Starting phenix.real_space_refine on Sat Mar 16 08:08:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plw_20378/03_2024/6plw_20378_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plw_20378/03_2024/6plw_20378.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plw_20378/03_2024/6plw_20378.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plw_20378/03_2024/6plw_20378.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plw_20378/03_2024/6plw_20378_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plw_20378/03_2024/6plw_20378_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9180 2.51 5 N 2265 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14095 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2773 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.28, per 1000 atoms: 0.52 Number of scatterers: 14095 At special positions: 0 Unit cell: (106.99, 105.344, 135.795, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2560 8.00 N 2265 7.00 C 9180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 154 " - pdb=" SG CYS A 168 " distance=2.04 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.04 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.04 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 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 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG G 1 " - " ASN B 54 " " NAG H 1 " - " ASN C 54 " " NAG I 1 " - " ASN D 54 " " NAG J 1 " - " ASN E 54 " Time building additional restraints: 5.64 Conformation dependent library (CDL) restraints added in 2.4 seconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 55 helices and 20 sheets defined 35.5% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.880A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.573A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP A 107 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.675A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 284 removed outlier: 4.548A pdb=" N GLY A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU A 271 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 273 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A 274 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 278 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET A 279 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 280 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 282 " --> pdb=" O MET A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 324 removed outlier: 3.803A pdb=" N VAL A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 399 removed outlier: 3.723A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 426 removed outlier: 4.101A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 3.577A pdb=" N PHE A 420 " --> pdb=" O ILE A 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 33 removed outlier: 3.881A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.573A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP B 107 " --> pdb=" O SER B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.675A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 284 removed outlier: 4.548A pdb=" N GLY B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU B 271 " --> pdb=" O ARG B 268 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 273 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR B 274 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 278 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET B 279 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 280 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN B 282 " --> pdb=" O MET B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 324 removed outlier: 3.803A pdb=" N VAL B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 399 removed outlier: 3.722A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 399 " --> pdb=" O PHE B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 426 removed outlier: 4.101A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 3.577A pdb=" N PHE B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 33 removed outlier: 3.881A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.573A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP C 107 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.675A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 284 removed outlier: 4.549A pdb=" N GLY C 270 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU C 271 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 273 " --> pdb=" O GLY C 270 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR C 274 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 278 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET C 279 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR C 280 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN C 282 " --> pdb=" O MET C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 324 removed outlier: 3.803A pdb=" N VAL C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 399 removed outlier: 3.723A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C 399 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 426 removed outlier: 4.101A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 3.577A pdb=" N PHE C 420 " --> pdb=" O ILE C 416 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE C 423 " --> pdb=" O ILE C 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.880A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.573A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP D 107 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.675A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 284 removed outlier: 4.549A pdb=" N GLY D 270 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU D 271 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE D 273 " --> pdb=" O GLY D 270 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR D 274 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 278 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET D 279 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR D 280 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN D 282 " --> pdb=" O MET D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 324 removed outlier: 3.803A pdb=" N VAL D 305 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 399 removed outlier: 3.723A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA D 399 " --> pdb=" O PHE D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 426 removed outlier: 4.101A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 3.577A pdb=" N PHE D 420 " --> pdb=" O ILE D 416 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 33 removed outlier: 3.880A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.573A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ASP E 107 " --> pdb=" O SER E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 236 through 242 Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.674A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 284 removed outlier: 4.548A pdb=" N GLY E 270 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N LEU E 271 " --> pdb=" O ARG E 268 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE E 273 " --> pdb=" O GLY E 270 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR E 274 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR E 278 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET E 279 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR E 280 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN E 282 " --> pdb=" O MET E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 324 removed outlier: 3.803A pdb=" N VAL E 305 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 399 removed outlier: 3.723A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA E 399 " --> pdb=" O PHE E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 426 removed outlier: 4.101A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 3.577A pdb=" N PHE E 420 " --> pdb=" O ILE E 416 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ILE E 423 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR E 425 " --> pdb=" O TYR E 421 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 6.140A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 59 through 61 Processing sheet with id= C, first strand: chain 'A' and resid 114 through 116 Processing sheet with id= D, first strand: chain 'A' and resid 210 through 213 Processing sheet with id= E, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.140A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 59 through 61 Processing sheet with id= G, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= H, first strand: chain 'B' and resid 210 through 213 Processing sheet with id= I, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.140A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASN C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 59 through 61 Processing sheet with id= K, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= L, first strand: chain 'C' and resid 210 through 213 Processing sheet with id= M, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.140A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 59 through 61 Processing sheet with id= O, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= P, first strand: chain 'D' and resid 210 through 213 Processing sheet with id= Q, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.140A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 59 through 61 Processing sheet with id= S, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= T, first strand: chain 'E' and resid 210 through 213 500 hydrogen bonds defined for protein. 1350 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: 4.23 Time building geometry restraints manager: 6.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4350 1.35 - 1.47: 3927 1.47 - 1.60: 6013 1.60 - 1.73: 0 1.73 - 1.86: 150 Bond restraints: 14440 Sorted by residual: bond pdb=" CB ARG A 234 " pdb=" CG ARG A 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB ARG D 234 " pdb=" CG ARG D 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.70e+00 bond pdb=" CB ARG E 234 " pdb=" CG ARG E 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.69e+00 bond pdb=" CB ARG B 234 " pdb=" CG ARG B 234 " ideal model delta sigma weight residual 1.520 1.455 0.065 3.00e-02 1.11e+03 4.66e+00 bond pdb=" CB ARG C 234 " pdb=" CG ARG C 234 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.57e+00 ... (remaining 14435 not shown) Histogram of bond angle deviations from ideal: 98.78 - 105.93: 372 105.93 - 113.08: 7930 113.08 - 120.23: 5529 120.23 - 127.38: 5623 127.38 - 134.53: 156 Bond angle restraints: 19610 Sorted by residual: angle pdb=" C VAL E 127 " pdb=" N THR E 128 " pdb=" CA THR E 128 " ideal model delta sigma weight residual 121.54 134.53 -12.99 1.91e+00 2.74e-01 4.62e+01 angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 134.51 -12.97 1.91e+00 2.74e-01 4.61e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 134.50 -12.96 1.91e+00 2.74e-01 4.60e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 134.49 -12.95 1.91e+00 2.74e-01 4.60e+01 ... (remaining 19605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.59: 8531 21.59 - 43.18: 194 43.18 - 64.77: 25 64.77 - 86.36: 35 86.36 - 107.95: 20 Dihedral angle restraints: 8805 sinusoidal: 3690 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS E 154 " pdb=" SG CYS E 154 " pdb=" SG CYS E 168 " pdb=" CB CYS E 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.65 43.35 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.67 43.33 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS C 154 " pdb=" SG CYS C 154 " pdb=" SG CYS C 168 " pdb=" CB CYS C 168 " ideal model delta sinusoidal sigma weight residual 93.00 49.67 43.33 1 1.00e+01 1.00e-02 2.62e+01 ... (remaining 8802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1606 0.059 - 0.118: 541 0.118 - 0.177: 88 0.177 - 0.236: 19 0.236 - 0.295: 6 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C5 BMA J 3 " pdb=" C4 BMA J 3 " pdb=" C6 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 128 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C THR B 128 " -0.040 2.00e-02 2.50e+03 pdb=" O THR B 128 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 129 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 128 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C THR E 128 " 0.040 2.00e-02 2.50e+03 pdb=" O THR E 128 " -0.015 2.00e-02 2.50e+03 pdb=" N THR E 129 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 128 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C THR A 128 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 128 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A 129 " -0.013 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4143 2.80 - 3.33: 12318 3.33 - 3.85: 23379 3.85 - 4.38: 27571 4.38 - 4.90: 45579 Nonbonded interactions: 112990 Sorted by model distance: nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.277 2.440 ... (remaining 112985 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' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.490 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 38.920 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 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 : 0.010 0.065 14440 Z= 0.637 Angle : 1.017 12.987 19610 Z= 0.525 Chirality : 0.060 0.295 2260 Planarity : 0.007 0.047 2435 Dihedral : 13.315 107.951 5455 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.15), residues: 1710 helix: -4.53 (0.10), residues: 600 sheet: -1.36 (0.24), residues: 345 loop : -2.80 (0.17), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 110 HIS 0.006 0.002 HIS D 231 PHE 0.023 0.003 PHE B 115 TYR 0.026 0.003 TYR C 425 ARG 0.011 0.001 ARG C 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8392 (ttp) cc_final: 0.7531 (ttt) REVERT: A 28 GLU cc_start: 0.8966 (tp30) cc_final: 0.8739 (tm-30) REVERT: A 105 MET cc_start: 0.8435 (mmp) cc_final: 0.8130 (mpp) REVERT: A 249 LEU cc_start: 0.9356 (mt) cc_final: 0.9012 (pp) REVERT: A 317 TYR cc_start: 0.8371 (t80) cc_final: 0.7818 (t80) REVERT: B 173 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7715 (mp0) REVERT: B 249 LEU cc_start: 0.9329 (mt) cc_final: 0.8999 (pp) REVERT: C 105 MET cc_start: 0.8458 (mmp) cc_final: 0.8231 (mpp) REVERT: C 249 LEU cc_start: 0.9315 (mt) cc_final: 0.9031 (pp) REVERT: D 72 MET cc_start: 0.8996 (mtm) cc_final: 0.8753 (mtm) REVERT: D 173 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7616 (mm-30) REVERT: D 249 LEU cc_start: 0.9290 (mt) cc_final: 0.8993 (pp) REVERT: D 292 LYS cc_start: 0.9260 (mttt) cc_final: 0.9004 (mmmm) REVERT: D 317 TYR cc_start: 0.8351 (t80) cc_final: 0.8087 (t80) REVERT: E 249 LEU cc_start: 0.9299 (mt) cc_final: 0.8934 (pp) REVERT: E 416 ILE cc_start: 0.9509 (tp) cc_final: 0.9292 (tp) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 1.2119 time to fit residues: 427.7387 Evaluate side-chains 176 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.0010 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 82 GLN ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN B 82 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 82 GLN ** C 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN D 77 ASN D 82 GLN ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 82 GLN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14440 Z= 0.219 Angle : 0.687 10.202 19610 Z= 0.343 Chirality : 0.044 0.200 2260 Planarity : 0.005 0.052 2435 Dihedral : 11.257 69.670 2195 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.78 % Allowed : 10.66 % Favored : 86.56 % 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: -3.61 (0.17), residues: 1710 helix: -3.19 (0.15), residues: 610 sheet: -0.78 (0.26), residues: 345 loop : -2.37 (0.18), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 186 HIS 0.002 0.000 HIS B 231 PHE 0.021 0.001 PHE D 258 TYR 0.015 0.001 TYR C 425 ARG 0.009 0.001 ARG A 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 213 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8419 (mmm) REVERT: A 300 ASP cc_start: 0.9061 (m-30) cc_final: 0.8732 (m-30) REVERT: B 173 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7271 (mp0) REVERT: B 235 GLN cc_start: 0.9270 (mm-40) cc_final: 0.9018 (mm110) REVERT: B 243 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8390 (mmm) REVERT: B 262 MET cc_start: 0.7033 (mpm) cc_final: 0.6800 (mpt) REVERT: B 317 TYR cc_start: 0.8487 (t80) cc_final: 0.8172 (t80) REVERT: C 243 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8277 (mmm) REVERT: C 300 ASP cc_start: 0.9105 (m-30) cc_final: 0.8788 (m-30) REVERT: C 317 TYR cc_start: 0.8446 (t80) cc_final: 0.7954 (t80) REVERT: D 105 MET cc_start: 0.8541 (mmp) cc_final: 0.8174 (mmp) REVERT: D 235 GLN cc_start: 0.9263 (mm-40) cc_final: 0.9019 (mm110) REVERT: D 243 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8442 (mmm) REVERT: E 236 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7479 (tmm) REVERT: E 243 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8333 (mmm) REVERT: E 317 TYR cc_start: 0.8460 (t80) cc_final: 0.8190 (t80) REVERT: E 391 MET cc_start: 0.0538 (tpt) cc_final: 0.0217 (tpp) outliers start: 42 outliers final: 13 residues processed: 232 average time/residue: 0.9848 time to fit residues: 256.5594 Evaluate side-chains 187 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 168 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 416 ILE Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 0.0980 chunk 105 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 0.0040 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 ASN A 231 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN B 231 HIS C 62 ASN C 231 HIS D 231 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14440 Z= 0.158 Angle : 0.615 9.573 19610 Z= 0.303 Chirality : 0.043 0.159 2260 Planarity : 0.003 0.036 2435 Dihedral : 8.436 59.836 2195 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.19 % Allowed : 12.72 % Favored : 85.10 % 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: -2.58 (0.18), residues: 1710 helix: -2.21 (0.17), residues: 610 sheet: -0.19 (0.28), residues: 340 loop : -1.90 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 186 HIS 0.001 0.000 HIS B 217 PHE 0.013 0.001 PHE D 258 TYR 0.018 0.001 TYR D 317 ARG 0.005 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 190 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 243 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8350 (mmm) REVERT: A 300 ASP cc_start: 0.9065 (m-30) cc_final: 0.8774 (m-30) REVERT: A 306 CYS cc_start: 0.8758 (m) cc_final: 0.8069 (t) REVERT: A 317 TYR cc_start: 0.8467 (t80) cc_final: 0.7958 (t80) REVERT: B 156 MET cc_start: 0.9146 (mmt) cc_final: 0.8761 (mmt) REVERT: B 166 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7907 (mm110) REVERT: B 214 CYS cc_start: 0.4989 (p) cc_final: 0.4725 (p) REVERT: B 243 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8353 (mmm) REVERT: B 262 MET cc_start: 0.7121 (mpm) cc_final: 0.6904 (mpt) REVERT: B 300 ASP cc_start: 0.9093 (m-30) cc_final: 0.8777 (m-30) REVERT: B 306 CYS cc_start: 0.8646 (m) cc_final: 0.8001 (t) REVERT: B 317 TYR cc_start: 0.8525 (t80) cc_final: 0.8165 (t80) REVERT: C 163 MET cc_start: 0.8771 (mpp) cc_final: 0.8328 (mtp) REVERT: C 243 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8267 (mmm) REVERT: C 292 LYS cc_start: 0.9473 (OUTLIER) cc_final: 0.9247 (mttp) REVERT: C 300 ASP cc_start: 0.9069 (m-30) cc_final: 0.8762 (m-30) REVERT: C 306 CYS cc_start: 0.8453 (m) cc_final: 0.8110 (t) REVERT: C 317 TYR cc_start: 0.8401 (t80) cc_final: 0.7965 (t80) REVERT: D 31 ASP cc_start: 0.8779 (m-30) cc_final: 0.8299 (m-30) REVERT: D 173 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7495 (mm-30) REVERT: D 235 GLN cc_start: 0.9323 (mm-40) cc_final: 0.9091 (mm110) REVERT: D 243 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8401 (mmm) REVERT: D 292 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.8955 (mmmm) REVERT: D 300 ASP cc_start: 0.9064 (m-30) cc_final: 0.8697 (m-30) REVERT: E 243 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8296 (mmm) REVERT: E 292 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.8943 (mmmm) REVERT: E 300 ASP cc_start: 0.9067 (m-30) cc_final: 0.8798 (m-30) REVERT: E 306 CYS cc_start: 0.8583 (m) cc_final: 0.8091 (t) REVERT: E 317 TYR cc_start: 0.8486 (t80) cc_final: 0.8271 (t80) outliers start: 33 outliers final: 17 residues processed: 206 average time/residue: 0.9243 time to fit residues: 214.9238 Evaluate side-chains 191 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 292 LYS Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 226 ILE Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.0370 chunk 116 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 166 GLN D 77 ASN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14440 Z= 0.312 Angle : 0.630 9.029 19610 Z= 0.314 Chirality : 0.044 0.151 2260 Planarity : 0.003 0.031 2435 Dihedral : 7.001 59.934 2195 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.84 % Allowed : 12.25 % Favored : 83.91 % 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: -1.94 (0.19), residues: 1710 helix: -1.61 (0.19), residues: 610 sheet: 0.14 (0.30), residues: 345 loop : -1.59 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 186 HIS 0.001 0.000 HIS E 231 PHE 0.009 0.001 PHE A 258 TYR 0.018 0.002 TYR D 317 ARG 0.003 0.000 ARG E 287 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 170 time to evaluate : 1.613 Fit side-chains REVERT: A 243 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8266 (mpp) REVERT: A 300 ASP cc_start: 0.9095 (m-30) cc_final: 0.8764 (m-30) REVERT: A 306 CYS cc_start: 0.8775 (m) cc_final: 0.8157 (t) REVERT: A 317 TYR cc_start: 0.8563 (t80) cc_final: 0.8021 (t80) REVERT: B 105 MET cc_start: 0.8565 (mmp) cc_final: 0.8346 (mmp) REVERT: B 243 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8136 (mpp) REVERT: B 300 ASP cc_start: 0.9108 (m-30) cc_final: 0.8760 (m-30) REVERT: B 306 CYS cc_start: 0.8651 (m) cc_final: 0.8116 (t) REVERT: B 317 TYR cc_start: 0.8634 (t80) cc_final: 0.8200 (t80) REVERT: C 243 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8315 (mmm) REVERT: C 300 ASP cc_start: 0.9106 (m-30) cc_final: 0.8783 (m-30) REVERT: C 306 CYS cc_start: 0.8469 (m) cc_final: 0.8148 (t) REVERT: C 317 TYR cc_start: 0.8511 (t80) cc_final: 0.8111 (t80) REVERT: D 31 ASP cc_start: 0.8781 (m-30) cc_final: 0.8311 (m-30) REVERT: D 72 MET cc_start: 0.8943 (mtm) cc_final: 0.8626 (mmm) REVERT: D 105 MET cc_start: 0.8625 (mmp) cc_final: 0.8316 (mmp) REVERT: D 300 ASP cc_start: 0.9048 (m-30) cc_final: 0.8657 (m-30) REVERT: D 317 TYR cc_start: 0.8477 (t80) cc_final: 0.8256 (t80) REVERT: D 391 MET cc_start: 0.0134 (tpt) cc_final: -0.0272 (tpp) REVERT: E 156 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8651 (tpp) REVERT: E 243 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: E 300 ASP cc_start: 0.9092 (m-30) cc_final: 0.8809 (m-30) REVERT: E 306 CYS cc_start: 0.8561 (m) cc_final: 0.8187 (t) REVERT: E 317 TYR cc_start: 0.8587 (t80) cc_final: 0.8277 (t80) outliers start: 58 outliers final: 26 residues processed: 206 average time/residue: 0.9783 time to fit residues: 226.7725 Evaluate side-chains 189 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.2980 chunk 93 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN ** D 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14440 Z= 0.192 Angle : 0.593 9.593 19610 Z= 0.294 Chirality : 0.043 0.161 2260 Planarity : 0.003 0.039 2435 Dihedral : 6.426 59.208 2195 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.98 % Allowed : 13.64 % Favored : 83.38 % 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: -1.52 (0.20), residues: 1710 helix: -1.19 (0.20), residues: 610 sheet: 0.25 (0.29), residues: 345 loop : -1.35 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 186 HIS 0.001 0.000 HIS B 125 PHE 0.009 0.001 PHE E 258 TYR 0.014 0.001 TYR D 317 ARG 0.003 0.000 ARG A 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 1.585 Fit side-chains REVERT: A 156 MET cc_start: 0.9144 (tpp) cc_final: 0.8749 (tpp) REVERT: A 241 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8897 (mp) REVERT: A 300 ASP cc_start: 0.9055 (m-30) cc_final: 0.8737 (m-30) REVERT: A 306 CYS cc_start: 0.8615 (m) cc_final: 0.8156 (t) REVERT: A 317 TYR cc_start: 0.8528 (t80) cc_final: 0.8004 (t80) REVERT: B 105 MET cc_start: 0.8557 (mmp) cc_final: 0.8331 (mmp) REVERT: B 300 ASP cc_start: 0.9105 (m-30) cc_final: 0.8757 (m-30) REVERT: B 306 CYS cc_start: 0.8575 (m) cc_final: 0.8111 (t) REVERT: C 236 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7353 (tmm) REVERT: C 243 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8302 (mmm) REVERT: C 300 ASP cc_start: 0.9068 (m-30) cc_final: 0.8744 (m-30) REVERT: C 306 CYS cc_start: 0.8372 (m) cc_final: 0.8057 (t) REVERT: C 317 TYR cc_start: 0.8509 (t80) cc_final: 0.8137 (t80) REVERT: D 31 ASP cc_start: 0.8772 (m-30) cc_final: 0.8293 (m-30) REVERT: D 72 MET cc_start: 0.8906 (mtm) cc_final: 0.8616 (mmm) REVERT: D 243 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8342 (mmm) REVERT: D 300 ASP cc_start: 0.9000 (m-30) cc_final: 0.8626 (m-30) REVERT: D 317 TYR cc_start: 0.8460 (t80) cc_final: 0.8257 (t80) REVERT: D 391 MET cc_start: 0.0216 (tpt) cc_final: -0.0079 (tpp) REVERT: E 156 MET cc_start: 0.9077 (tpp) cc_final: 0.8650 (tpp) REVERT: E 236 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7056 (tmm) REVERT: E 300 ASP cc_start: 0.9054 (m-30) cc_final: 0.8792 (m-30) REVERT: E 306 CYS cc_start: 0.8445 (m) cc_final: 0.8152 (t) REVERT: E 317 TYR cc_start: 0.8481 (t80) cc_final: 0.8202 (t80) REVERT: E 391 MET cc_start: 0.0234 (tpt) cc_final: -0.0152 (tpp) outliers start: 45 outliers final: 19 residues processed: 191 average time/residue: 0.9472 time to fit residues: 203.6763 Evaluate side-chains 184 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 160 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 136 optimal weight: 0.0020 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 ASN C 202 GLN D 166 GLN D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 14440 Z= 0.322 Angle : 0.627 9.507 19610 Z= 0.312 Chirality : 0.043 0.149 2260 Planarity : 0.003 0.047 2435 Dihedral : 6.289 58.498 2195 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.38 % Allowed : 14.70 % Favored : 81.92 % 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: -1.33 (0.20), residues: 1710 helix: -1.01 (0.20), residues: 615 sheet: 0.35 (0.29), residues: 345 loop : -1.26 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 186 HIS 0.001 0.000 HIS E 231 PHE 0.009 0.001 PHE A 115 TYR 0.022 0.001 TYR B 317 ARG 0.013 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 160 time to evaluate : 1.603 Fit side-chains REVERT: A 156 MET cc_start: 0.9082 (tpp) cc_final: 0.8308 (tpp) REVERT: A 241 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8890 (mp) REVERT: A 243 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: A 300 ASP cc_start: 0.9070 (m-30) cc_final: 0.8724 (m-30) REVERT: A 306 CYS cc_start: 0.8576 (m) cc_final: 0.8210 (t) REVERT: B 75 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8271 (ttm110) REVERT: B 105 MET cc_start: 0.8632 (mmp) cc_final: 0.8374 (mmp) REVERT: B 241 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8862 (mp) REVERT: B 243 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8064 (mpp) REVERT: B 300 ASP cc_start: 0.9118 (m-30) cc_final: 0.8719 (m-30) REVERT: B 306 CYS cc_start: 0.8520 (m) cc_final: 0.8166 (t) REVERT: B 317 TYR cc_start: 0.8239 (t80) cc_final: 0.7829 (t80) REVERT: C 242 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: C 243 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.7868 (mmm) REVERT: C 248 LEU cc_start: 0.9532 (tp) cc_final: 0.9328 (tm) REVERT: C 300 ASP cc_start: 0.9077 (m-30) cc_final: 0.8733 (m-30) REVERT: D 31 ASP cc_start: 0.8786 (m-30) cc_final: 0.8281 (m-30) REVERT: D 72 MET cc_start: 0.8934 (mtm) cc_final: 0.8618 (mmm) REVERT: D 243 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8381 (mmm) REVERT: D 300 ASP cc_start: 0.9010 (m-30) cc_final: 0.8611 (m-30) REVERT: D 391 MET cc_start: 0.0183 (tpt) cc_final: -0.0073 (tpp) REVERT: D 420 PHE cc_start: 0.8534 (m-80) cc_final: 0.8300 (m-80) REVERT: E 156 MET cc_start: 0.9008 (tpp) cc_final: 0.8662 (tpp) REVERT: E 243 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8363 (mmm) REVERT: E 300 ASP cc_start: 0.9056 (m-30) cc_final: 0.8772 (m-30) REVERT: E 306 CYS cc_start: 0.8519 (m) cc_final: 0.8216 (t) REVERT: E 317 TYR cc_start: 0.8547 (t80) cc_final: 0.8281 (t80) REVERT: E 391 MET cc_start: 0.0445 (tpt) cc_final: 0.0144 (tpp) outliers start: 51 outliers final: 29 residues processed: 185 average time/residue: 0.9107 time to fit residues: 190.8874 Evaluate side-chains 195 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 242 GLN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 93 optimal weight: 0.0470 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 202 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14440 Z= 0.154 Angle : 0.580 9.736 19610 Z= 0.287 Chirality : 0.043 0.168 2260 Planarity : 0.003 0.043 2435 Dihedral : 5.943 59.017 2195 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.85 % Allowed : 15.36 % Favored : 81.79 % 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: -0.92 (0.20), residues: 1710 helix: -0.63 (0.20), residues: 595 sheet: 0.48 (0.29), residues: 345 loop : -1.01 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 186 HIS 0.001 0.000 HIS A 217 PHE 0.010 0.001 PHE A 258 TYR 0.023 0.001 TYR B 317 ARG 0.008 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8876 (tpp) cc_final: 0.8673 (tpp) REVERT: A 166 GLN cc_start: 0.7180 (mt0) cc_final: 0.6968 (tt0) REVERT: A 241 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 300 ASP cc_start: 0.8996 (m-30) cc_final: 0.8695 (m-30) REVERT: A 306 CYS cc_start: 0.8521 (m) cc_final: 0.8214 (t) REVERT: A 317 TYR cc_start: 0.8446 (t80) cc_final: 0.7983 (t80) REVERT: B 105 MET cc_start: 0.8600 (mmp) cc_final: 0.8377 (mmp) REVERT: B 241 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8820 (mp) REVERT: B 243 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8011 (mpp) REVERT: B 300 ASP cc_start: 0.9090 (m-30) cc_final: 0.8734 (m-30) REVERT: B 306 CYS cc_start: 0.8472 (m) cc_final: 0.8125 (t) REVERT: B 317 TYR cc_start: 0.8228 (t80) cc_final: 0.7852 (t80) REVERT: C 105 MET cc_start: 0.8614 (mmm) cc_final: 0.7857 (mpt) REVERT: C 156 MET cc_start: 0.9080 (tpp) cc_final: 0.8871 (tpp) REVERT: C 243 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: C 262 MET cc_start: 0.6445 (pmm) cc_final: 0.6085 (pmm) REVERT: C 300 ASP cc_start: 0.9028 (m-30) cc_final: 0.8695 (m-30) REVERT: C 317 TYR cc_start: 0.8399 (t80) cc_final: 0.8045 (t80) REVERT: D 31 ASP cc_start: 0.8754 (m-30) cc_final: 0.8460 (m-30) REVERT: D 72 MET cc_start: 0.8905 (mtm) cc_final: 0.8705 (mmm) REVERT: D 243 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8362 (mmm) REVERT: D 262 MET cc_start: 0.6340 (pmm) cc_final: 0.6130 (pmm) REVERT: D 300 ASP cc_start: 0.8931 (m-30) cc_final: 0.8560 (m-30) REVERT: D 306 CYS cc_start: 0.8713 (m) cc_final: 0.8286 (t) REVERT: D 317 TYR cc_start: 0.8056 (t80) cc_final: 0.7847 (t80) REVERT: D 391 MET cc_start: 0.0190 (tpt) cc_final: -0.0027 (tpp) REVERT: D 420 PHE cc_start: 0.8507 (m-80) cc_final: 0.8252 (m-80) REVERT: E 156 MET cc_start: 0.8949 (tpp) cc_final: 0.8064 (tpp) REVERT: E 202 GLN cc_start: 0.8901 (mt0) cc_final: 0.8665 (mm-40) REVERT: E 243 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8375 (mmm) REVERT: E 300 ASP cc_start: 0.9010 (m-30) cc_final: 0.8765 (m-30) REVERT: E 306 CYS cc_start: 0.8435 (m) cc_final: 0.8189 (t) REVERT: E 391 MET cc_start: 0.0332 (tpt) cc_final: 0.0045 (tpp) outliers start: 43 outliers final: 26 residues processed: 198 average time/residue: 0.9447 time to fit residues: 210.8394 Evaluate side-chains 198 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14440 Z= 0.286 Angle : 0.618 7.453 19610 Z= 0.310 Chirality : 0.043 0.156 2260 Planarity : 0.004 0.075 2435 Dihedral : 5.801 57.919 2195 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.91 % Allowed : 16.23 % Favored : 80.86 % 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: -0.83 (0.20), residues: 1710 helix: -0.48 (0.20), residues: 600 sheet: 0.59 (0.29), residues: 345 loop : -1.07 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP C 255 HIS 0.001 0.000 HIS D 231 PHE 0.009 0.001 PHE E 258 TYR 0.021 0.001 TYR E 317 ARG 0.017 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 167 time to evaluate : 1.701 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.9126 (ptp) cc_final: 0.8902 (mpp) REVERT: A 202 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8593 (mm-40) REVERT: A 241 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8859 (mp) REVERT: A 243 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8087 (mpp) REVERT: A 300 ASP cc_start: 0.9023 (m-30) cc_final: 0.8710 (m-30) REVERT: A 306 CYS cc_start: 0.8496 (m) cc_final: 0.8222 (t) REVERT: A 317 TYR cc_start: 0.8551 (t80) cc_final: 0.8047 (t80) REVERT: B 105 MET cc_start: 0.8629 (mmp) cc_final: 0.8378 (mmp) REVERT: B 241 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8807 (mp) REVERT: B 243 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8281 (mmm) REVERT: B 300 ASP cc_start: 0.9104 (m-30) cc_final: 0.8718 (m-30) REVERT: B 306 CYS cc_start: 0.8449 (m) cc_final: 0.8184 (t) REVERT: B 317 TYR cc_start: 0.8255 (t80) cc_final: 0.7854 (t80) REVERT: C 243 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8358 (mmm) REVERT: C 262 MET cc_start: 0.6446 (pmm) cc_final: 0.6121 (pmm) REVERT: C 300 ASP cc_start: 0.9048 (m-30) cc_final: 0.8701 (m-30) REVERT: C 317 TYR cc_start: 0.8494 (t80) cc_final: 0.8142 (t80) REVERT: D 72 MET cc_start: 0.8918 (mtm) cc_final: 0.8683 (mmm) REVERT: D 243 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8388 (mmm) REVERT: D 300 ASP cc_start: 0.8955 (m-30) cc_final: 0.8574 (m-30) REVERT: D 306 CYS cc_start: 0.8735 (m) cc_final: 0.8305 (t) REVERT: D 317 TYR cc_start: 0.8101 (t80) cc_final: 0.7888 (t80) REVERT: D 420 PHE cc_start: 0.8550 (m-80) cc_final: 0.8311 (m-80) REVERT: E 202 GLN cc_start: 0.8912 (mt0) cc_final: 0.8663 (mm-40) REVERT: E 243 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8387 (mmm) REVERT: E 300 ASP cc_start: 0.9032 (m-30) cc_final: 0.8773 (m-30) REVERT: E 306 CYS cc_start: 0.8465 (m) cc_final: 0.8240 (t) REVERT: E 317 TYR cc_start: 0.8349 (t80) cc_final: 0.7967 (t80) REVERT: E 391 MET cc_start: 0.0277 (tpt) cc_final: 0.0027 (tpp) outliers start: 44 outliers final: 27 residues processed: 192 average time/residue: 0.9188 time to fit residues: 200.4973 Evaluate side-chains 197 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 202 GLN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14440 Z= 0.210 Angle : 0.636 11.144 19610 Z= 0.312 Chirality : 0.043 0.161 2260 Planarity : 0.004 0.087 2435 Dihedral : 5.703 56.947 2195 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.52 % Allowed : 17.28 % Favored : 80.20 % 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: -0.73 (0.20), residues: 1710 helix: -0.32 (0.20), residues: 600 sheet: 0.65 (0.29), residues: 345 loop : -1.09 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP C 255 HIS 0.001 0.000 HIS C 231 PHE 0.008 0.001 PHE E 258 TYR 0.019 0.001 TYR B 317 ARG 0.019 0.001 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 164 time to evaluate : 1.603 Fit side-chains REVERT: A 163 MET cc_start: 0.9113 (ptp) cc_final: 0.8889 (mpp) REVERT: A 241 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8852 (mp) REVERT: A 243 MET cc_start: 0.8761 (mmm) cc_final: 0.8080 (mpp) REVERT: A 300 ASP cc_start: 0.9005 (m-30) cc_final: 0.8693 (m-30) REVERT: A 306 CYS cc_start: 0.8509 (m) cc_final: 0.8259 (t) REVERT: A 317 TYR cc_start: 0.8553 (t80) cc_final: 0.8088 (t80) REVERT: B 105 MET cc_start: 0.8622 (mmp) cc_final: 0.8375 (mmp) REVERT: B 241 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8783 (mp) REVERT: B 300 ASP cc_start: 0.9086 (m-30) cc_final: 0.8707 (m-30) REVERT: B 306 CYS cc_start: 0.8450 (m) cc_final: 0.8196 (t) REVERT: B 317 TYR cc_start: 0.8242 (t80) cc_final: 0.7858 (t80) REVERT: C 243 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8340 (mmm) REVERT: C 262 MET cc_start: 0.6509 (pmm) cc_final: 0.6155 (pmm) REVERT: C 300 ASP cc_start: 0.9026 (m-30) cc_final: 0.8684 (m-30) REVERT: C 317 TYR cc_start: 0.8466 (t80) cc_final: 0.8135 (t80) REVERT: D 72 MET cc_start: 0.8924 (mtm) cc_final: 0.8710 (mmm) REVERT: D 243 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8384 (mmm) REVERT: D 300 ASP cc_start: 0.8964 (m-30) cc_final: 0.8579 (m-30) REVERT: D 306 CYS cc_start: 0.8662 (m) cc_final: 0.8237 (t) REVERT: D 317 TYR cc_start: 0.8113 (t80) cc_final: 0.7586 (t80) REVERT: D 420 PHE cc_start: 0.8528 (m-80) cc_final: 0.8292 (m-80) REVERT: E 28 GLU cc_start: 0.8586 (mp0) cc_final: 0.8309 (mp0) REVERT: E 202 GLN cc_start: 0.8900 (mt0) cc_final: 0.8601 (mm-40) REVERT: E 243 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8391 (mmm) REVERT: E 300 ASP cc_start: 0.9001 (m-30) cc_final: 0.8739 (m-30) REVERT: E 317 TYR cc_start: 0.8244 (t80) cc_final: 0.7967 (t80) REVERT: E 391 MET cc_start: 0.0269 (tpt) cc_final: 0.0011 (tpp) outliers start: 38 outliers final: 27 residues processed: 187 average time/residue: 0.8991 time to fit residues: 190.9419 Evaluate side-chains 192 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 306 CYS Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN C 202 GLN D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14440 Z= 0.156 Angle : 0.613 10.238 19610 Z= 0.297 Chirality : 0.043 0.165 2260 Planarity : 0.004 0.080 2435 Dihedral : 5.446 54.599 2195 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.45 % Allowed : 17.42 % Favored : 80.13 % 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: -0.43 (0.20), residues: 1710 helix: -0.08 (0.21), residues: 595 sheet: 0.88 (0.30), residues: 320 loop : -0.88 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C 255 HIS 0.001 0.000 HIS B 231 PHE 0.012 0.001 PHE E 258 TYR 0.018 0.001 TYR B 317 ARG 0.019 0.000 ARG B 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 163 MET cc_start: 0.9112 (ptp) cc_final: 0.8870 (mpp) REVERT: A 241 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 243 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8141 (mpp) REVERT: A 300 ASP cc_start: 0.8994 (m-30) cc_final: 0.8689 (m-30) REVERT: A 306 CYS cc_start: 0.8494 (m) cc_final: 0.8226 (t) REVERT: A 317 TYR cc_start: 0.8486 (t80) cc_final: 0.8026 (t80) REVERT: B 241 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8795 (mp) REVERT: B 300 ASP cc_start: 0.9082 (m-30) cc_final: 0.8738 (m-30) REVERT: B 317 TYR cc_start: 0.8167 (t80) cc_final: 0.7804 (t80) REVERT: C 243 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: C 262 MET cc_start: 0.6423 (pmm) cc_final: 0.6058 (pmm) REVERT: C 300 ASP cc_start: 0.9022 (m-30) cc_final: 0.8680 (m-30) REVERT: C 317 TYR cc_start: 0.8428 (t80) cc_final: 0.8157 (t80) REVERT: D 105 MET cc_start: 0.8509 (mpp) cc_final: 0.8122 (mpm) REVERT: D 243 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8336 (mmm) REVERT: D 300 ASP cc_start: 0.8953 (m-30) cc_final: 0.8581 (m-30) REVERT: D 306 CYS cc_start: 0.8606 (m) cc_final: 0.8230 (t) REVERT: D 317 TYR cc_start: 0.8099 (t80) cc_final: 0.7577 (t80) REVERT: D 420 PHE cc_start: 0.8517 (m-80) cc_final: 0.8276 (m-80) REVERT: E 28 GLU cc_start: 0.8598 (mp0) cc_final: 0.8335 (mp0) REVERT: E 317 TYR cc_start: 0.8086 (t80) cc_final: 0.7804 (t80) REVERT: E 391 MET cc_start: 0.0339 (tpt) cc_final: 0.0082 (tpp) outliers start: 37 outliers final: 21 residues processed: 195 average time/residue: 0.8635 time to fit residues: 191.4820 Evaluate side-chains 195 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 243 MET Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 219 ASN Chi-restraints excluded: chain E residue 310 VAL Chi-restraints excluded: chain E residue 412 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 0.1980 chunk 124 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 17 optimal weight: 0.0170 chunk 24 optimal weight: 0.3980 chunk 118 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 overall best weight: 0.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.094158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.063969 restraints weight = 33775.355| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.87 r_work: 0.2762 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14440 Z= 0.137 Angle : 0.604 10.635 19610 Z= 0.293 Chirality : 0.043 0.178 2260 Planarity : 0.004 0.079 2435 Dihedral : 5.277 51.243 2195 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.05 % Allowed : 18.08 % Favored : 79.87 % 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: -0.36 (0.20), residues: 1710 helix: 0.07 (0.21), residues: 595 sheet: 0.95 (0.29), residues: 315 loop : -0.93 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP E 255 HIS 0.000 0.000 HIS C 231 PHE 0.014 0.001 PHE E 258 TYR 0.017 0.001 TYR B 317 ARG 0.018 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4526.98 seconds wall clock time: 83 minutes 9.86 seconds (4989.86 seconds total)