Starting phenix.real_space_refine on Fri Feb 16 02:36:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/02_2024/7u2o_26317_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/02_2024/7u2o_26317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/02_2024/7u2o_26317.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/02_2024/7u2o_26317.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/02_2024/7u2o_26317_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2o_26317/02_2024/7u2o_26317_trim_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.220 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 9145 2.51 5 N 2265 2.21 5 O 2565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 45": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 229": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 229": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 229": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 229": "NH1" <-> "NH2" Residue "D ARG 268": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 229": "NH1" <-> "NH2" Residue "E ARG 268": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14075 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2770 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 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: "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: "N" 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: "R" 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: "V" 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'L2L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.85, per 1000 atoms: 0.56 Number of scatterers: 14075 At special positions: 0 Unit cell: (105.537, 107.199, 132.129, 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 2565 8.00 N 2265 7.00 C 9145 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=2.03 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 225 " distance=2.02 Simple disulfide: pdb=" SG CYS B 154 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 225 " distance=2.02 Simple disulfide: pdb=" SG CYS C 154 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 225 " distance=2.02 Simple disulfide: pdb=" SG CYS D 154 " - pdb=" SG CYS D 168 " distance=2.03 Simple disulfide: pdb=" SG CYS D 214 " - pdb=" SG CYS D 225 " distance=2.02 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 168 " distance=2.03 Simple disulfide: pdb=" SG CYS E 214 " - pdb=" SG CYS E 225 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG F 1 " - " ASN A 54 " " NAG J 1 " - " ASN B 54 " " NAG N 1 " - " ASN C 54 " " NAG R 1 " - " ASN D 54 " " NAG V 1 " - " ASN E 54 " Time building additional restraints: 7.84 Conformation dependent library (CDL) restraints added in 2.9 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: 40 helices and 25 sheets defined 35.0% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.07 Creating SS restraints... Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.842A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (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 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.603A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 286 removed outlier: 3.949A pdb=" N ILE A 273 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 326 removed outlier: 3.534A pdb=" N LEU A 307 " --> pdb=" O MET A 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 314 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 425 removed outlier: 4.139A pdb=" N SER A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Proline residue: A 411 - end of helix Processing helix chain 'B' and resid 26 through 33 removed outlier: 3.843A pdb=" N LYS B 32 " --> pdb=" O GLU B 28 " (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 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 244 through 256 removed outlier: 3.602A pdb=" N ILE B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 286 removed outlier: 3.948A pdb=" N ILE B 273 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 326 removed outlier: 3.534A pdb=" N LEU B 307 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 314 " --> pdb=" O VAL B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 425 removed outlier: 4.139A pdb=" N SER B 397 " --> pdb=" O LYS B 393 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 408 " --> pdb=" O THR B 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Proline residue: B 411 - end of helix Processing helix chain 'C' and resid 26 through 33 removed outlier: 3.841A pdb=" N LYS C 32 " --> pdb=" O GLU C 28 " (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 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 244 through 256 removed outlier: 3.602A pdb=" N ILE C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 286 removed outlier: 3.949A pdb=" N ILE C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 326 removed outlier: 3.533A pdb=" N LEU C 307 " --> pdb=" O MET C 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU C 314 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 425 removed outlier: 4.140A pdb=" N SER C 397 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 401 " --> pdb=" O SER C 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) Proline residue: C 411 - end of helix Processing helix chain 'D' and resid 26 through 33 removed outlier: 3.842A pdb=" N LYS D 32 " --> pdb=" O GLU D 28 " (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 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 244 through 256 removed outlier: 3.603A pdb=" N ILE D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL D 251 " --> pdb=" O SER D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 286 removed outlier: 3.948A pdb=" N ILE D 273 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 326 removed outlier: 3.534A pdb=" N LEU D 307 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 425 removed outlier: 4.139A pdb=" N SER D 397 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 401 " --> pdb=" O SER D 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL D 408 " --> pdb=" O THR D 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Proline residue: D 411 - end of helix Processing helix chain 'E' and resid 26 through 33 removed outlier: 3.843A pdb=" N LYS E 32 " --> pdb=" O GLU E 28 " (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 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 236 through 242 Processing helix chain 'E' and resid 244 through 256 removed outlier: 3.602A pdb=" N ILE E 250 " --> pdb=" O PRO E 246 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VAL E 251 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 286 removed outlier: 3.949A pdb=" N ILE E 273 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 326 removed outlier: 3.534A pdb=" N LEU E 307 " --> pdb=" O MET E 303 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU E 314 " --> pdb=" O VAL E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 425 removed outlier: 4.138A pdb=" N SER E 397 " --> pdb=" O LYS E 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG E 401 " --> pdb=" O SER E 397 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL E 408 " --> pdb=" O THR E 404 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Proline residue: E 411 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 182 through 186 removed outlier: 5.705A pdb=" N VAL A 53 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU A 185 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A 55 " --> pdb=" O GLU A 185 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 54 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.758A 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: 6.194A pdb=" N ILE A 59 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN A 77 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 64 " --> pdb=" O ARG A 75 " (cutoff:3.500A) removed outlier: 7.205A 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 removed outlier: 3.592A pdb=" N GLU A 233 " --> pdb=" O ILE A 204 " (cutoff:3.500A) 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 209 through 213 Processing sheet with id= F, first strand: chain 'B' and resid 182 through 186 removed outlier: 5.706A pdb=" N VAL B 53 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU B 185 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL B 55 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 54 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.758A 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: 6.194A pdb=" N ILE B 59 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN B 77 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 64 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 7.205A 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 removed outlier: 3.592A pdb=" N GLU B 233 " --> pdb=" O ILE B 204 " (cutoff:3.500A) 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 209 through 213 Processing sheet with id= K, first strand: chain 'C' and resid 182 through 186 removed outlier: 5.706A pdb=" N VAL C 53 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU C 185 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL C 55 " --> pdb=" O GLU C 185 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN C 54 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.758A 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: 6.194A pdb=" N ILE C 59 " --> pdb=" O GLN C 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN C 77 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE C 64 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 7.205A 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 removed outlier: 3.592A pdb=" N GLU C 233 " --> pdb=" O ILE C 204 " (cutoff:3.500A) 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 209 through 213 Processing sheet with id= P, first strand: chain 'D' and resid 182 through 186 removed outlier: 5.705A pdb=" N VAL D 53 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU D 185 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL D 55 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN D 54 " --> pdb=" O ASN D 85 " (cutoff:3.500A) removed outlier: 4.758A 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: 6.195A pdb=" N ILE D 59 " --> pdb=" O GLN D 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN D 77 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE D 64 " --> pdb=" O ARG D 75 " (cutoff:3.500A) removed outlier: 7.206A 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 removed outlier: 3.592A pdb=" N GLU D 233 " --> pdb=" O ILE D 204 " (cutoff:3.500A) 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 209 through 212 Processing sheet with id= U, first strand: chain 'E' and resid 182 through 186 removed outlier: 5.706A pdb=" N VAL E 53 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLU E 185 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL E 55 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN E 54 " --> pdb=" O ASN E 85 " (cutoff:3.500A) removed outlier: 4.758A 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: 6.194A pdb=" N ILE E 59 " --> pdb=" O GLN E 193 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN E 77 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE E 64 " --> pdb=" O ARG E 75 " (cutoff:3.500A) removed outlier: 7.205A 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 removed outlier: 3.592A pdb=" N GLU E 233 " --> pdb=" O ILE E 204 " (cutoff:3.500A) 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 209 through 213 575 hydrogen bonds defined for protein. 1722 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: 4.26 Time building geometry restraints manager: 8.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4340 1.34 - 1.47: 3687 1.47 - 1.60: 6223 1.60 - 1.72: 0 1.72 - 1.85: 165 Bond restraints: 14415 Sorted by residual: bond pdb=" C1 BMA J 3 " pdb=" C2 BMA J 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C1 BMA N 3 " pdb=" C2 BMA N 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 BMA V 3 " pdb=" C2 BMA V 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 BMA R 3 " pdb=" C2 BMA R 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.39e+00 ... (remaining 14410 not shown) Histogram of bond angle deviations from ideal: 98.65 - 105.72: 369 105.72 - 112.79: 7757 112.79 - 119.87: 4655 119.87 - 126.94: 6632 126.94 - 134.01: 172 Bond angle restraints: 19585 Sorted by residual: angle pdb=" O04 L2L C 600 " pdb=" S03 L2L C 600 " pdb=" O05 L2L C 600 " ideal model delta sigma weight residual 112.97 101.87 11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" O04 L2L A 600 " pdb=" S03 L2L A 600 " pdb=" O05 L2L A 600 " ideal model delta sigma weight residual 112.97 101.89 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L B 600 " pdb=" S03 L2L B 600 " pdb=" O05 L2L B 600 " ideal model delta sigma weight residual 112.97 101.89 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L D 600 " pdb=" S03 L2L D 600 " pdb=" O05 L2L D 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 angle pdb=" O04 L2L E 600 " pdb=" S03 L2L E 600 " pdb=" O05 L2L E 600 " ideal model delta sigma weight residual 112.97 101.90 11.07 3.00e+00 1.11e-01 1.36e+01 ... (remaining 19580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.49: 8540 22.49 - 44.98: 200 44.98 - 67.47: 10 67.47 - 89.97: 40 89.97 - 112.46: 20 Dihedral angle restraints: 8810 sinusoidal: 3695 harmonic: 5115 Sorted by residual: dihedral pdb=" CB CYS D 154 " pdb=" SG CYS D 154 " pdb=" SG CYS D 168 " pdb=" CB CYS D 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.18 50.82 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS B 154 " pdb=" SG CYS B 154 " pdb=" SG CYS B 168 " pdb=" CB CYS B 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.19 50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS A 154 " pdb=" SG CYS A 154 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual 93.00 42.20 50.80 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 8807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1853 0.054 - 0.107: 345 0.107 - 0.161: 52 0.161 - 0.215: 0 0.215 - 0.269: 10 Chirality restraints: 2260 Sorted by residual: chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C6 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2257 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 151 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL B 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 151 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU B 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 151 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C VAL A 151 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 152 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 151 " 0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C VAL D 151 " -0.035 2.00e-02 2.50e+03 pdb=" O VAL D 151 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU D 152 " 0.012 2.00e-02 2.50e+03 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 292 2.66 - 3.22: 14590 3.22 - 3.78: 21300 3.78 - 4.34: 30898 4.34 - 4.90: 47906 Nonbonded interactions: 114986 Sorted by model distance: nonbonded pdb=" OG1 THR C 178 " pdb=" OD1 ASN C 180 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR B 178 " pdb=" OD1 ASN B 180 " model vdw 2.101 2.440 nonbonded pdb=" OG1 THR A 178 " pdb=" OD1 ASN A 180 " model vdw 2.102 2.440 nonbonded pdb=" OG1 THR E 178 " pdb=" OD1 ASN E 180 " model vdw 2.102 2.440 nonbonded pdb=" OG1 THR D 178 " pdb=" OD1 ASN D 180 " model vdw 2.102 2.440 ... (remaining 114981 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 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' } 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: 1.410 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: 7.540 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 42.310 Find NCS groups from input model: 0.860 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 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 0.043 14415 Z= 0.414 Angle : 0.837 11.097 19585 Z= 0.455 Chirality : 0.048 0.269 2260 Planarity : 0.005 0.051 2425 Dihedral : 13.058 112.457 5460 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 37.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % 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: -4.77 (0.16), residues: 1710 helix: -3.68 (0.14), residues: 585 sheet: -3.06 (0.18), residues: 390 loop : -2.55 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 422 HIS 0.003 0.002 HIS C 217 PHE 0.017 0.002 PHE C 309 TYR 0.017 0.003 TYR C 144 ARG 0.007 0.001 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.9032 (mtm-85) cc_final: 0.8653 (mtm-85) REVERT: A 104 SER cc_start: 0.8212 (p) cc_final: 0.7601 (t) REVERT: A 127 VAL cc_start: 0.9007 (t) cc_final: 0.8648 (p) REVERT: A 206 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8281 (mttp) REVERT: A 295 TYR cc_start: 0.8847 (p90) cc_final: 0.8646 (p90) REVERT: B 105 MET cc_start: 0.6200 (mmp) cc_final: 0.5754 (mmp) REVERT: B 127 VAL cc_start: 0.9003 (t) cc_final: 0.8655 (p) REVERT: B 206 LYS cc_start: 0.8611 (mtpt) cc_final: 0.8231 (mttp) REVERT: B 239 TYR cc_start: 0.8761 (m-80) cc_final: 0.8139 (m-80) REVERT: B 295 TYR cc_start: 0.8867 (p90) cc_final: 0.8567 (p90) REVERT: C 43 ARG cc_start: 0.9024 (mtm-85) cc_final: 0.8525 (mtm-85) REVERT: C 104 SER cc_start: 0.8295 (p) cc_final: 0.7557 (p) REVERT: C 105 MET cc_start: 0.6121 (mmp) cc_final: 0.5865 (mmp) REVERT: C 127 VAL cc_start: 0.9038 (t) cc_final: 0.8621 (p) REVERT: C 137 SER cc_start: 0.9171 (m) cc_final: 0.8472 (p) REVERT: C 206 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8394 (mttm) REVERT: C 210 ASP cc_start: 0.8513 (m-30) cc_final: 0.8156 (m-30) REVERT: C 239 TYR cc_start: 0.8718 (m-80) cc_final: 0.8508 (m-80) REVERT: D 43 ARG cc_start: 0.9046 (mtm-85) cc_final: 0.8758 (mtm-85) REVERT: D 104 SER cc_start: 0.8210 (p) cc_final: 0.7547 (t) REVERT: D 105 MET cc_start: 0.6113 (mmp) cc_final: 0.5834 (mmp) REVERT: D 127 VAL cc_start: 0.9005 (t) cc_final: 0.8629 (p) REVERT: D 206 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8359 (mttm) REVERT: D 299 ILE cc_start: 0.9091 (tp) cc_final: 0.8874 (tp) REVERT: E 43 ARG cc_start: 0.9019 (mtm-85) cc_final: 0.8689 (mtm-85) REVERT: E 104 SER cc_start: 0.8121 (p) cc_final: 0.7090 (p) REVERT: E 127 VAL cc_start: 0.8846 (t) cc_final: 0.8524 (p) REVERT: E 130 ASP cc_start: 0.8342 (m-30) cc_final: 0.8110 (m-30) REVERT: E 206 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8368 (mttp) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.2801 time to fit residues: 218.3440 Evaluate side-chains 386 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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: 1.9990 chunk 128 optimal weight: 0.0070 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 154 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 82 GLN A 141 ASN B 77 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 ASN B 235 GLN C 77 ASN C 82 GLN C 141 ASN C 171 GLN D 77 ASN D 82 GLN D 141 ASN D 202 GLN ** D 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14415 Z= 0.229 Angle : 0.760 7.163 19585 Z= 0.388 Chirality : 0.049 0.231 2260 Planarity : 0.005 0.046 2425 Dihedral : 10.635 69.657 2195 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.98 % Allowed : 11.06 % Favored : 85.96 % 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: -2.81 (0.19), residues: 1710 helix: -1.49 (0.19), residues: 590 sheet: -2.07 (0.22), residues: 390 loop : -1.88 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 110 HIS 0.003 0.001 HIS A 125 PHE 0.021 0.002 PHE D 322 TYR 0.023 0.002 TYR A 421 ARG 0.004 0.000 ARG C 398 *********************** 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 521 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 476 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7830 (tptt) REVERT: A 43 ARG cc_start: 0.8961 (mtm-85) cc_final: 0.8442 (mtm-85) REVERT: A 133 LEU cc_start: 0.8529 (tp) cc_final: 0.8211 (tt) REVERT: A 159 LYS cc_start: 0.8600 (mttt) cc_final: 0.8271 (mtmt) REVERT: A 206 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8251 (mttp) REVERT: A 210 ASP cc_start: 0.8337 (m-30) cc_final: 0.7771 (m-30) REVERT: A 282 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8517 (mm-40) REVERT: B 32 LYS cc_start: 0.8528 (pttp) cc_final: 0.7884 (tptt) REVERT: B 105 MET cc_start: 0.6177 (mmp) cc_final: 0.5951 (mmp) REVERT: B 133 LEU cc_start: 0.8573 (tp) cc_final: 0.8246 (tt) REVERT: B 159 LYS cc_start: 0.8680 (mttt) cc_final: 0.8402 (mtpt) REVERT: B 206 LYS cc_start: 0.8580 (mtpt) cc_final: 0.8241 (mttp) REVERT: B 208 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7197 (tm-30) REVERT: B 210 ASP cc_start: 0.8245 (m-30) cc_final: 0.7515 (m-30) REVERT: B 239 TYR cc_start: 0.8544 (m-80) cc_final: 0.8258 (m-80) REVERT: B 295 TYR cc_start: 0.8924 (p90) cc_final: 0.8640 (p90) REVERT: C 32 LYS cc_start: 0.8509 (pttp) cc_final: 0.7779 (tptt) REVERT: C 133 LEU cc_start: 0.8577 (tp) cc_final: 0.8219 (tt) REVERT: C 206 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8330 (mttp) REVERT: C 208 GLU cc_start: 0.7650 (tm-30) cc_final: 0.6875 (pp20) REVERT: C 210 ASP cc_start: 0.8380 (m-30) cc_final: 0.8018 (m-30) REVERT: C 239 TYR cc_start: 0.8558 (m-80) cc_final: 0.8158 (m-80) REVERT: C 282 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8487 (mm-40) REVERT: D 130 ASP cc_start: 0.8262 (m-30) cc_final: 0.7994 (m-30) REVERT: D 133 LEU cc_start: 0.8538 (tp) cc_final: 0.8223 (tt) REVERT: D 159 LYS cc_start: 0.8633 (mttt) cc_final: 0.8345 (mtpt) REVERT: D 165 VAL cc_start: 0.9255 (t) cc_final: 0.9032 (p) REVERT: D 206 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8415 (mttp) REVERT: D 282 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8288 (mm-40) REVERT: D 418 ASN cc_start: 0.9060 (m-40) cc_final: 0.8858 (m-40) REVERT: E 32 LYS cc_start: 0.8483 (pttp) cc_final: 0.7849 (tptt) REVERT: E 105 MET cc_start: 0.5729 (mmp) cc_final: 0.5489 (mmp) REVERT: E 133 LEU cc_start: 0.8421 (tp) cc_final: 0.8094 (tt) REVERT: E 149 THR cc_start: 0.8664 (m) cc_final: 0.8377 (m) REVERT: E 159 LYS cc_start: 0.8607 (mttt) cc_final: 0.8331 (mtpt) REVERT: E 206 LYS cc_start: 0.8649 (mtpt) cc_final: 0.8447 (mttp) outliers start: 45 outliers final: 28 residues processed: 499 average time/residue: 0.2578 time to fit residues: 186.6381 Evaluate side-chains 431 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 402 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 301 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 47 ASN C 85 ASN C 141 ASN D 231 HIS ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14415 Z= 0.229 Angle : 0.700 7.690 19585 Z= 0.354 Chirality : 0.046 0.194 2260 Planarity : 0.005 0.044 2425 Dihedral : 8.412 50.316 2195 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.24 % Allowed : 14.24 % Favored : 81.52 % 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: -2.00 (0.19), residues: 1710 helix: -0.57 (0.20), residues: 600 sheet: -1.40 (0.25), residues: 345 loop : -1.83 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 422 HIS 0.003 0.001 HIS B 125 PHE 0.023 0.001 PHE E 414 TYR 0.020 0.002 TYR A 421 ARG 0.003 0.000 ARG C 229 *********************** 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 480 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 416 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8565 (pttp) cc_final: 0.7853 (tptt) REVERT: A 133 LEU cc_start: 0.8538 (tp) cc_final: 0.8313 (tt) REVERT: A 141 ASN cc_start: 0.8530 (m110) cc_final: 0.8254 (m110) REVERT: A 159 LYS cc_start: 0.8613 (mttt) cc_final: 0.8385 (mtpt) REVERT: A 206 LYS cc_start: 0.8702 (mtpt) cc_final: 0.8236 (mttp) REVERT: A 210 ASP cc_start: 0.8334 (m-30) cc_final: 0.7723 (m-30) REVERT: A 428 ILE cc_start: 0.7298 (mp) cc_final: 0.7030 (mt) REVERT: B 32 LYS cc_start: 0.8593 (pttp) cc_final: 0.7917 (tptt) REVERT: B 104 SER cc_start: 0.8423 (p) cc_final: 0.7771 (t) REVERT: B 105 MET cc_start: 0.6176 (mmp) cc_final: 0.5901 (mmp) REVERT: B 133 LEU cc_start: 0.8579 (tp) cc_final: 0.8315 (tt) REVERT: B 141 ASN cc_start: 0.8607 (m110) cc_final: 0.8301 (m110) REVERT: B 159 LYS cc_start: 0.8662 (mttt) cc_final: 0.8398 (mtpt) REVERT: B 206 LYS cc_start: 0.8618 (mtpt) cc_final: 0.8275 (mttp) REVERT: B 208 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 210 ASP cc_start: 0.8360 (m-30) cc_final: 0.7624 (m-30) REVERT: B 227 GLU cc_start: 0.8244 (pt0) cc_final: 0.8001 (pt0) REVERT: B 239 TYR cc_start: 0.8637 (m-80) cc_final: 0.8013 (m-80) REVERT: B 295 TYR cc_start: 0.8956 (p90) cc_final: 0.8707 (p90) REVERT: C 105 MET cc_start: 0.7535 (ppp) cc_final: 0.7195 (ptm) REVERT: C 113 ASP cc_start: 0.9028 (p0) cc_final: 0.8803 (p0) REVERT: C 133 LEU cc_start: 0.8618 (tp) cc_final: 0.8364 (tt) REVERT: C 137 SER cc_start: 0.9018 (m) cc_final: 0.8164 (p) REVERT: C 159 LYS cc_start: 0.8578 (mttt) cc_final: 0.8350 (mtpt) REVERT: C 206 LYS cc_start: 0.8579 (mtpt) cc_final: 0.8368 (mttp) REVERT: C 210 ASP cc_start: 0.8406 (m-30) cc_final: 0.8127 (m-30) REVERT: C 239 TYR cc_start: 0.8526 (m-80) cc_final: 0.8199 (m-80) REVERT: D 133 LEU cc_start: 0.8596 (tp) cc_final: 0.8309 (tt) REVERT: D 159 LYS cc_start: 0.8653 (mttt) cc_final: 0.8389 (mtpt) REVERT: D 206 LYS cc_start: 0.8651 (mtpt) cc_final: 0.8419 (mttp) REVERT: D 282 GLN cc_start: 0.8806 (mm-40) cc_final: 0.8388 (mm-40) REVERT: E 159 LYS cc_start: 0.8619 (mttt) cc_final: 0.8363 (mtpt) outliers start: 64 outliers final: 50 residues processed: 438 average time/residue: 0.2362 time to fit residues: 153.1688 Evaluate side-chains 435 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 385 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU 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: 2.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 164 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 141 ASN C 171 GLN D 85 ASN D 141 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14415 Z= 0.243 Angle : 0.725 8.044 19585 Z= 0.376 Chirality : 0.053 0.603 2260 Planarity : 0.005 0.047 2425 Dihedral : 7.064 48.693 2195 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.17 % Allowed : 14.64 % Favored : 80.20 % Cbeta Deviations : 0.06 % 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: -1.41 (0.19), residues: 1710 helix: -0.01 (0.21), residues: 600 sheet: -0.69 (0.26), residues: 310 loop : -1.74 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.003 0.001 HIS B 125 PHE 0.026 0.002 PHE A 322 TYR 0.018 0.002 TYR A 421 ARG 0.003 0.000 ARG C 229 *********************** 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 471 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 393 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7842 (tptt) REVERT: A 133 LEU cc_start: 0.8573 (tp) cc_final: 0.8291 (tt) REVERT: A 206 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8216 (mttp) REVERT: A 240 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 282 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8442 (mm-40) REVERT: A 428 ILE cc_start: 0.7207 (mp) cc_final: 0.6952 (mt) REVERT: B 32 LYS cc_start: 0.8587 (pttp) cc_final: 0.7982 (tptt) REVERT: B 105 MET cc_start: 0.6245 (mmp) cc_final: 0.5992 (mmp) REVERT: B 159 LYS cc_start: 0.8668 (mttt) cc_final: 0.8393 (mtpt) REVERT: B 206 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8306 (mttp) REVERT: B 208 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 210 ASP cc_start: 0.8359 (m-30) cc_final: 0.7601 (m-30) REVERT: B 239 TYR cc_start: 0.8617 (m-80) cc_final: 0.8052 (m-80) REVERT: B 240 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 105 MET cc_start: 0.7380 (ppp) cc_final: 0.6999 (ptm) REVERT: C 123 ASN cc_start: 0.9099 (p0) cc_final: 0.8888 (p0) REVERT: C 133 LEU cc_start: 0.8593 (tp) cc_final: 0.8339 (tt) REVERT: C 159 LYS cc_start: 0.8613 (mttt) cc_final: 0.8362 (mtpt) REVERT: C 239 TYR cc_start: 0.8527 (m-80) cc_final: 0.8205 (m-80) REVERT: D 159 LYS cc_start: 0.8674 (mttt) cc_final: 0.8406 (mtpt) REVERT: D 206 LYS cc_start: 0.8664 (mtpt) cc_final: 0.8436 (mttm) REVERT: D 282 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8341 (mm-40) REVERT: E 159 LYS cc_start: 0.8634 (mttt) cc_final: 0.8369 (mtpt) REVERT: E 188 GLU cc_start: 0.7149 (pm20) cc_final: 0.5964 (pm20) REVERT: E 189 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8057 (mmmt) outliers start: 78 outliers final: 62 residues processed: 421 average time/residue: 0.2254 time to fit residues: 142.6732 Evaluate side-chains 440 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 375 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 140 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 41 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 HIS E 47 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14415 Z= 0.209 Angle : 0.693 9.098 19585 Z= 0.357 Chirality : 0.053 0.721 2260 Planarity : 0.004 0.041 2425 Dihedral : 6.521 55.474 2195 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.23 % Allowed : 15.89 % Favored : 78.87 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.20), residues: 1710 helix: 0.48 (0.22), residues: 595 sheet: -0.49 (0.26), residues: 310 loop : -1.63 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.002 0.001 HIS B 125 PHE 0.026 0.001 PHE A 322 TYR 0.018 0.002 TYR A 421 ARG 0.002 0.000 ARG A 229 *********************** 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 466 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 387 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7847 (tptt) REVERT: A 105 MET cc_start: 0.5688 (mmt) cc_final: 0.5353 (mmt) REVERT: A 133 LEU cc_start: 0.8567 (tp) cc_final: 0.8327 (tt) REVERT: A 206 LYS cc_start: 0.8725 (mtpt) cc_final: 0.8210 (mttp) REVERT: A 240 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8711 (mp) REVERT: A 282 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8465 (mm-40) REVERT: A 428 ILE cc_start: 0.7182 (mp) cc_final: 0.6932 (mt) REVERT: B 32 LYS cc_start: 0.8578 (pttp) cc_final: 0.7964 (tptt) REVERT: B 104 SER cc_start: 0.8789 (p) cc_final: 0.7782 (t) REVERT: B 105 MET cc_start: 0.6176 (mmp) cc_final: 0.5904 (mmp) REVERT: B 159 LYS cc_start: 0.8666 (mttt) cc_final: 0.8376 (mtpt) REVERT: B 206 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8301 (mttp) REVERT: B 208 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7246 (tm-30) REVERT: B 210 ASP cc_start: 0.8305 (m-30) cc_final: 0.7561 (m-30) REVERT: B 239 TYR cc_start: 0.8565 (m-80) cc_final: 0.8050 (m-80) REVERT: B 240 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8649 (mp) REVERT: B 250 ILE cc_start: 0.8364 (mm) cc_final: 0.7996 (mt) REVERT: B 282 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8440 (mm-40) REVERT: B 428 ILE cc_start: 0.7122 (mp) cc_final: 0.6686 (mt) REVERT: C 123 ASN cc_start: 0.9047 (p0) cc_final: 0.8806 (p0) REVERT: C 133 LEU cc_start: 0.8569 (tp) cc_final: 0.8321 (tt) REVERT: C 159 LYS cc_start: 0.8594 (mttt) cc_final: 0.8327 (mtpt) REVERT: C 163 MET cc_start: 0.8599 (mtm) cc_final: 0.8370 (mtm) REVERT: C 236 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6411 (tpp) REVERT: C 239 TYR cc_start: 0.8440 (m-80) cc_final: 0.8097 (m-80) REVERT: C 240 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 250 ILE cc_start: 0.8493 (mm) cc_final: 0.8174 (mt) REVERT: C 282 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8530 (mm-40) REVERT: D 159 LYS cc_start: 0.8672 (mttt) cc_final: 0.8370 (mtpt) REVERT: D 206 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8449 (mttm) REVERT: D 229 ARG cc_start: 0.8477 (mtp180) cc_final: 0.8175 (mtp180) REVERT: D 282 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8425 (mm-40) REVERT: E 159 LYS cc_start: 0.8619 (mttt) cc_final: 0.8344 (mtpt) REVERT: E 189 LYS cc_start: 0.8417 (mmmt) cc_final: 0.7971 (mmmt) outliers start: 79 outliers final: 62 residues processed: 417 average time/residue: 0.2345 time to fit residues: 146.6325 Evaluate side-chains 440 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 373 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU 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: 1.9990 chunk 147 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14415 Z= 0.233 Angle : 0.685 9.111 19585 Z= 0.357 Chirality : 0.052 0.711 2260 Planarity : 0.004 0.046 2425 Dihedral : 6.589 58.510 2195 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.76 % Allowed : 16.16 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.20), residues: 1710 helix: 0.77 (0.22), residues: 595 sheet: -0.56 (0.25), residues: 355 loop : -1.43 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 302 HIS 0.003 0.001 HIS B 125 PHE 0.028 0.002 PHE B 414 TYR 0.017 0.002 TYR A 421 ARG 0.002 0.000 ARG A 43 *********************** 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 456 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 369 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7836 (tptt) REVERT: A 47 ASN cc_start: 0.8728 (m-40) cc_final: 0.8463 (m-40) REVERT: A 133 LEU cc_start: 0.8614 (tp) cc_final: 0.8374 (tt) REVERT: A 206 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8194 (mttp) REVERT: A 240 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 282 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8497 (mm-40) REVERT: B 32 LYS cc_start: 0.8619 (pttp) cc_final: 0.8017 (tptt) REVERT: B 128 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.8016 (m) REVERT: B 159 LYS cc_start: 0.8694 (mttt) cc_final: 0.8388 (mtpt) REVERT: B 206 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8353 (mttp) REVERT: B 208 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 239 TYR cc_start: 0.8583 (m-80) cc_final: 0.8035 (m-80) REVERT: B 240 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8661 (mp) REVERT: B 250 ILE cc_start: 0.8479 (mm) cc_final: 0.8113 (mt) REVERT: B 282 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8392 (mm-40) REVERT: C 123 ASN cc_start: 0.9008 (p0) cc_final: 0.8764 (p0) REVERT: C 133 LEU cc_start: 0.8601 (tp) cc_final: 0.8360 (tt) REVERT: C 159 LYS cc_start: 0.8647 (mttt) cc_final: 0.8360 (mtpt) REVERT: C 239 TYR cc_start: 0.8431 (m-80) cc_final: 0.8108 (m-80) REVERT: C 240 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8619 (mp) REVERT: C 250 ILE cc_start: 0.8509 (mm) cc_final: 0.8200 (mt) REVERT: C 282 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8538 (mm-40) REVERT: D 105 MET cc_start: 0.7809 (ppp) cc_final: 0.7463 (ppp) REVERT: D 113 ASP cc_start: 0.9034 (p0) cc_final: 0.8806 (p0) REVERT: D 133 LEU cc_start: 0.8669 (tp) cc_final: 0.8400 (tt) REVERT: D 159 LYS cc_start: 0.8680 (mttt) cc_final: 0.8414 (mtpt) REVERT: D 206 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8478 (mttm) REVERT: E 159 LYS cc_start: 0.8641 (mttt) cc_final: 0.8365 (mtpt) REVERT: E 240 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8706 (mp) REVERT: E 250 ILE cc_start: 0.8346 (mm) cc_final: 0.8061 (mt) REVERT: E 282 GLN cc_start: 0.8769 (mm-40) cc_final: 0.8521 (mm-40) outliers start: 87 outliers final: 66 residues processed: 409 average time/residue: 0.2242 time to fit residues: 138.2195 Evaluate side-chains 428 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 356 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 301 ILE Chi-restraints excluded: chain E residue 308 LEU 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: 0.0870 chunk 18 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 163 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN B 85 ASN B 141 ASN C 171 GLN D 47 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14415 Z= 0.198 Angle : 0.674 9.133 19585 Z= 0.348 Chirality : 0.051 0.617 2260 Planarity : 0.004 0.043 2425 Dihedral : 6.668 57.181 2195 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.50 % Allowed : 18.34 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1710 helix: 0.90 (0.22), residues: 595 sheet: -0.29 (0.26), residues: 315 loop : -1.55 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 186 HIS 0.002 0.001 HIS B 125 PHE 0.028 0.001 PHE A 322 TYR 0.017 0.002 TYR A 421 ARG 0.002 0.000 ARG C 229 *********************** 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 440 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 372 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7839 (tptt) REVERT: A 47 ASN cc_start: 0.8700 (m-40) cc_final: 0.8448 (m-40) REVERT: A 133 LEU cc_start: 0.8604 (tp) cc_final: 0.8365 (tt) REVERT: A 206 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8208 (mttp) REVERT: A 240 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8703 (mp) REVERT: A 282 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8484 (mm-40) REVERT: B 32 LYS cc_start: 0.8615 (pttp) cc_final: 0.8024 (tptt) REVERT: B 159 LYS cc_start: 0.8669 (mttt) cc_final: 0.8365 (mtpt) REVERT: B 206 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8372 (mttp) REVERT: B 239 TYR cc_start: 0.8458 (m-80) cc_final: 0.8018 (m-80) REVERT: B 250 ILE cc_start: 0.8482 (mm) cc_final: 0.8130 (mt) REVERT: B 282 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8425 (mm-40) REVERT: C 32 LYS cc_start: 0.8698 (pttp) cc_final: 0.8070 (tptt) REVERT: C 123 ASN cc_start: 0.8964 (p0) cc_final: 0.8731 (p0) REVERT: C 133 LEU cc_start: 0.8599 (tp) cc_final: 0.8362 (tt) REVERT: C 159 LYS cc_start: 0.8637 (mttt) cc_final: 0.8332 (mtpt) REVERT: C 163 MET cc_start: 0.8634 (mtm) cc_final: 0.8386 (mtm) REVERT: C 236 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6362 (tpp) REVERT: C 239 TYR cc_start: 0.8410 (m-80) cc_final: 0.8070 (m-80) REVERT: C 250 ILE cc_start: 0.8518 (mm) cc_final: 0.8223 (mt) REVERT: C 282 GLN cc_start: 0.8749 (mm-40) cc_final: 0.8537 (mm-40) REVERT: D 133 LEU cc_start: 0.8663 (tp) cc_final: 0.8407 (tt) REVERT: D 159 LYS cc_start: 0.8705 (mttt) cc_final: 0.8420 (mtpt) REVERT: D 206 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8483 (mttm) REVERT: E 159 LYS cc_start: 0.8633 (mttt) cc_final: 0.8342 (mtpt) REVERT: E 240 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8702 (mp) REVERT: E 250 ILE cc_start: 0.8331 (mm) cc_final: 0.8065 (mt) REVERT: E 282 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8473 (mm-40) outliers start: 68 outliers final: 56 residues processed: 405 average time/residue: 0.2260 time to fit residues: 138.1694 Evaluate side-chains 426 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 366 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 308 LEU 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: 4.9990 chunk 97 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 128 optimal weight: 0.9990 chunk 149 optimal weight: 0.0010 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 GLN B 231 HIS C 171 GLN E 131 ASN E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14415 Z= 0.215 Angle : 0.687 13.049 19585 Z= 0.356 Chirality : 0.052 0.704 2260 Planarity : 0.004 0.046 2425 Dihedral : 6.696 56.381 2195 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.03 % Allowed : 18.08 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1710 helix: 0.98 (0.22), residues: 595 sheet: -0.26 (0.26), residues: 315 loop : -1.51 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 186 HIS 0.002 0.001 HIS B 125 PHE 0.028 0.001 PHE A 322 TYR 0.017 0.002 TYR A 421 ARG 0.003 0.000 ARG A 229 *********************** 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 447 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 371 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7920 (tptt) REVERT: A 47 ASN cc_start: 0.8712 (m-40) cc_final: 0.8446 (m-40) REVERT: A 133 LEU cc_start: 0.8616 (tp) cc_final: 0.8386 (tt) REVERT: A 206 LYS cc_start: 0.8703 (mtpt) cc_final: 0.8184 (mttp) REVERT: A 240 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 282 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8470 (mm-40) REVERT: B 32 LYS cc_start: 0.8618 (pttp) cc_final: 0.8033 (tptt) REVERT: B 141 ASN cc_start: 0.8501 (m-40) cc_final: 0.8241 (m-40) REVERT: B 159 LYS cc_start: 0.8636 (mttt) cc_final: 0.8354 (mtpt) REVERT: B 206 LYS cc_start: 0.8670 (mtpt) cc_final: 0.8381 (mttp) REVERT: B 239 TYR cc_start: 0.8523 (m-80) cc_final: 0.7995 (m-80) REVERT: B 250 ILE cc_start: 0.8477 (mm) cc_final: 0.8127 (mt) REVERT: B 282 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8396 (mm-40) REVERT: C 32 LYS cc_start: 0.8668 (pttp) cc_final: 0.8047 (tptt) REVERT: C 105 MET cc_start: 0.7752 (ppp) cc_final: 0.7051 (ppp) REVERT: C 123 ASN cc_start: 0.8969 (p0) cc_final: 0.8752 (p0) REVERT: C 133 LEU cc_start: 0.8610 (tp) cc_final: 0.8383 (tt) REVERT: C 159 LYS cc_start: 0.8634 (mttt) cc_final: 0.8337 (mtpt) REVERT: C 163 MET cc_start: 0.8581 (mtm) cc_final: 0.8360 (mtm) REVERT: C 236 MET cc_start: 0.6597 (OUTLIER) cc_final: 0.6070 (tpp) REVERT: C 239 TYR cc_start: 0.8401 (m-80) cc_final: 0.8054 (m-80) REVERT: C 240 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8552 (mp) REVERT: C 250 ILE cc_start: 0.8533 (mm) cc_final: 0.8242 (mt) REVERT: C 282 GLN cc_start: 0.8792 (mm-40) cc_final: 0.8570 (mm-40) REVERT: D 133 LEU cc_start: 0.8675 (tp) cc_final: 0.8418 (tt) REVERT: D 159 LYS cc_start: 0.8686 (mttt) cc_final: 0.8450 (mtpt) REVERT: D 206 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8507 (mttm) REVERT: D 282 GLN cc_start: 0.8725 (mm-40) cc_final: 0.8441 (mm-40) REVERT: E 159 LYS cc_start: 0.8639 (mttt) cc_final: 0.8341 (mtpt) REVERT: E 240 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8708 (mp) REVERT: E 250 ILE cc_start: 0.8353 (mm) cc_final: 0.8088 (mt) REVERT: E 282 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8456 (mm-40) outliers start: 76 outliers final: 62 residues processed: 404 average time/residue: 0.2213 time to fit residues: 134.7242 Evaluate side-chains 436 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 369 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 160 ASN Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 ASN Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 308 LEU 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: 0.8980 chunk 143 optimal weight: 0.0170 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN C 171 GLN E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14415 Z= 0.183 Angle : 0.673 13.172 19585 Z= 0.346 Chirality : 0.051 0.668 2260 Planarity : 0.004 0.051 2425 Dihedral : 6.683 58.464 2195 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.57 % Allowed : 18.61 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1710 helix: 1.07 (0.22), residues: 590 sheet: -0.21 (0.26), residues: 315 loop : -1.56 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 186 HIS 0.002 0.001 HIS B 125 PHE 0.029 0.001 PHE A 322 TYR 0.017 0.001 TYR A 421 ARG 0.002 0.000 ARG C 229 *********************** 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 451 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 382 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8676 (m-40) cc_final: 0.8438 (m-40) REVERT: A 133 LEU cc_start: 0.8587 (tp) cc_final: 0.8357 (tt) REVERT: A 206 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8361 (mtpp) REVERT: A 282 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8498 (mm-40) REVERT: B 141 ASN cc_start: 0.8446 (m-40) cc_final: 0.8212 (m-40) REVERT: B 159 LYS cc_start: 0.8603 (mttt) cc_final: 0.8292 (mtpt) REVERT: B 206 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8388 (mttm) REVERT: B 239 TYR cc_start: 0.8478 (m-80) cc_final: 0.7995 (m-80) REVERT: B 250 ILE cc_start: 0.8484 (mm) cc_final: 0.8147 (mt) REVERT: B 282 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8386 (mm-40) REVERT: C 32 LYS cc_start: 0.8660 (pttp) cc_final: 0.8028 (tptt) REVERT: C 105 MET cc_start: 0.7540 (ppp) cc_final: 0.7041 (ppp) REVERT: C 133 LEU cc_start: 0.8595 (tp) cc_final: 0.8366 (tt) REVERT: C 159 LYS cc_start: 0.8616 (mttt) cc_final: 0.8331 (mtpt) REVERT: C 163 MET cc_start: 0.8577 (mtm) cc_final: 0.8318 (mtm) REVERT: C 236 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5924 (tpp) REVERT: C 239 TYR cc_start: 0.8346 (m-80) cc_final: 0.8057 (m-80) REVERT: C 240 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8551 (mp) REVERT: C 250 ILE cc_start: 0.8537 (mm) cc_final: 0.8263 (mt) REVERT: C 295 TYR cc_start: 0.8851 (p90) cc_final: 0.8562 (p90) REVERT: D 133 LEU cc_start: 0.8656 (tp) cc_final: 0.8399 (tt) REVERT: D 159 LYS cc_start: 0.8660 (mttt) cc_final: 0.8424 (mtpt) REVERT: D 206 LYS cc_start: 0.8730 (mtpt) cc_final: 0.8510 (mttm) REVERT: D 282 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8419 (mm-40) REVERT: E 133 LEU cc_start: 0.8452 (tp) cc_final: 0.8225 (tt) REVERT: E 159 LYS cc_start: 0.8611 (mttt) cc_final: 0.8319 (mtpt) REVERT: E 240 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8660 (mp) REVERT: E 250 ILE cc_start: 0.8328 (mm) cc_final: 0.8087 (mt) REVERT: E 282 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8443 (mm-40) outliers start: 69 outliers final: 55 residues processed: 415 average time/residue: 0.2306 time to fit residues: 143.8662 Evaluate side-chains 435 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 377 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 391 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 308 LEU 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: 3.9990 chunk 76 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 171 GLN B 235 GLN C 131 ASN C 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 14415 Z= 0.225 Angle : 0.710 14.101 19585 Z= 0.362 Chirality : 0.053 0.764 2260 Planarity : 0.004 0.057 2425 Dihedral : 6.658 59.334 2195 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.44 % Allowed : 19.21 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1710 helix: 1.03 (0.22), residues: 590 sheet: -0.17 (0.26), residues: 315 loop : -1.53 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 186 HIS 0.002 0.001 HIS B 125 PHE 0.029 0.001 PHE A 322 TYR 0.030 0.002 TYR C 238 ARG 0.002 0.000 ARG B 392 ********************** 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 445 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 378 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8673 (m-40) cc_final: 0.8424 (m-40) REVERT: A 133 LEU cc_start: 0.8615 (tp) cc_final: 0.8396 (tt) REVERT: A 206 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8370 (mtpp) REVERT: A 282 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8494 (mm-40) REVERT: B 141 ASN cc_start: 0.8429 (m-40) cc_final: 0.8217 (m-40) REVERT: B 159 LYS cc_start: 0.8584 (mttt) cc_final: 0.8289 (mtpt) REVERT: B 206 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8396 (mttm) REVERT: B 239 TYR cc_start: 0.8502 (m-80) cc_final: 0.8047 (m-80) REVERT: B 250 ILE cc_start: 0.8503 (mm) cc_final: 0.8168 (mt) REVERT: B 282 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8395 (mm-40) REVERT: C 105 MET cc_start: 0.7590 (ppp) cc_final: 0.7070 (ppp) REVERT: C 133 LEU cc_start: 0.8611 (tp) cc_final: 0.8389 (tt) REVERT: C 159 LYS cc_start: 0.8660 (mttt) cc_final: 0.8395 (mtpt) REVERT: C 226 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8597 (pt) REVERT: C 236 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5800 (tpp) REVERT: C 239 TYR cc_start: 0.8362 (m-80) cc_final: 0.8081 (m-80) REVERT: C 240 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8526 (mp) REVERT: C 250 ILE cc_start: 0.8552 (mm) cc_final: 0.8271 (mt) REVERT: C 295 TYR cc_start: 0.8842 (p90) cc_final: 0.8584 (p90) REVERT: D 133 LEU cc_start: 0.8668 (tp) cc_final: 0.8414 (tt) REVERT: D 159 LYS cc_start: 0.8678 (mttt) cc_final: 0.8431 (mtpt) REVERT: D 206 LYS cc_start: 0.8745 (mtpt) cc_final: 0.8522 (mttm) REVERT: E 133 LEU cc_start: 0.8482 (tp) cc_final: 0.8248 (tt) REVERT: E 159 LYS cc_start: 0.8623 (mttt) cc_final: 0.8378 (mtpt) REVERT: E 240 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8689 (mp) REVERT: E 282 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8437 (mm-40) outliers start: 67 outliers final: 59 residues processed: 411 average time/residue: 0.2250 time to fit residues: 140.2738 Evaluate side-chains 435 residues out of total 1555 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 372 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 160 ASN Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 245 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 ASN Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 ASN Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 160 ASN Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 391 MET Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 160 ASN Chi-restraints excluded: chain E residue 170 MET Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 308 LEU 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: 5.9990 chunk 124 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 171 GLN ** C 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.171453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129328 restraints weight = 20825.115| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.15 r_work: 0.3222 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14415 Z= 0.209 Angle : 0.711 14.742 19585 Z= 0.359 Chirality : 0.052 0.695 2260 Planarity : 0.004 0.060 2425 Dihedral : 6.589 58.887 2195 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.17 % Allowed : 20.13 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1710 helix: 1.02 (0.22), residues: 590 sheet: -0.18 (0.26), residues: 315 loop : -1.50 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 186 HIS 0.002 0.001 HIS A 125 PHE 0.030 0.001 PHE A 322 TYR 0.017 0.002 TYR A 421 ARG 0.002 0.000 ARG C 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3860.59 seconds wall clock time: 70 minutes 38.89 seconds (4238.89 seconds total)