0000 chunk 331 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN C 48 ASN D 48 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 45736 Z= 0.360 Angle : 0.663 9.935 62724 Z= 0.344 Chirality : 0.045 0.283 7672 Planarity : 0.004 0.031 8064 Dihedral : 7.883 82.611 7052 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 7.30 % Allowed : 21.32 % Favored : 71.38 % 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: 1.19 (0.11), residues: 6464 helix: 1.75 (0.08), residues: 3972 sheet: -0.77 (0.22), residues: 516 loop : -0.71 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 688 HIS 0.005 0.001 HIS G 36 PHE 0.031 0.002 PHE F 169 TYR 0.018 0.002 TYR G1181 ARG 0.005 0.001 ARG H1145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 900 time to evaluate : 4.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.4978 (mmm160) cc_final: 0.4554 (mtt-85) REVERT: A 163 MET cc_start: 0.6784 (tmm) cc_final: 0.6421 (ttp) REVERT: B 32 ARG cc_start: 0.4992 (mmm160) cc_final: 0.4565 (mtt-85) REVERT: C 32 ARG cc_start: 0.5029 (mmm160) cc_final: 0.4603 (mtt-85) REVERT: D 32 ARG cc_start: 0.4953 (mmm160) cc_final: 0.4478 (mmt180) REVERT: D 43 ASN cc_start: 0.7568 (p0) cc_final: 0.7150 (p0) REVERT: E 102 ARG cc_start: 0.8283 (mmt180) cc_final: 0.7571 (mmp80) REVERT: E 257 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8482 (mtt) REVERT: E 264 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8348 (tm-30) REVERT: E 298 ARG cc_start: 0.8285 (tpt170) cc_final: 0.7834 (mmm-85) REVERT: E 402 MET cc_start: 0.5049 (tmm) cc_final: 0.4035 (tmm) REVERT: E 432 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8427 (t80) REVERT: E 483 GLN cc_start: 0.7742 (mt0) cc_final: 0.7482 (mt0) REVERT: E 574 SER cc_start: 0.7921 (p) cc_final: 0.7587 (p) REVERT: E 739 TRP cc_start: 0.6980 (OUTLIER) cc_final: 0.6027 (t60) REVERT: E 1125 PHE cc_start: 0.7523 (t80) cc_final: 0.7250 (t80) REVERT: E 1177 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8786 (m-10) REVERT: E 1186 SER cc_start: 0.8694 (t) cc_final: 0.8303 (p) REVERT: E 1188 ASP cc_start: 0.8500 (m-30) cc_final: 0.8252 (m-30) REVERT: E 1225 GLN cc_start: 0.8746 (mm-40) cc_final: 0.7907 (mm-40) REVERT: E 1226 LYS cc_start: 0.9059 (mttt) cc_final: 0.8430 (mttp) REVERT: E 1229 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8313 (mp0) REVERT: E 1230 TYR cc_start: 0.9019 (m-10) cc_final: 0.8364 (m-80) REVERT: E 1298 MET cc_start: 0.8458 (tmm) cc_final: 0.8211 (tmm) REVERT: F 96 ASP cc_start: 0.8705 (t70) cc_final: 0.8063 (t0) REVERT: F 102 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7567 (mmp80) REVERT: F 257 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8510 (mtt) REVERT: F 264 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8356 (tm-30) REVERT: F 298 ARG cc_start: 0.8299 (tpt170) cc_final: 0.7840 (mmm-85) REVERT: F 402 MET cc_start: 0.5034 (tmm) cc_final: 0.4007 (tmm) REVERT: F 432 PHE cc_start: 0.8877 (OUTLIER) cc_final: 0.8448 (t80) REVERT: F 483 GLN cc_start: 0.7737 (mt0) cc_final: 0.7481 (mt0) REVERT: F 574 SER cc_start: 0.7913 (p) cc_final: 0.7579 (p) REVERT: F 739 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.6004 (t60) REVERT: F 1186 SER cc_start: 0.8901 (t) cc_final: 0.8466 (p) REVERT: F 1226 LYS cc_start: 0.9019 (mttt) cc_final: 0.8668 (mttp) REVERT: F 1230 TYR cc_start: 0.9037 (m-10) cc_final: 0.8423 (m-80) REVERT: G 96 ASP cc_start: 0.8775 (t0) cc_final: 0.8118 (t0) REVERT: G 102 ARG cc_start: 0.8228 (mmt180) cc_final: 0.7626 (mmp80) REVERT: G 257 MET cc_start: 0.8759 (mtt) cc_final: 0.8530 (mtt) REVERT: G 264 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8347 (tm-30) REVERT: G 298 ARG cc_start: 0.8271 (tpt170) cc_final: 0.7832 (mmm-85) REVERT: G 402 MET cc_start: 0.5022 (tmm) cc_final: 0.3999 (tmm) REVERT: G 432 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8445 (t80) REVERT: G 574 SER cc_start: 0.7923 (p) cc_final: 0.7598 (p) REVERT: G 739 TRP cc_start: 0.6960 (OUTLIER) cc_final: 0.6008 (t60) REVERT: G 1145 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8113 (ttp80) REVERT: G 1186 SER cc_start: 0.8852 (t) cc_final: 0.8407 (p) REVERT: G 1226 LYS cc_start: 0.9016 (mttt) cc_final: 0.8686 (mttp) REVERT: G 1230 TYR cc_start: 0.9052 (m-10) cc_final: 0.8439 (m-80) REVERT: H 102 ARG cc_start: 0.8303 (mmt180) cc_final: 0.7581 (mmp80) REVERT: H 128 GLU cc_start: 0.8752 (tt0) cc_final: 0.7759 (tt0) REVERT: H 181 MET cc_start: 0.8325 (tpt) cc_final: 0.8098 (mmt) REVERT: H 257 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8530 (mtt) REVERT: H 264 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8348 (tm-30) REVERT: H 298 ARG cc_start: 0.8334 (tpt170) cc_final: 0.7919 (mmm-85) REVERT: H 402 MET cc_start: 0.5006 (tmm) cc_final: 0.3956 (tmm) REVERT: H 432 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.8437 (t80) REVERT: H 483 GLN cc_start: 0.7719 (mt0) cc_final: 0.7460 (mt0) REVERT: H 574 SER cc_start: 0.7905 (p) cc_final: 0.7575 (p) REVERT: H 739 TRP cc_start: 0.6970 (OUTLIER) cc_final: 0.6021 (t60) REVERT: H 1186 SER cc_start: 0.8695 (t) cc_final: 0.8279 (p) REVERT: H 1226 LYS cc_start: 0.9039 (mttt) cc_final: 0.8406 (mttp) REVERT: H 1229 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8490 (mt-10) REVERT: H 1230 TYR cc_start: 0.9036 (m-10) cc_final: 0.8411 (m-80) REVERT: H 1249 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8736 (tm-30) REVERT: H 1298 MET cc_start: 0.8421 (tmm) cc_final: 0.8172 (tmm) outliers start: 260 outliers final: 213 residues processed: 1055 average time/residue: 0.5115 time to fit residues: 932.2529 Evaluate side-chains 1088 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 863 time to evaluate : 5.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 351 GLU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 198 PHE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 257 MET Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 581 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1129 CYS Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1157 ILE Chi-restraints excluded: chain E residue 1169 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1261 LEU Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1155 THR Chi-restraints excluded: chain F residue 1157 ILE Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1204 PHE Chi-restraints excluded: chain F residue 1211 LEU Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1261 LEU Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1146 SER Chi-restraints excluded: chain G residue 1155 THR Chi-restraints excluded: chain G residue 1157 ILE Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1211 LEU Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1267 SER Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1283 LEU Chi-restraints excluded: chain G residue 1285 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 198 PHE Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 257 MET Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 449 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1155 THR Chi-restraints excluded: chain H residue 1157 ILE Chi-restraints excluded: chain H residue 1169 LEU Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1211 LEU Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 608 optimal weight: 40.0000 chunk 71 optimal weight: 10.0000 chunk 359 optimal weight: 6.9990 chunk 460 optimal weight: 20.0000 chunk 356 optimal weight: 0.6980 chunk 531 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 628 optimal weight: 0.9980 chunk 393 optimal weight: 0.9980 chunk 383 optimal weight: 50.0000 chunk 290 optimal weight: 8.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 128 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1179 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1179 GLN F1224 GLN G 166 GLN ** G 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1179 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45736 Z= 0.223 Angle : 0.605 12.918 62724 Z= 0.305 Chirality : 0.043 0.148 7672 Planarity : 0.004 0.034 8064 Dihedral : 7.671 82.353 7052 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 6.12 % Allowed : 22.78 % Favored : 71.10 % 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: 1.44 (0.11), residues: 6464 helix: 1.96 (0.08), residues: 3972 sheet: -0.75 (0.22), residues: 500 loop : -0.61 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 688 HIS 0.004 0.001 HIS F 36 PHE 0.027 0.001 PHE E 169 TYR 0.015 0.001 TYR E 107 ARG 0.006 0.001 ARG E1145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 953 time to evaluate : 5.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.4816 (mmm160) cc_final: 0.4495 (mmt180) REVERT: B 32 ARG cc_start: 0.4796 (mmm160) cc_final: 0.4365 (mtt180) REVERT: C 32 ARG cc_start: 0.4819 (mmm160) cc_final: 0.4391 (mtt180) REVERT: D 32 ARG cc_start: 0.4787 (mmm160) cc_final: 0.4391 (mmt180) REVERT: D 43 ASN cc_start: 0.7516 (p0) cc_final: 0.7109 (p0) REVERT: E 102 ARG cc_start: 0.8295 (mmt180) cc_final: 0.7563 (mmp80) REVERT: E 257 MET cc_start: 0.8642 (mtt) cc_final: 0.8387 (mtt) REVERT: E 264 GLN cc_start: 0.8663 (tp-100) cc_final: 0.8325 (tm-30) REVERT: E 298 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7721 (mmm-85) REVERT: E 402 MET cc_start: 0.5032 (tmm) cc_final: 0.4134 (tmm) REVERT: E 432 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8387 (t80) REVERT: E 739 TRP cc_start: 0.6982 (OUTLIER) cc_final: 0.6054 (t60) REVERT: E 1125 PHE cc_start: 0.7552 (t80) cc_final: 0.7289 (t80) REVERT: E 1177 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8769 (m-10) REVERT: E 1186 SER cc_start: 0.8616 (t) cc_final: 0.8182 (p) REVERT: E 1188 ASP cc_start: 0.8503 (m-30) cc_final: 0.8203 (m-30) REVERT: E 1225 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8272 (mm-40) REVERT: E 1229 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8444 (mp0) REVERT: E 1298 MET cc_start: 0.8435 (tmm) cc_final: 0.8153 (tmm) REVERT: F 96 ASP cc_start: 0.8635 (t70) cc_final: 0.7566 (t70) REVERT: F 102 ARG cc_start: 0.8290 (mmt180) cc_final: 0.7578 (mmp80) REVERT: F 257 MET cc_start: 0.8679 (mtt) cc_final: 0.8425 (mtt) REVERT: F 264 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8343 (tm-30) REVERT: F 298 ARG cc_start: 0.8194 (tpt170) cc_final: 0.7710 (mmm-85) REVERT: F 402 MET cc_start: 0.4979 (tmm) cc_final: 0.4073 (tmm) REVERT: F 432 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8374 (t80) REVERT: F 584 HIS cc_start: 0.8641 (m-70) cc_final: 0.8415 (m-70) REVERT: F 739 TRP cc_start: 0.6958 (OUTLIER) cc_final: 0.6031 (t60) REVERT: F 1125 PHE cc_start: 0.7554 (t80) cc_final: 0.7312 (t80) REVERT: F 1186 SER cc_start: 0.8852 (t) cc_final: 0.8389 (p) REVERT: F 1224 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8301 (tp40) REVERT: F 1226 LYS cc_start: 0.8987 (mttt) cc_final: 0.8648 (mttp) REVERT: F 1230 TYR cc_start: 0.9084 (m-10) cc_final: 0.8507 (m-80) REVERT: F 1298 MET cc_start: 0.8420 (tmm) cc_final: 0.8135 (tmm) REVERT: G 96 ASP cc_start: 0.8688 (t0) cc_final: 0.7928 (t0) REVERT: G 102 ARG cc_start: 0.8245 (mmt180) cc_final: 0.7630 (mmp80) REVERT: G 128 GLU cc_start: 0.8811 (tt0) cc_final: 0.7742 (tt0) REVERT: G 264 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8329 (tm-30) REVERT: G 298 ARG cc_start: 0.8198 (tpt170) cc_final: 0.7706 (mmm-85) REVERT: G 402 MET cc_start: 0.4991 (tmm) cc_final: 0.4070 (tmm) REVERT: G 432 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8371 (t80) REVERT: G 739 TRP cc_start: 0.6977 (OUTLIER) cc_final: 0.6044 (t60) REVERT: G 1125 PHE cc_start: 0.7552 (t80) cc_final: 0.7312 (t80) REVERT: G 1177 PHE cc_start: 0.9078 (OUTLIER) cc_final: 0.8738 (m-10) REVERT: G 1186 SER cc_start: 0.8794 (t) cc_final: 0.8319 (p) REVERT: G 1226 LYS cc_start: 0.8995 (mttt) cc_final: 0.8646 (mttp) REVERT: G 1229 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8509 (mt-10) REVERT: G 1298 MET cc_start: 0.8432 (tmm) cc_final: 0.8140 (tmm) REVERT: H 102 ARG cc_start: 0.8309 (mmt180) cc_final: 0.7582 (mmp80) REVERT: H 128 GLU cc_start: 0.8735 (tt0) cc_final: 0.7471 (tt0) REVERT: H 257 MET cc_start: 0.8681 (mtt) cc_final: 0.8437 (mtt) REVERT: H 264 GLN cc_start: 0.8667 (tp-100) cc_final: 0.8323 (tm-30) REVERT: H 298 ARG cc_start: 0.8236 (tpt170) cc_final: 0.7755 (mmm-85) REVERT: H 402 MET cc_start: 0.5020 (tmm) cc_final: 0.4057 (tmm) REVERT: H 432 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8355 (t80) REVERT: H 739 TRP cc_start: 0.6993 (OUTLIER) cc_final: 0.6071 (t60) REVERT: H 1125 PHE cc_start: 0.7523 (t80) cc_final: 0.7266 (t80) REVERT: H 1145 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7477 (tmm160) REVERT: H 1186 SER cc_start: 0.8555 (t) cc_final: 0.8092 (p) REVERT: H 1226 LYS cc_start: 0.9006 (mttt) cc_final: 0.8394 (mttp) REVERT: H 1229 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8509 (mt-10) REVERT: H 1230 TYR cc_start: 0.9071 (m-10) cc_final: 0.8475 (m-80) REVERT: H 1249 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8714 (tm-30) REVERT: H 1298 MET cc_start: 0.8408 (tmm) cc_final: 0.8124 (tmm) outliers start: 218 outliers final: 173 residues processed: 1083 average time/residue: 0.5007 time to fit residues: 933.6198 Evaluate side-chains 1074 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 890 time to evaluate : 4.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 428 LEU Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 543 SER Chi-restraints excluded: chain E residue 581 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1179 GLN Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 94 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1129 CYS Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1155 THR Chi-restraints excluded: chain F residue 1168 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1179 GLN Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1204 PHE Chi-restraints excluded: chain F residue 1211 LEU Chi-restraints excluded: chain F residue 1224 GLN Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 94 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1129 CYS Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1155 THR Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1177 PHE Chi-restraints excluded: chain G residue 1179 GLN Chi-restraints excluded: chain G residue 1211 LEU Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1283 LEU Chi-restraints excluded: chain G residue 1307 ILE Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1155 THR Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1211 LEU Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1255 ILE Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 388 optimal weight: 50.0000 chunk 250 optimal weight: 50.0000 chunk 375 optimal weight: 40.0000 chunk 189 optimal weight: 50.0000 chunk 123 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 399 optimal weight: 7.9990 chunk 428 optimal weight: 0.9980 chunk 310 optimal weight: 50.0000 chunk 58 optimal weight: 10.0000 chunk 493 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN B 313 GLN C 313 GLN D 48 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1179 GLN ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 262 ASN ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 45736 Z= 0.398 Angle : 0.700 13.017 62724 Z= 0.362 Chirality : 0.046 0.243 7672 Planarity : 0.004 0.045 8064 Dihedral : 7.888 89.926 7052 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.76 % Allowed : 22.84 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.11), residues: 6464 helix: 1.70 (0.08), residues: 3936 sheet: -0.91 (0.21), residues: 556 loop : -0.72 (0.15), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP H 688 HIS 0.006 0.001 HIS G 867 PHE 0.030 0.002 PHE H 169 TYR 0.017 0.002 TYR A 330 ARG 0.007 0.001 ARG F1145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 889 time to evaluate : 5.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.5146 (mmm160) cc_final: 0.4667 (mtt180) REVERT: A 163 MET cc_start: 0.6709 (tmm) cc_final: 0.6417 (ttp) REVERT: B 32 ARG cc_start: 0.4975 (mmm160) cc_final: 0.4282 (mtt-85) REVERT: C 32 ARG cc_start: 0.5009 (mmm160) cc_final: 0.4312 (mtt-85) REVERT: D 32 ARG cc_start: 0.5083 (mmm160) cc_final: 0.4522 (mtt180) REVERT: E 102 ARG cc_start: 0.8263 (mmt180) cc_final: 0.7528 (mmp80) REVERT: E 257 MET cc_start: 0.8730 (mtt) cc_final: 0.8517 (mtt) REVERT: E 264 GLN cc_start: 0.8719 (tp-100) cc_final: 0.8383 (tm-30) REVERT: E 298 ARG cc_start: 0.8303 (tpt170) cc_final: 0.7817 (mmm-85) REVERT: E 402 MET cc_start: 0.5183 (tmm) cc_final: 0.4266 (tmm) REVERT: E 432 PHE cc_start: 0.8849 (OUTLIER) cc_final: 0.8400 (t80) REVERT: E 574 SER cc_start: 0.7894 (p) cc_final: 0.7579 (p) REVERT: E 739 TRP cc_start: 0.7054 (OUTLIER) cc_final: 0.5940 (t60) REVERT: E 1177 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8808 (m-10) REVERT: E 1188 ASP cc_start: 0.8519 (m-30) cc_final: 0.8240 (m-30) REVERT: E 1225 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8022 (mm-40) REVERT: E 1229 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8359 (mp0) REVERT: E 1230 TYR cc_start: 0.8938 (m-80) cc_final: 0.8385 (m-80) REVERT: E 1298 MET cc_start: 0.8403 (tmm) cc_final: 0.8151 (tmm) REVERT: E 1531 ARG cc_start: 0.5843 (mtt180) cc_final: 0.4813 (mtp180) REVERT: F 53 SER cc_start: 0.7391 (OUTLIER) cc_final: 0.7187 (t) REVERT: F 96 ASP cc_start: 0.8682 (t70) cc_final: 0.7847 (t0) REVERT: F 102 ARG cc_start: 0.8281 (mmt180) cc_final: 0.7572 (mmp80) REVERT: F 128 GLU cc_start: 0.8771 (tt0) cc_final: 0.7819 (tt0) REVERT: F 257 MET cc_start: 0.8717 (mtt) cc_final: 0.8491 (mtt) REVERT: F 264 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8395 (tm-30) REVERT: F 298 ARG cc_start: 0.8309 (tpt170) cc_final: 0.7849 (mmm-85) REVERT: F 402 MET cc_start: 0.5082 (tmm) cc_final: 0.4166 (tmm) REVERT: F 432 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8401 (t80) REVERT: F 483 GLN cc_start: 0.7747 (mt0) cc_final: 0.7528 (mt0) REVERT: F 574 SER cc_start: 0.7878 (p) cc_final: 0.7564 (p) REVERT: F 739 TRP cc_start: 0.7068 (OUTLIER) cc_final: 0.5938 (t60) REVERT: F 1186 SER cc_start: 0.8911 (t) cc_final: 0.8466 (p) REVERT: F 1226 LYS cc_start: 0.9017 (mttt) cc_final: 0.8685 (mttp) REVERT: F 1230 TYR cc_start: 0.9027 (m-10) cc_final: 0.8432 (m-80) REVERT: F 1298 MET cc_start: 0.8362 (tmm) cc_final: 0.8110 (tmm) REVERT: F 1531 ARG cc_start: 0.5801 (mtt180) cc_final: 0.4772 (mtp180) REVERT: G 53 SER cc_start: 0.7403 (OUTLIER) cc_final: 0.7185 (t) REVERT: G 96 ASP cc_start: 0.8709 (t0) cc_final: 0.7641 (t0) REVERT: G 102 ARG cc_start: 0.8229 (mmt180) cc_final: 0.7558 (mmp80) REVERT: G 264 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8397 (tm-30) REVERT: G 298 ARG cc_start: 0.8316 (tpt170) cc_final: 0.7818 (mmm-85) REVERT: G 402 MET cc_start: 0.5152 (tmm) cc_final: 0.4226 (tmm) REVERT: G 432 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8403 (t80) REVERT: G 574 SER cc_start: 0.7930 (p) cc_final: 0.7610 (p) REVERT: G 739 TRP cc_start: 0.7028 (OUTLIER) cc_final: 0.5880 (t60) REVERT: G 1177 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8833 (m-10) REVERT: G 1179 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8618 (tm-30) REVERT: G 1186 SER cc_start: 0.8918 (t) cc_final: 0.8359 (p) REVERT: G 1226 LYS cc_start: 0.9019 (mttt) cc_final: 0.8803 (mttp) REVERT: G 1230 TYR cc_start: 0.8992 (m-80) cc_final: 0.8477 (m-80) REVERT: G 1298 MET cc_start: 0.8348 (tmm) cc_final: 0.8094 (tmm) REVERT: G 1531 ARG cc_start: 0.5793 (mtt180) cc_final: 0.4745 (mtp180) REVERT: H 102 ARG cc_start: 0.8294 (mmt180) cc_final: 0.7534 (mmp80) REVERT: H 128 GLU cc_start: 0.8754 (tt0) cc_final: 0.7812 (tt0) REVERT: H 257 MET cc_start: 0.8726 (mtt) cc_final: 0.8500 (mtt) REVERT: H 264 GLN cc_start: 0.8707 (tp-100) cc_final: 0.8369 (tm-30) REVERT: H 298 ARG cc_start: 0.8336 (tpt170) cc_final: 0.7915 (mmm-85) REVERT: H 402 MET cc_start: 0.5114 (tmm) cc_final: 0.4167 (tmm) REVERT: H 432 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8398 (t80) REVERT: H 574 SER cc_start: 0.7942 (p) cc_final: 0.7615 (p) REVERT: H 739 TRP cc_start: 0.7065 (OUTLIER) cc_final: 0.5948 (t60) REVERT: H 1226 LYS cc_start: 0.9045 (mttt) cc_final: 0.8472 (mttp) REVERT: H 1229 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8465 (mt-10) REVERT: H 1230 TYR cc_start: 0.9039 (m-10) cc_final: 0.8447 (m-80) REVERT: H 1249 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8589 (tm-30) REVERT: H 1298 MET cc_start: 0.8422 (tmm) cc_final: 0.8157 (tmm) REVERT: H 1307 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7994 (tp) REVERT: H 1531 ARG cc_start: 0.5879 (mtt180) cc_final: 0.4854 (mtp180) outliers start: 241 outliers final: 200 residues processed: 1037 average time/residue: 0.5099 time to fit residues: 907.6931 Evaluate side-chains 1065 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 851 time to evaluate : 4.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 424 ASP Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 443 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 543 SER Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 581 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1211 LEU Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 424 ASP Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1155 THR Chi-restraints excluded: chain F residue 1168 LEU Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1211 LEU Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1267 SER Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 428 LEU Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1155 THR Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1177 PHE Chi-restraints excluded: chain G residue 1179 GLN Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1211 LEU Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1283 LEU Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 177 ILE Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 543 SER Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1129 CYS Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1155 THR Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1211 LEU Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1267 SER Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1307 ILE Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 571 optimal weight: 8.9990 chunk 602 optimal weight: 50.0000 chunk 549 optimal weight: 0.9990 chunk 585 optimal weight: 50.0000 chunk 601 optimal weight: 10.0000 chunk 352 optimal weight: 0.9990 chunk 255 optimal weight: 9.9990 chunk 459 optimal weight: 30.0000 chunk 179 optimal weight: 50.0000 chunk 529 optimal weight: 5.9990 chunk 553 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 ASN ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 386 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 45736 Z= 0.261 Angle : 0.640 11.678 62724 Z= 0.324 Chirality : 0.044 0.177 7672 Planarity : 0.004 0.035 8064 Dihedral : 7.627 88.434 7052 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.84 % Allowed : 24.35 % Favored : 69.81 % 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: 1.27 (0.11), residues: 6464 helix: 1.84 (0.08), residues: 3944 sheet: -0.78 (0.23), residues: 500 loop : -0.69 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP H 688 HIS 0.004 0.001 HIS G 36 PHE 0.025 0.001 PHE A 75 TYR 0.013 0.001 TYR F 123 ARG 0.008 0.001 ARG F1145 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 887 time to evaluate : 4.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.4983 (mmm160) cc_final: 0.4646 (mtt-85) REVERT: A 163 MET cc_start: 0.6682 (tmm) cc_final: 0.6404 (ttp) REVERT: B 32 ARG cc_start: 0.4899 (mmm160) cc_final: 0.4467 (mtt180) REVERT: C 32 ARG cc_start: 0.4931 (mmm160) cc_final: 0.4488 (mtt180) REVERT: D 32 ARG cc_start: 0.4942 (mmm160) cc_final: 0.4568 (mtt-85) REVERT: E 96 ASP cc_start: 0.8609 (t70) cc_final: 0.7375 (t0) REVERT: E 102 ARG cc_start: 0.8290 (mmt180) cc_final: 0.7591 (mmp80) REVERT: E 257 MET cc_start: 0.8643 (mtt) cc_final: 0.8395 (mtt) REVERT: E 264 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8366 (tm-30) REVERT: E 298 ARG cc_start: 0.8272 (tpt170) cc_final: 0.7779 (mmm-85) REVERT: E 402 MET cc_start: 0.5077 (tmm) cc_final: 0.4276 (tmm) REVERT: E 432 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8298 (t80) REVERT: E 739 TRP cc_start: 0.7035 (OUTLIER) cc_final: 0.5931 (t60) REVERT: E 1177 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8789 (m-10) REVERT: E 1186 SER cc_start: 0.8662 (t) cc_final: 0.8207 (p) REVERT: E 1188 ASP cc_start: 0.8501 (m-30) cc_final: 0.8178 (m-30) REVERT: E 1225 GLN cc_start: 0.8781 (mm-40) cc_final: 0.7923 (mm-40) REVERT: E 1229 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8322 (mp0) REVERT: E 1230 TYR cc_start: 0.8974 (m-80) cc_final: 0.8421 (m-80) REVERT: E 1298 MET cc_start: 0.8346 (tmm) cc_final: 0.8104 (tmm) REVERT: E 1531 ARG cc_start: 0.5838 (mtt180) cc_final: 0.4769 (mtp-110) REVERT: F 96 ASP cc_start: 0.8612 (t70) cc_final: 0.7732 (t0) REVERT: F 102 ARG cc_start: 0.8292 (mmt180) cc_final: 0.7574 (mmp80) REVERT: F 257 MET cc_start: 0.8669 (mtt) cc_final: 0.8389 (mtt) REVERT: F 264 GLN cc_start: 0.8721 (tp-100) cc_final: 0.8379 (tm-30) REVERT: F 298 ARG cc_start: 0.8248 (tpt170) cc_final: 0.7775 (mmm-85) REVERT: F 402 MET cc_start: 0.5062 (tmm) cc_final: 0.4247 (tmm) REVERT: F 432 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8327 (t80) REVERT: F 739 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.5902 (t60) REVERT: F 1186 SER cc_start: 0.8818 (t) cc_final: 0.8369 (p) REVERT: F 1226 LYS cc_start: 0.8997 (mttt) cc_final: 0.8690 (mttp) REVERT: F 1230 TYR cc_start: 0.9063 (m-10) cc_final: 0.8489 (m-80) REVERT: F 1298 MET cc_start: 0.8332 (tmm) cc_final: 0.8089 (tmm) REVERT: F 1531 ARG cc_start: 0.5788 (mtt180) cc_final: 0.4721 (mtp-110) REVERT: G 96 ASP cc_start: 0.8650 (t0) cc_final: 0.7726 (t0) REVERT: G 102 ARG cc_start: 0.8260 (mmt180) cc_final: 0.7578 (mmp80) REVERT: G 264 GLN cc_start: 0.8717 (tp-100) cc_final: 0.8353 (tm-30) REVERT: G 298 ARG cc_start: 0.8262 (tpt170) cc_final: 0.7792 (mmm-85) REVERT: G 402 MET cc_start: 0.5080 (tmm) cc_final: 0.4264 (tmm) REVERT: G 432 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8314 (t80) REVERT: G 739 TRP cc_start: 0.7044 (OUTLIER) cc_final: 0.5911 (t60) REVERT: G 1145 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7531 (tmm160) REVERT: G 1177 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8777 (m-10) REVERT: G 1186 SER cc_start: 0.8692 (t) cc_final: 0.8276 (p) REVERT: G 1226 LYS cc_start: 0.8995 (mttt) cc_final: 0.8772 (mttp) REVERT: G 1230 TYR cc_start: 0.9016 (m-80) cc_final: 0.8493 (m-80) REVERT: G 1298 MET cc_start: 0.8341 (tmm) cc_final: 0.8095 (tmm) REVERT: G 1531 ARG cc_start: 0.5788 (mtt180) cc_final: 0.4733 (mtp-110) REVERT: H 102 ARG cc_start: 0.8322 (mmt180) cc_final: 0.7555 (mmp80) REVERT: H 128 GLU cc_start: 0.8755 (tt0) cc_final: 0.7645 (tt0) REVERT: H 257 MET cc_start: 0.8664 (mtt) cc_final: 0.8416 (mtt) REVERT: H 264 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8429 (tm-30) REVERT: H 298 ARG cc_start: 0.8283 (tpt170) cc_final: 0.7813 (mmm-85) REVERT: H 402 MET cc_start: 0.5048 (tmm) cc_final: 0.4192 (tmm) REVERT: H 432 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8295 (t80) REVERT: H 739 TRP cc_start: 0.7049 (OUTLIER) cc_final: 0.5933 (t60) REVERT: H 1125 PHE cc_start: 0.7538 (t80) cc_final: 0.7285 (t80) REVERT: H 1145 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7514 (tmm160) REVERT: H 1226 LYS cc_start: 0.9022 (mttt) cc_final: 0.8440 (mttp) REVERT: H 1229 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8453 (mt-10) REVERT: H 1230 TYR cc_start: 0.9059 (m-10) cc_final: 0.8468 (m-80) REVERT: H 1249 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8663 (tm-30) REVERT: H 1298 MET cc_start: 0.8341 (tmm) cc_final: 0.8090 (tmm) REVERT: H 1306 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8628 (tm-30) REVERT: H 1307 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7901 (tp) REVERT: H 1531 ARG cc_start: 0.5816 (mtt180) cc_final: 0.4745 (mtp-110) outliers start: 208 outliers final: 172 residues processed: 1018 average time/residue: 0.5010 time to fit residues: 875.2624 Evaluate side-chains 1037 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 854 time to evaluate : 5.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 543 SER Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 581 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1155 THR Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1307 ILE Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 443 VAL Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1155 THR Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1177 PHE Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1267 SER Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1283 LEU Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 443 VAL Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 543 SER Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1155 THR Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1307 ILE Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 583 optimal weight: 20.0000 chunk 384 optimal weight: 50.0000 chunk 619 optimal weight: 6.9990 chunk 377 optimal weight: 20.0000 chunk 293 optimal weight: 2.9990 chunk 430 optimal weight: 2.9990 chunk 649 optimal weight: 50.0000 chunk 597 optimal weight: 30.0000 chunk 517 optimal weight: 50.0000 chunk 53 optimal weight: 9.9990 chunk 399 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 45736 Z= 0.342 Angle : 0.685 11.457 62724 Z= 0.350 Chirality : 0.045 0.198 7672 Planarity : 0.004 0.038 8064 Dihedral : 7.494 84.800 7052 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.78 % Allowed : 24.66 % Favored : 69.56 % 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: 1.13 (0.11), residues: 6464 helix: 1.72 (0.08), residues: 3940 sheet: -0.85 (0.23), residues: 504 loop : -0.71 (0.15), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 688 HIS 0.005 0.001 HIS G 867 PHE 0.026 0.002 PHE A 75 TYR 0.013 0.001 TYR F 179 ARG 0.016 0.001 ARG H 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12928 Ramachandran restraints generated. 6464 Oldfield, 0 Emsley, 6464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 863 time to evaluate : 5.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.5015 (mmm160) cc_final: 0.4533 (mtt180) REVERT: A 163 MET cc_start: 0.6705 (tmm) cc_final: 0.6415 (ttp) REVERT: B 32 ARG cc_start: 0.5077 (mmm160) cc_final: 0.4821 (mtt-85) REVERT: C 32 ARG cc_start: 0.5111 (mmm160) cc_final: 0.4838 (mtt-85) REVERT: D 32 ARG cc_start: 0.5073 (mmm160) cc_final: 0.4742 (mtt-85) REVERT: E 102 ARG cc_start: 0.8284 (mmt180) cc_final: 0.7488 (mmp80) REVERT: E 257 MET cc_start: 0.8676 (mtt) cc_final: 0.8458 (mtt) REVERT: E 264 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8402 (tm-30) REVERT: E 298 ARG cc_start: 0.8271 (tpt170) cc_final: 0.7825 (mmm-85) REVERT: E 402 MET cc_start: 0.5108 (tmm) cc_final: 0.4323 (tmm) REVERT: E 432 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8304 (t80) REVERT: E 574 SER cc_start: 0.7856 (p) cc_final: 0.7535 (p) REVERT: E 739 TRP cc_start: 0.7079 (OUTLIER) cc_final: 0.5821 (t60) REVERT: E 1177 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8813 (m-10) REVERT: E 1188 ASP cc_start: 0.8464 (m-30) cc_final: 0.8111 (m-30) REVERT: E 1225 GLN cc_start: 0.8781 (mm-40) cc_final: 0.7932 (mm-40) REVERT: E 1229 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8310 (mp0) REVERT: E 1230 TYR cc_start: 0.8966 (m-80) cc_final: 0.8346 (m-80) REVERT: E 1298 MET cc_start: 0.8338 (tmm) cc_final: 0.8075 (tmm) REVERT: E 1306 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8565 (tm-30) REVERT: F 96 ASP cc_start: 0.8617 (t70) cc_final: 0.7315 (t0) REVERT: F 102 ARG cc_start: 0.8277 (mmt180) cc_final: 0.7542 (mmp80) REVERT: F 257 MET cc_start: 0.8696 (mtt) cc_final: 0.8454 (mtt) REVERT: F 264 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8393 (tm-30) REVERT: F 298 ARG cc_start: 0.8282 (tpt170) cc_final: 0.7819 (mmm-85) REVERT: F 402 MET cc_start: 0.5091 (tmm) cc_final: 0.4309 (tmm) REVERT: F 432 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8274 (t80) REVERT: F 574 SER cc_start: 0.7848 (p) cc_final: 0.7525 (p) REVERT: F 739 TRP cc_start: 0.6979 (OUTLIER) cc_final: 0.5720 (t60) REVERT: F 1186 SER cc_start: 0.8885 (t) cc_final: 0.8350 (p) REVERT: F 1226 LYS cc_start: 0.9022 (mttt) cc_final: 0.8719 (mttp) REVERT: F 1230 TYR cc_start: 0.9043 (m-10) cc_final: 0.8469 (m-80) REVERT: F 1298 MET cc_start: 0.8312 (tmm) cc_final: 0.8043 (tmm) REVERT: G 102 ARG cc_start: 0.8273 (mmt180) cc_final: 0.7431 (mmp-170) REVERT: G 264 GLN cc_start: 0.8738 (tp-100) cc_final: 0.8388 (tm-30) REVERT: G 298 ARG cc_start: 0.8302 (tpt170) cc_final: 0.7848 (mmm-85) REVERT: G 402 MET cc_start: 0.5135 (tmm) cc_final: 0.4322 (tmm) REVERT: G 432 PHE cc_start: 0.8748 (OUTLIER) cc_final: 0.8305 (t80) REVERT: G 739 TRP cc_start: 0.7015 (OUTLIER) cc_final: 0.5728 (t60) REVERT: G 1177 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8815 (m-10) REVERT: G 1186 SER cc_start: 0.8766 (t) cc_final: 0.8328 (p) REVERT: G 1226 LYS cc_start: 0.9009 (mttt) cc_final: 0.8807 (mttp) REVERT: G 1230 TYR cc_start: 0.9018 (m-80) cc_final: 0.8500 (m-80) REVERT: G 1298 MET cc_start: 0.8312 (tmm) cc_final: 0.8041 (tmm) REVERT: H 73 LEU cc_start: 0.9128 (pt) cc_final: 0.8814 (tt) REVERT: H 96 ASP cc_start: 0.8648 (t70) cc_final: 0.8098 (t0) REVERT: H 102 ARG cc_start: 0.8308 (mmt180) cc_final: 0.7488 (mmp-170) REVERT: H 128 GLU cc_start: 0.8758 (tt0) cc_final: 0.7680 (tt0) REVERT: H 257 MET cc_start: 0.8702 (mtt) cc_final: 0.8475 (mtt) REVERT: H 264 GLN cc_start: 0.8726 (tp-100) cc_final: 0.8382 (tm-30) REVERT: H 298 ARG cc_start: 0.8303 (tpt170) cc_final: 0.7868 (mmm-85) REVERT: H 402 MET cc_start: 0.5115 (tmm) cc_final: 0.4250 (tmm) REVERT: H 432 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8313 (t80) REVERT: H 739 TRP cc_start: 0.7083 (OUTLIER) cc_final: 0.5826 (t60) REVERT: H 1145 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7520 (tmm160) REVERT: H 1158 SER cc_start: 0.9072 (m) cc_final: 0.8740 (p) REVERT: H 1226 LYS cc_start: 0.9030 (mttt) cc_final: 0.8479 (mttp) REVERT: H 1229 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8464 (mt-10) REVERT: H 1230 TYR cc_start: 0.9045 (m-10) cc_final: 0.8457 (m-80) REVERT: H 1249 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8636 (tm-30) REVERT: H 1298 MET cc_start: 0.8331 (tmm) cc_final: 0.8063 (tmm) REVERT: H 1306 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8602 (tm-30) REVERT: H 1307 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7941 (tp) outliers start: 206 outliers final: 186 residues processed: 997 average time/residue: 0.4957 time to fit residues: 849.9710 Evaluate side-chains 1040 residues out of total 5700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 843 time to evaluate : 4.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 215 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 140 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 88 MET Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 71 HIS Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 221 PHE Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 320 ILE Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 357 VAL Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain E residue 421 VAL Chi-restraints excluded: chain E residue 432 PHE Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 473 VAL Chi-restraints excluded: chain E residue 543 SER Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain E residue 581 SER Chi-restraints excluded: chain E residue 585 ILE Chi-restraints excluded: chain E residue 739 TRP Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1155 THR Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1177 PHE Chi-restraints excluded: chain E residue 1202 SER Chi-restraints excluded: chain E residue 1227 LEU Chi-restraints excluded: chain E residue 1250 VAL Chi-restraints excluded: chain E residue 1267 SER Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1316 HIS Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 65 TRP Chi-restraints excluded: chain F residue 71 HIS Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 152 ILE Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 221 PHE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 327 LEU Chi-restraints excluded: chain F residue 357 VAL Chi-restraints excluded: chain F residue 421 VAL Chi-restraints excluded: chain F residue 432 PHE Chi-restraints excluded: chain F residue 443 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 581 SER Chi-restraints excluded: chain F residue 585 ILE Chi-restraints excluded: chain F residue 610 LEU Chi-restraints excluded: chain F residue 739 TRP Chi-restraints excluded: chain F residue 1140 LEU Chi-restraints excluded: chain F residue 1146 SER Chi-restraints excluded: chain F residue 1155 THR Chi-restraints excluded: chain F residue 1175 CYS Chi-restraints excluded: chain F residue 1202 SER Chi-restraints excluded: chain F residue 1227 LEU Chi-restraints excluded: chain F residue 1250 VAL Chi-restraints excluded: chain F residue 1272 LEU Chi-restraints excluded: chain F residue 1283 LEU Chi-restraints excluded: chain F residue 1285 LEU Chi-restraints excluded: chain F residue 1316 HIS Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 129 THR Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain G residue 174 LEU Chi-restraints excluded: chain G residue 177 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 221 PHE Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain G residue 304 THR Chi-restraints excluded: chain G residue 327 LEU Chi-restraints excluded: chain G residue 357 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 421 VAL Chi-restraints excluded: chain G residue 432 PHE Chi-restraints excluded: chain G residue 449 VAL Chi-restraints excluded: chain G residue 473 VAL Chi-restraints excluded: chain G residue 543 SER Chi-restraints excluded: chain G residue 581 SER Chi-restraints excluded: chain G residue 610 LEU Chi-restraints excluded: chain G residue 739 TRP Chi-restraints excluded: chain G residue 1140 LEU Chi-restraints excluded: chain G residue 1155 THR Chi-restraints excluded: chain G residue 1175 CYS Chi-restraints excluded: chain G residue 1177 PHE Chi-restraints excluded: chain G residue 1202 SER Chi-restraints excluded: chain G residue 1227 LEU Chi-restraints excluded: chain G residue 1267 SER Chi-restraints excluded: chain G residue 1272 LEU Chi-restraints excluded: chain G residue 1283 LEU Chi-restraints excluded: chain G residue 1316 HIS Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 65 TRP Chi-restraints excluded: chain H residue 71 HIS Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 152 ILE Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 LEU Chi-restraints excluded: chain H residue 357 VAL Chi-restraints excluded: chain H residue 361 LEU Chi-restraints excluded: chain H residue 368 LEU Chi-restraints excluded: chain H residue 421 VAL Chi-restraints excluded: chain H residue 424 ASP Chi-restraints excluded: chain H residue 432 PHE Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain H residue 473 VAL Chi-restraints excluded: chain H residue 543 SER Chi-restraints excluded: chain H residue 581 SER Chi-restraints excluded: chain H residue 739 TRP Chi-restraints excluded: chain H residue 1140 LEU Chi-restraints excluded: chain H residue 1155 THR Chi-restraints excluded: chain H residue 1175 CYS Chi-restraints excluded: chain H residue 1202 SER Chi-restraints excluded: chain H residue 1227 LEU Chi-restraints excluded: chain H residue 1250 VAL Chi-restraints excluded: chain H residue 1255 ILE Chi-restraints excluded: chain H residue 1272 LEU Chi-restraints excluded: chain H residue 1283 LEU Chi-restraints excluded: chain H residue 1285 LEU Chi-restraints excluded: chain H residue 1307 ILE Chi-restraints excluded: chain H residue 1316 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 317 optimal weight: 9.9990 chunk 410 optimal weight: 4.9990 chunk 550 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 476 optimal weight: 50.0000 chunk 76 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 518 optimal weight: 50.0000 chunk 216 optimal weight: 6.9990 chunk 531 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.131991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104238 restraints weight = 121828.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106988 restraints weight = 57936.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108808 restraints weight = 35115.909| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 45736 Z= 0.260 Angle : 0.654 11.494 62724 Z= 0.329 Chirality : 0.044 0.238 7672 Planarity : 0.004 0.033 8064 Dihedral : 6.823 84.112 7052 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 5.58 % Allowed : 24.92 % Favored : 69.50 % 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: 1.25 (0.11), residues: 6464 helix: 1.83 (0.08), residues: 3932 sheet: -0.91 (0.22), residues: 520 loop : -0.64 (0.15), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 688 HIS 0.004 0.001 HIS C 70 PHE 0.059 0.001 PHE F1164 TYR 0.013 0.001 TYR H 123 ARG 0.009 0.001 ARG E1145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14184.32 seconds wall clock time: 255 minutes 19.37 seconds (15319.37 seconds total)