Starting phenix.real_space_refine on Fri Feb 16 03:23:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/02_2024/6plo_20370_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/02_2024/6plo_20370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/02_2024/6plo_20370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/02_2024/6plo_20370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/02_2024/6plo_20370_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6plo_20370/02_2024/6plo_20370_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 100 5.16 5 C 9230 2.51 5 N 2275 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 TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14165 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 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: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 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: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 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: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 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: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2787 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 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: 7.48, per 1000 atoms: 0.53 Number of scatterers: 14165 At special positions: 0 Unit cell: (104.48, 105.786, 134.518, 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 100 16.00 O 2560 8.00 N 2275 7.00 C 9230 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.04 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.03 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=2.03 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: 5.42 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: 50 helices and 25 sheets defined 30.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.656A pdb=" N LEU A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) 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 106 removed outlier: 3.579A pdb=" N LEU A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 106' 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 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 244 through 258 removed outlier: 3.735A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 284 removed outlier: 3.960A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET A 279 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 323 removed outlier: 3.513A pdb=" N VAL A 310 " --> pdb=" O CYS A 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 400 removed outlier: 4.024A pdb=" N ILE A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 427 removed outlier: 3.566A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.199A pdb=" N LEU A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 423 " --> pdb=" O ILE A 419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 34 removed outlier: 3.656A pdb=" N LEU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) 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 106 removed outlier: 3.580A pdb=" N LEU B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 103 through 106' 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 239 through 242 No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 244 through 258 removed outlier: 3.735A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 284 removed outlier: 3.960A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 282 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 323 removed outlier: 3.513A pdb=" N VAL B 310 " --> pdb=" O CYS B 306 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 400 removed outlier: 4.024A pdb=" N ILE B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 427 removed outlier: 3.566A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix removed outlier: 4.199A pdb=" N LEU B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 423 " --> pdb=" O ILE B 419 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 34 removed outlier: 3.657A pdb=" N LEU C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) 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 106 removed outlier: 3.580A pdb=" N LEU C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' 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 239 through 242 No H-bonds generated for 'chain 'C' and resid 239 through 242' Processing helix chain 'C' and resid 244 through 258 removed outlier: 3.736A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP C 255 " --> pdb=" O VAL C 251 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 284 removed outlier: 3.960A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 323 removed outlier: 3.513A pdb=" N VAL C 310 " --> pdb=" O CYS C 306 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 400 removed outlier: 4.024A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 427 removed outlier: 3.566A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix removed outlier: 4.198A pdb=" N LEU C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 425 " --> pdb=" O TYR C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.657A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) 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 106 removed outlier: 3.580A pdb=" N LEU D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 103 through 106' 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 239 through 242 No H-bonds generated for 'chain 'D' and resid 239 through 242' Processing helix chain 'D' and resid 244 through 258 removed outlier: 3.735A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP D 255 " --> pdb=" O VAL D 251 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 284 removed outlier: 3.960A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 282 " --> pdb=" O THR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 323 removed outlier: 3.513A pdb=" N VAL D 310 " --> pdb=" O CYS D 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA D 313 " --> pdb=" O PHE D 309 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 400 removed outlier: 4.024A pdb=" N ILE D 396 " --> pdb=" O ARG D 392 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 427 removed outlier: 3.566A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix removed outlier: 4.198A pdb=" N LEU D 415 " --> pdb=" O PRO D 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 424 " --> pdb=" O PHE D 420 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 425 " --> pdb=" O TYR D 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 34 removed outlier: 3.657A pdb=" N LEU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) 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 106 removed outlier: 3.580A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 106' 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 239 through 242 No H-bonds generated for 'chain 'E' and resid 239 through 242' Processing helix chain 'E' and resid 244 through 258 removed outlier: 3.735A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TRP E 255 " --> pdb=" O VAL E 251 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL E 256 " --> pdb=" O ILE E 252 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER E 257 " --> pdb=" O LEU E 253 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE E 258 " --> pdb=" O SER E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 3.960A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL E 276 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N MET E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 323 removed outlier: 3.512A pdb=" N VAL E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 313 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 400 removed outlier: 4.024A pdb=" N ILE E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 427 removed outlier: 3.567A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix removed outlier: 4.198A pdb=" N LEU E 415 " --> pdb=" O PRO E 411 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TRP E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR E 424 " --> pdb=" O PHE E 420 " (cutoff:3.500A) removed outlier: 3.516A 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: 6.187A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN A 85 " --> pdb=" O ASN A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 192 through 194 removed outlier: 6.247A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG A 75 " --> pdb=" O PHE A 64 " (cutoff:3.500A) 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 132 through 136 Processing sheet with id= E, first strand: chain 'A' and resid 211 through 213 Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 6.187A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN B 85 " --> pdb=" O ASN B 54 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 192 through 194 removed outlier: 6.247A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 114 through 116 Processing sheet with id= I, first strand: chain 'B' and resid 132 through 136 Processing sheet with id= J, first strand: chain 'B' and resid 211 through 213 Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 6.187A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN C 85 " --> pdb=" O ASN C 54 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 192 through 194 removed outlier: 6.247A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG C 75 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 114 through 116 Processing sheet with id= N, first strand: chain 'C' and resid 132 through 136 Processing sheet with id= O, first strand: chain 'C' and resid 211 through 213 Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 6.187A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN D 85 " --> pdb=" O ASN D 54 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 192 through 194 removed outlier: 6.247A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG D 75 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= S, first strand: chain 'D' and resid 132 through 136 Processing sheet with id= T, first strand: chain 'D' and resid 211 through 213 Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.186A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN E 85 " --> pdb=" O ASN E 54 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 192 through 194 removed outlier: 6.246A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ARG E 75 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 114 through 116 Processing sheet with id= X, first strand: chain 'E' and resid 132 through 136 Processing sheet with id= Y, first strand: chain 'E' and resid 211 through 213 392 hydrogen bonds defined for protein. 1176 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: 4.06 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4247 1.34 - 1.46: 3535 1.46 - 1.58: 6558 1.58 - 1.70: 0 1.70 - 1.83: 170 Bond restraints: 14510 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.13e+00 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.12e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.554 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 ... (remaining 14505 not shown) Histogram of bond angle deviations from ideal: 97.78 - 105.03: 328 105.03 - 112.29: 7108 112.29 - 119.54: 4918 119.54 - 126.80: 7101 126.80 - 134.05: 225 Bond angle restraints: 19680 Sorted by residual: angle pdb=" C VAL A 127 " pdb=" N THR A 128 " pdb=" CA THR A 128 " ideal model delta sigma weight residual 121.54 132.23 -10.69 1.91e+00 2.74e-01 3.13e+01 angle pdb=" C VAL D 127 " pdb=" N THR D 128 " pdb=" CA THR D 128 " ideal model delta sigma weight residual 121.54 132.22 -10.68 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C VAL C 127 " pdb=" N THR C 128 " pdb=" CA THR C 128 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" C VAL B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta sigma weight residual 121.54 132.20 -10.66 1.91e+00 2.74e-01 3.12e+01 angle pdb=" N VAL E 37 " pdb=" CA VAL E 37 " pdb=" C VAL E 37 " ideal model delta sigma weight residual 113.53 108.06 5.47 9.80e-01 1.04e+00 3.12e+01 ... (remaining 19675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 8625 21.71 - 43.42: 185 43.42 - 65.13: 10 65.13 - 86.85: 35 86.85 - 108.56: 20 Dihedral angle restraints: 8875 sinusoidal: 3760 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASN D 261 " pdb=" C ASN D 261 " pdb=" N MET D 262 " pdb=" CA MET D 262 " ideal model delta harmonic sigma weight residual 180.00 151.85 28.15 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASN E 261 " pdb=" C ASN E 261 " pdb=" N MET E 262 " pdb=" CA MET E 262 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA ASN B 261 " pdb=" C ASN B 261 " pdb=" N MET B 262 " pdb=" CA MET B 262 " ideal model delta harmonic sigma weight residual 180.00 151.86 28.14 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 8872 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1574 0.055 - 0.110: 563 0.110 - 0.165: 93 0.165 - 0.220: 25 0.220 - 0.276: 5 Chirality restraints: 2260 Sorted by residual: 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 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 2257 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 410 " 0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 411 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 410 " -0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO C 411 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 411 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 411 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 410 " -0.043 5.00e-02 4.00e+02 6.39e-02 6.54e+00 pdb=" N PRO B 411 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 411 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 411 " -0.036 5.00e-02 4.00e+02 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 4568 2.84 - 3.35: 12176 3.35 - 3.87: 23281 3.87 - 4.38: 27372 4.38 - 4.90: 46105 Nonbonded interactions: 113502 Sorted by model distance: nonbonded pdb=" OE2 GLU C 69 " pdb=" NH2 ARG C 234 " model vdw 2.321 2.520 nonbonded pdb=" OE2 GLU D 69 " pdb=" NH2 ARG D 234 " model vdw 2.321 2.520 nonbonded pdb=" OE2 GLU A 69 " pdb=" NH2 ARG A 234 " model vdw 2.321 2.520 nonbonded pdb=" OE2 GLU B 69 " pdb=" NH2 ARG B 234 " model vdw 2.322 2.520 nonbonded pdb=" OE2 GLU E 69 " pdb=" NH2 ARG E 234 " model vdw 2.322 2.520 ... (remaining 113497 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.440 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 38.620 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 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 : 0.007 0.051 14510 Z= 0.473 Angle : 1.063 12.024 19680 Z= 0.542 Chirality : 0.058 0.276 2260 Planarity : 0.007 0.064 2435 Dihedral : 12.903 108.558 5525 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -5.29 (0.14), residues: 1710 helix: -4.71 (0.08), residues: 530 sheet: -2.76 (0.23), residues: 345 loop : -2.92 (0.17), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 302 HIS 0.004 0.002 HIS E 231 PHE 0.025 0.003 PHE C 115 TYR 0.024 0.003 TYR D 425 ARG 0.007 0.001 ARG A 234 *********************** 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 441 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.625 Fit side-chains REVERT: A 156 MET cc_start: 0.8587 (mmm) cc_final: 0.8137 (mmm) REVERT: A 426 LYS cc_start: 0.7044 (ttmt) cc_final: 0.6313 (mptt) REVERT: B 63 SER cc_start: 0.8825 (t) cc_final: 0.8590 (m) REVERT: B 113 ASP cc_start: 0.9085 (p0) cc_final: 0.8795 (p0) REVERT: B 156 MET cc_start: 0.8611 (mmm) cc_final: 0.8081 (mmm) REVERT: B 426 LYS cc_start: 0.7095 (ttmt) cc_final: 0.6306 (mmtm) REVERT: C 156 MET cc_start: 0.8607 (mmm) cc_final: 0.8149 (mmm) REVERT: C 173 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7611 (mt-10) REVERT: C 426 LYS cc_start: 0.6978 (ttmt) cc_final: 0.6227 (mptt) REVERT: D 43 ARG cc_start: 0.9018 (mtm-85) cc_final: 0.8801 (mtm180) REVERT: D 63 SER cc_start: 0.8777 (t) cc_final: 0.8575 (m) REVERT: D 156 MET cc_start: 0.8622 (mmm) cc_final: 0.8219 (mmm) REVERT: D 426 LYS cc_start: 0.7082 (ttmt) cc_final: 0.6244 (mmtm) REVERT: E 156 MET cc_start: 0.8592 (mmm) cc_final: 0.8237 (mmm) REVERT: E 426 LYS cc_start: 0.7024 (ttmt) cc_final: 0.6205 (mmtt) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.2914 time to fit residues: 179.7330 Evaluate side-chains 288 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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: 10.0000 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.0980 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 141 ASN A 231 HIS A 235 GLN A 242 GLN A 261 ASN A 282 GLN A 321 ASN B 62 ASN B 139 ASN B 141 ASN B 231 HIS B 235 GLN B 242 GLN B 261 ASN B 282 GLN B 321 ASN C 62 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS C 235 GLN C 242 GLN ** C 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN C 321 ASN D 62 ASN ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 HIS D 235 GLN D 242 GLN D 261 ASN D 282 GLN ** D 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 139 ASN E 141 ASN E 231 HIS E 235 GLN E 242 GLN E 261 ASN E 282 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14510 Z= 0.261 Angle : 0.696 5.574 19680 Z= 0.360 Chirality : 0.046 0.164 2260 Planarity : 0.005 0.040 2435 Dihedral : 10.869 68.094 2195 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.92 % Allowed : 10.92 % Favored : 85.16 % 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: -4.21 (0.16), residues: 1710 helix: -3.56 (0.13), residues: 555 sheet: -2.20 (0.24), residues: 350 loop : -2.37 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 84 HIS 0.004 0.001 HIS E 231 PHE 0.016 0.002 PHE D 322 TYR 0.012 0.001 TYR A 317 ARG 0.005 0.001 ARG D 147 *********************** 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 373 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 313 time to evaluate : 1.559 Fit side-chains REVERT: A 301 ILE cc_start: 0.8862 (pt) cc_final: 0.8511 (mt) REVERT: A 314 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7663 (tt) REVERT: A 416 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8435 (pt) REVERT: A 420 PHE cc_start: 0.7516 (t80) cc_final: 0.7060 (m-80) REVERT: A 426 LYS cc_start: 0.7104 (ttmt) cc_final: 0.6099 (mmtm) REVERT: B 63 SER cc_start: 0.8786 (t) cc_final: 0.8544 (m) REVERT: B 204 ILE cc_start: 0.9009 (pt) cc_final: 0.8793 (pt) REVERT: B 301 ILE cc_start: 0.8877 (pt) cc_final: 0.8507 (mt) REVERT: B 314 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7623 (tt) REVERT: B 398 ARG cc_start: 0.6562 (mtt90) cc_final: 0.6315 (mmt-90) REVERT: B 415 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7593 (tt) REVERT: B 416 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8384 (pt) REVERT: B 420 PHE cc_start: 0.7621 (t80) cc_final: 0.7306 (t80) REVERT: B 426 LYS cc_start: 0.7182 (ttmt) cc_final: 0.6210 (mmtm) REVERT: C 179 MET cc_start: 0.8484 (mpp) cc_final: 0.8282 (mmm) REVERT: C 301 ILE cc_start: 0.8853 (pt) cc_final: 0.8521 (mt) REVERT: C 398 ARG cc_start: 0.6415 (mtt90) cc_final: 0.6199 (mmt-90) REVERT: C 415 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7550 (tt) REVERT: C 426 LYS cc_start: 0.7113 (ttmt) cc_final: 0.6009 (mmtt) REVERT: D 43 ARG cc_start: 0.9031 (mtm-85) cc_final: 0.8632 (mtm180) REVERT: D 301 ILE cc_start: 0.8843 (pt) cc_final: 0.8474 (mt) REVERT: D 398 ARG cc_start: 0.6407 (mtt90) cc_final: 0.6195 (mmt-90) REVERT: D 415 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7680 (tt) REVERT: D 416 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8367 (pt) REVERT: D 426 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6225 (mmtm) REVERT: E 301 ILE cc_start: 0.8829 (pt) cc_final: 0.8508 (mt) REVERT: E 398 ARG cc_start: 0.6605 (mtt90) cc_final: 0.6388 (mmt-90) REVERT: E 426 LYS cc_start: 0.7059 (ttmt) cc_final: 0.5989 (mmtt) outliers start: 60 outliers final: 24 residues processed: 346 average time/residue: 0.2738 time to fit residues: 135.2532 Evaluate side-chains 320 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 288 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.0670 chunk 47 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 52 optimal weight: 0.0870 chunk 124 optimal weight: 0.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 321 ASN B 62 ASN B 242 GLN B 321 ASN C 62 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN C 321 ASN D 62 ASN D 139 ASN D 141 ASN D 242 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14510 Z= 0.153 Angle : 0.612 9.005 19680 Z= 0.309 Chirality : 0.045 0.134 2260 Planarity : 0.004 0.032 2435 Dihedral : 7.456 38.724 2195 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.59 % Allowed : 14.05 % Favored : 82.35 % 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: -3.33 (0.18), residues: 1710 helix: -2.43 (0.18), residues: 580 sheet: -1.57 (0.25), residues: 350 loop : -2.22 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 84 HIS 0.001 0.000 HIS E 217 PHE 0.019 0.002 PHE E 322 TYR 0.014 0.001 TYR B 317 ARG 0.004 0.000 ARG D 147 *********************** 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 355 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 300 time to evaluate : 1.872 Fit side-chains REVERT: A 229 ARG cc_start: 0.8670 (mmm-85) cc_final: 0.8358 (mtt-85) REVERT: A 301 ILE cc_start: 0.8677 (pt) cc_final: 0.8442 (mt) REVERT: A 416 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8418 (pt) REVERT: A 420 PHE cc_start: 0.7446 (t80) cc_final: 0.7044 (m-80) REVERT: A 426 LYS cc_start: 0.7018 (ttmt) cc_final: 0.6084 (mptt) REVERT: B 63 SER cc_start: 0.8759 (t) cc_final: 0.8514 (m) REVERT: B 229 ARG cc_start: 0.8608 (mmt90) cc_final: 0.8233 (mtt-85) REVERT: B 301 ILE cc_start: 0.8679 (pt) cc_final: 0.8400 (mt) REVERT: B 416 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8356 (pt) REVERT: B 420 PHE cc_start: 0.7483 (t80) cc_final: 0.7031 (m-80) REVERT: B 426 LYS cc_start: 0.7130 (ttmt) cc_final: 0.6068 (mmtm) REVERT: C 102 ASP cc_start: 0.7313 (p0) cc_final: 0.6957 (p0) REVERT: C 179 MET cc_start: 0.8520 (tpp) cc_final: 0.8315 (mmm) REVERT: C 301 ILE cc_start: 0.8607 (pt) cc_final: 0.8397 (mt) REVERT: C 398 ARG cc_start: 0.6192 (mtt90) cc_final: 0.5964 (mmt-90) REVERT: C 426 LYS cc_start: 0.7004 (ttmt) cc_final: 0.6021 (mmtm) REVERT: D 43 ARG cc_start: 0.8970 (mtm-85) cc_final: 0.8686 (mtp180) REVERT: D 229 ARG cc_start: 0.8546 (mmt90) cc_final: 0.8203 (mtt-85) REVERT: D 301 ILE cc_start: 0.8663 (pt) cc_final: 0.8390 (mt) REVERT: D 398 ARG cc_start: 0.6277 (mtt90) cc_final: 0.6022 (mmt-90) REVERT: D 416 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8302 (pt) REVERT: D 420 PHE cc_start: 0.7400 (t80) cc_final: 0.7029 (m-80) REVERT: D 426 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6052 (mmtt) REVERT: E 229 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8229 (mtt-85) REVERT: E 301 ILE cc_start: 0.8641 (pt) cc_final: 0.8435 (mt) REVERT: E 398 ARG cc_start: 0.6439 (mtt90) cc_final: 0.6200 (mmt-90) REVERT: E 426 LYS cc_start: 0.7036 (ttmt) cc_final: 0.6022 (mmtm) outliers start: 55 outliers final: 30 residues processed: 328 average time/residue: 0.2973 time to fit residues: 137.0225 Evaluate side-chains 314 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 281 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.0470 chunk 73 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN A 321 ASN B 242 GLN B 321 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 ASN D 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14510 Z= 0.249 Angle : 0.628 8.220 19680 Z= 0.317 Chirality : 0.045 0.134 2260 Planarity : 0.004 0.031 2435 Dihedral : 6.174 34.704 2195 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.10 % Allowed : 14.51 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.19), residues: 1710 helix: -1.67 (0.20), residues: 540 sheet: -1.33 (0.26), residues: 350 loop : -1.85 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 110 HIS 0.002 0.001 HIS E 125 PHE 0.033 0.002 PHE B 414 TYR 0.014 0.002 TYR A 317 ARG 0.003 0.000 ARG D 147 *********************** 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 375 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 297 time to evaluate : 1.635 Fit side-chains REVERT: A 204 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8768 (tt) REVERT: A 301 ILE cc_start: 0.8722 (pt) cc_final: 0.8474 (mt) REVERT: A 314 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7494 (tt) REVERT: A 416 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8464 (pt) REVERT: A 426 LYS cc_start: 0.7100 (ttmt) cc_final: 0.6187 (mptt) REVERT: B 63 SER cc_start: 0.8818 (t) cc_final: 0.8556 (m) REVERT: B 229 ARG cc_start: 0.8710 (mmt90) cc_final: 0.8428 (mtt-85) REVERT: B 258 PHE cc_start: 0.8184 (m-80) cc_final: 0.7973 (m-80) REVERT: B 301 ILE cc_start: 0.8647 (pt) cc_final: 0.8402 (mt) REVERT: B 314 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7443 (tt) REVERT: B 416 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8362 (pt) REVERT: B 420 PHE cc_start: 0.7381 (t80) cc_final: 0.7015 (m-80) REVERT: B 426 LYS cc_start: 0.7235 (ttmt) cc_final: 0.6186 (mmtm) REVERT: C 102 ASP cc_start: 0.7310 (p0) cc_final: 0.6965 (p0) REVERT: C 179 MET cc_start: 0.8562 (tpp) cc_final: 0.8344 (mmm) REVERT: C 204 ILE cc_start: 0.9019 (pt) cc_final: 0.8791 (tt) REVERT: C 314 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7589 (tt) REVERT: C 426 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6099 (mmtm) REVERT: D 229 ARG cc_start: 0.8651 (mmt90) cc_final: 0.8356 (mtt-85) REVERT: D 301 ILE cc_start: 0.8687 (pt) cc_final: 0.8420 (mt) REVERT: D 416 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8362 (pt) REVERT: D 426 LYS cc_start: 0.7137 (ttmt) cc_final: 0.5988 (mmtt) REVERT: E 229 ARG cc_start: 0.8690 (mmt90) cc_final: 0.8411 (mtt-85) REVERT: E 301 ILE cc_start: 0.8656 (pt) cc_final: 0.8454 (mt) REVERT: E 426 LYS cc_start: 0.7138 (ttmt) cc_final: 0.6111 (mmtm) outliers start: 78 outliers final: 52 residues processed: 346 average time/residue: 0.3070 time to fit residues: 152.0737 Evaluate side-chains 338 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 279 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 32 LYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 321 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS D 217 HIS E 217 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14510 Z= 0.309 Angle : 0.650 6.954 19680 Z= 0.327 Chirality : 0.045 0.144 2260 Planarity : 0.004 0.031 2435 Dihedral : 5.919 30.930 2195 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.69 % Allowed : 14.97 % Favored : 79.35 % 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: -2.21 (0.19), residues: 1710 helix: -1.37 (0.21), residues: 535 sheet: -1.04 (0.27), residues: 350 loop : -1.64 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 422 HIS 0.002 0.001 HIS C 231 PHE 0.037 0.002 PHE E 414 TYR 0.015 0.002 TYR B 175 ARG 0.003 0.001 ARG D 398 *********************** 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 375 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 288 time to evaluate : 1.539 Fit side-chains REVERT: A 204 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8774 (tt) REVERT: A 258 PHE cc_start: 0.8522 (m-80) cc_final: 0.8322 (m-80) REVERT: A 301 ILE cc_start: 0.8718 (pt) cc_final: 0.8513 (mt) REVERT: A 314 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7455 (tt) REVERT: A 416 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8462 (pt) REVERT: A 426 LYS cc_start: 0.7116 (ttmt) cc_final: 0.6092 (mmtm) REVERT: B 63 SER cc_start: 0.8885 (t) cc_final: 0.8576 (m) REVERT: B 229 ARG cc_start: 0.8751 (mmt90) cc_final: 0.8508 (mtt-85) REVERT: B 416 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8395 (pt) REVERT: B 426 LYS cc_start: 0.7224 (ttmt) cc_final: 0.6183 (mmtm) REVERT: C 102 ASP cc_start: 0.7349 (p0) cc_final: 0.7031 (p0) REVERT: C 179 MET cc_start: 0.8593 (tpp) cc_final: 0.8369 (mmm) REVERT: C 229 ARG cc_start: 0.8720 (mmt90) cc_final: 0.8400 (mtt-85) REVERT: C 314 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7647 (tt) REVERT: C 426 LYS cc_start: 0.7136 (ttmt) cc_final: 0.6096 (mmtm) REVERT: D 62 ASN cc_start: 0.8420 (m-40) cc_final: 0.8091 (m-40) REVERT: D 229 ARG cc_start: 0.8734 (mmt90) cc_final: 0.8478 (mtt-85) REVERT: D 301 ILE cc_start: 0.8656 (pt) cc_final: 0.8432 (mt) REVERT: D 416 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8309 (pt) REVERT: D 426 LYS cc_start: 0.7183 (ttmt) cc_final: 0.6082 (mmtm) REVERT: E 204 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8800 (tt) REVERT: E 229 ARG cc_start: 0.8737 (mmt90) cc_final: 0.8392 (mtt-85) REVERT: E 426 LYS cc_start: 0.7200 (ttmt) cc_final: 0.6157 (mmtm) outliers start: 87 outliers final: 60 residues processed: 332 average time/residue: 0.2799 time to fit residues: 131.3567 Evaluate side-chains 335 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 268 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.0020 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14510 Z= 0.247 Angle : 0.639 8.281 19680 Z= 0.316 Chirality : 0.044 0.138 2260 Planarity : 0.004 0.030 2435 Dihedral : 5.585 27.348 2195 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 5.49 % Allowed : 16.27 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.19), residues: 1710 helix: -1.14 (0.21), residues: 535 sheet: -0.81 (0.28), residues: 350 loop : -1.54 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 84 HIS 0.001 0.001 HIS C 231 PHE 0.029 0.002 PHE D 414 TYR 0.011 0.002 TYR A 425 ARG 0.007 0.001 ARG B 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 370 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 286 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7461 (tt) REVERT: A 416 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8432 (pt) REVERT: A 426 LYS cc_start: 0.7079 (ttmt) cc_final: 0.6158 (mmtm) REVERT: B 63 SER cc_start: 0.8888 (t) cc_final: 0.8595 (m) REVERT: B 229 ARG cc_start: 0.8755 (mmt90) cc_final: 0.8532 (mtt-85) REVERT: B 303 MET cc_start: 0.8383 (mmm) cc_final: 0.8160 (mmm) REVERT: B 314 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7456 (tt) REVERT: B 416 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8392 (pt) REVERT: B 426 LYS cc_start: 0.7227 (ttmt) cc_final: 0.6263 (mmtm) REVERT: C 102 ASP cc_start: 0.7297 (p0) cc_final: 0.7025 (p0) REVERT: C 229 ARG cc_start: 0.8728 (mmt90) cc_final: 0.8447 (mtt-85) REVERT: C 314 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7627 (tt) REVERT: C 426 LYS cc_start: 0.7133 (ttmt) cc_final: 0.6069 (mmtm) REVERT: D 62 ASN cc_start: 0.8427 (m-40) cc_final: 0.8100 (m-40) REVERT: D 229 ARG cc_start: 0.8751 (mmt90) cc_final: 0.8440 (mtt-85) REVERT: D 301 ILE cc_start: 0.8660 (pt) cc_final: 0.8458 (mt) REVERT: D 416 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8321 (pt) REVERT: D 426 LYS cc_start: 0.7154 (ttmt) cc_final: 0.6050 (mmtm) REVERT: E 204 ILE cc_start: 0.8981 (pt) cc_final: 0.8779 (tt) REVERT: E 229 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8458 (mtt-85) REVERT: E 426 LYS cc_start: 0.7213 (ttmt) cc_final: 0.6133 (mmtm) outliers start: 84 outliers final: 60 residues processed: 329 average time/residue: 0.2989 time to fit residues: 138.4025 Evaluate side-chains 346 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 279 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 99 optimal weight: 0.0980 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14510 Z= 0.171 Angle : 0.612 8.375 19680 Z= 0.301 Chirality : 0.043 0.140 2260 Planarity : 0.003 0.030 2435 Dihedral : 5.200 24.711 2195 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.69 % Allowed : 16.41 % Favored : 77.91 % 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: -1.73 (0.20), residues: 1710 helix: -0.85 (0.22), residues: 540 sheet: -0.69 (0.28), residues: 350 loop : -1.48 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.001 0.001 HIS E 217 PHE 0.031 0.002 PHE A 414 TYR 0.011 0.001 TYR A 317 ARG 0.006 0.000 ARG B 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 373 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 286 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7407 (tt) REVERT: A 416 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8446 (pt) REVERT: A 426 LYS cc_start: 0.7038 (ttmt) cc_final: 0.6097 (mmtm) REVERT: B 63 SER cc_start: 0.8881 (t) cc_final: 0.8609 (m) REVERT: B 227 GLU cc_start: 0.8241 (tt0) cc_final: 0.7421 (tt0) REVERT: B 229 ARG cc_start: 0.8749 (mmt90) cc_final: 0.8437 (mtt-85) REVERT: B 314 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7463 (tt) REVERT: B 416 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8385 (pt) REVERT: B 420 PHE cc_start: 0.7299 (t80) cc_final: 0.6977 (m-80) REVERT: B 426 LYS cc_start: 0.7159 (ttmt) cc_final: 0.6166 (mmtm) REVERT: C 102 ASP cc_start: 0.7270 (p0) cc_final: 0.6986 (p0) REVERT: C 227 GLU cc_start: 0.8282 (tt0) cc_final: 0.7369 (tt0) REVERT: C 229 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8449 (mtt-85) REVERT: C 314 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7605 (tt) REVERT: C 426 LYS cc_start: 0.7062 (ttmt) cc_final: 0.5992 (mmtm) REVERT: D 229 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8418 (mtt-85) REVERT: D 416 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8309 (pt) REVERT: D 426 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6083 (mmtm) REVERT: E 204 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8742 (tt) REVERT: E 229 ARG cc_start: 0.8740 (mmt90) cc_final: 0.8447 (mtt-85) REVERT: E 426 LYS cc_start: 0.7156 (ttmt) cc_final: 0.6084 (mmtm) outliers start: 87 outliers final: 61 residues processed: 335 average time/residue: 0.2856 time to fit residues: 135.3046 Evaluate side-chains 336 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 266 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 chunk 149 optimal weight: 0.0770 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14510 Z= 0.160 Angle : 0.617 9.801 19680 Z= 0.303 Chirality : 0.043 0.140 2260 Planarity : 0.004 0.035 2435 Dihedral : 5.142 38.501 2195 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.03 % Allowed : 16.86 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.20), residues: 1710 helix: -0.63 (0.22), residues: 540 sheet: -0.60 (0.28), residues: 350 loop : -1.42 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.002 0.001 HIS C 217 PHE 0.022 0.002 PHE E 322 TYR 0.011 0.001 TYR A 317 ARG 0.007 0.000 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 350 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 273 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8557 (tt) REVERT: A 314 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7399 (tt) REVERT: A 416 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8444 (pt) REVERT: A 426 LYS cc_start: 0.7004 (ttmt) cc_final: 0.6050 (mmtm) REVERT: B 63 SER cc_start: 0.8891 (t) cc_final: 0.8621 (m) REVERT: B 229 ARG cc_start: 0.8781 (mmt90) cc_final: 0.8473 (mtt-85) REVERT: B 314 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7453 (tt) REVERT: B 420 PHE cc_start: 0.7290 (t80) cc_final: 0.6968 (m-80) REVERT: B 426 LYS cc_start: 0.7088 (ttmt) cc_final: 0.6116 (mmtm) REVERT: C 102 ASP cc_start: 0.7206 (p0) cc_final: 0.6916 (p0) REVERT: C 229 ARG cc_start: 0.8743 (mmt90) cc_final: 0.8441 (mtt-85) REVERT: C 314 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7586 (tt) REVERT: C 426 LYS cc_start: 0.7052 (ttmt) cc_final: 0.5969 (mmtm) REVERT: D 229 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8457 (mtt-85) REVERT: D 416 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8317 (pt) REVERT: D 426 LYS cc_start: 0.7033 (ttmt) cc_final: 0.6043 (mmtm) REVERT: E 204 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8738 (tt) REVERT: E 229 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8465 (mtt-85) REVERT: E 426 LYS cc_start: 0.7103 (ttmt) cc_final: 0.6063 (mmtm) outliers start: 77 outliers final: 60 residues processed: 311 average time/residue: 0.2866 time to fit residues: 125.9896 Evaluate side-chains 334 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 265 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 300 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14510 Z= 0.164 Angle : 0.615 7.922 19680 Z= 0.301 Chirality : 0.043 0.137 2260 Planarity : 0.003 0.030 2435 Dihedral : 5.067 46.100 2195 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 5.36 % Allowed : 16.80 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.45 (0.20), residues: 1710 helix: -0.52 (0.22), residues: 545 sheet: -0.50 (0.28), residues: 350 loop : -1.42 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 84 HIS 0.001 0.001 HIS B 217 PHE 0.023 0.002 PHE E 322 TYR 0.011 0.001 TYR A 317 ARG 0.008 0.000 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 359 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 277 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8538 (tt) REVERT: A 314 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7467 (tt) REVERT: A 416 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8461 (pt) REVERT: A 426 LYS cc_start: 0.6976 (ttmt) cc_final: 0.6033 (mmtm) REVERT: B 63 SER cc_start: 0.8915 (t) cc_final: 0.8646 (m) REVERT: B 229 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8476 (mtt-85) REVERT: B 314 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7461 (tt) REVERT: B 426 LYS cc_start: 0.7046 (ttmt) cc_final: 0.6041 (mmtm) REVERT: C 102 ASP cc_start: 0.7228 (p0) cc_final: 0.6968 (p0) REVERT: C 229 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8477 (mtt-85) REVERT: C 314 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7576 (tt) REVERT: C 426 LYS cc_start: 0.7031 (ttmt) cc_final: 0.5957 (mmtm) REVERT: D 159 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7479 (mmtt) REVERT: D 229 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8459 (mtt-85) REVERT: D 416 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8322 (pt) REVERT: D 426 LYS cc_start: 0.7010 (ttmt) cc_final: 0.6002 (mmtm) REVERT: E 204 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8728 (tt) REVERT: E 229 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8495 (mtt-85) REVERT: E 426 LYS cc_start: 0.7006 (ttmt) cc_final: 0.5995 (mmtm) outliers start: 82 outliers final: 62 residues processed: 317 average time/residue: 0.2825 time to fit residues: 127.3642 Evaluate side-chains 338 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 265 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 196 ASP Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14510 Z= 0.233 Angle : 0.642 9.171 19680 Z= 0.315 Chirality : 0.044 0.136 2260 Planarity : 0.004 0.037 2435 Dihedral : 5.200 45.158 2195 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.84 % Allowed : 17.32 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.34 (0.20), residues: 1710 helix: -0.16 (0.22), residues: 515 sheet: -0.50 (0.28), residues: 350 loop : -1.49 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 422 HIS 0.002 0.001 HIS D 217 PHE 0.034 0.002 PHE A 414 TYR 0.011 0.001 TYR A 144 ARG 0.009 0.001 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 336 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 262 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8567 (tt) REVERT: A 314 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 416 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8469 (pt) REVERT: A 426 LYS cc_start: 0.7008 (ttmt) cc_final: 0.6065 (mmtm) REVERT: B 63 SER cc_start: 0.8936 (t) cc_final: 0.8630 (m) REVERT: B 229 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8519 (mtt-85) REVERT: B 314 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7458 (tt) REVERT: B 426 LYS cc_start: 0.7055 (ttmt) cc_final: 0.6061 (mmtm) REVERT: C 102 ASP cc_start: 0.7255 (p0) cc_final: 0.7028 (p0) REVERT: C 229 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8492 (mtt-85) REVERT: C 426 LYS cc_start: 0.7057 (ttmt) cc_final: 0.5980 (mmtm) REVERT: D 159 LYS cc_start: 0.7755 (mtpt) cc_final: 0.7512 (mmtt) REVERT: D 229 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8498 (mtt-85) REVERT: D 416 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8322 (pt) REVERT: D 426 LYS cc_start: 0.7036 (ttmt) cc_final: 0.6030 (mmtm) REVERT: E 229 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8519 (mtt-85) REVERT: E 426 LYS cc_start: 0.7055 (ttmt) cc_final: 0.6061 (mmtm) outliers start: 74 outliers final: 61 residues processed: 296 average time/residue: 0.2845 time to fit residues: 119.7429 Evaluate side-chains 326 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 256 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain B residue 24 MET Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain C residue 24 MET Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 118 ASN Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 24 MET Chi-restraints excluded: chain D residue 32 LYS Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 171 GLN Chi-restraints excluded: chain D residue 199 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain E residue 24 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 146 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain E residue 188 GLU Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 229 ARG Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 296 VAL Chi-restraints excluded: chain E residue 316 GLU Chi-restraints excluded: chain E residue 415 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 9.9990 chunk 124 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 138 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.162654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126008 restraints weight = 17269.570| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.33 r_work: 0.3203 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14510 Z= 0.153 Angle : 0.620 9.264 19680 Z= 0.301 Chirality : 0.043 0.144 2260 Planarity : 0.003 0.033 2435 Dihedral : 4.992 44.707 2195 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.51 % Allowed : 17.58 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1710 helix: -0.07 (0.23), residues: 515 sheet: -0.39 (0.28), residues: 350 loop : -1.49 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 186 HIS 0.001 0.000 HIS B 125 PHE 0.034 0.002 PHE E 414 TYR 0.010 0.001 TYR B 317 ARG 0.009 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3664.39 seconds wall clock time: 67 minutes 10.44 seconds (4030.44 seconds total)