Starting phenix.real_space_refine on Fri Feb 6 09:29:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9loc_63244/02_2026/9loc_63244.cif Found real_map, /net/cci-nas-00/data/ceres_data/9loc_63244/02_2026/9loc_63244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9loc_63244/02_2026/9loc_63244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9loc_63244/02_2026/9loc_63244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9loc_63244/02_2026/9loc_63244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9loc_63244/02_2026/9loc_63244.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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 107 5.16 5 C 14962 2.51 5 N 3937 2.21 5 O 4539 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23545 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 2121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2121 Classifications: {'peptide': 264} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 244} Chain: "B" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "C" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "D" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "E" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "F" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "G" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "H" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "I" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "J" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "K" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "L" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "M" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1764 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 202} Chain: "N" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 74 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.09, per 1000 atoms: 0.26 Number of scatterers: 23545 At special positions: 0 Unit cell: (78.11, 193.67, 192.6, 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 107 16.00 O 4539 8.00 N 3937 7.00 C 14962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 44 " - pdb=" SG CYS A 85 " distance=2.02 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 260 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 309 " - pdb=" SG CYS M 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 367 " - pdb=" SG CYS B 425 " distance=2.02 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 321 " distance=2.03 Simple disulfide: pdb=" SG CYS C 309 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 425 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 321 " distance=2.03 Simple disulfide: pdb=" SG CYS D 367 " - pdb=" SG CYS D 425 " distance=2.03 Simple disulfide: pdb=" SG CYS E 261 " - pdb=" SG CYS E 321 " distance=2.03 Simple disulfide: pdb=" SG CYS E 309 " - pdb=" SG CYS F 309 " distance=2.03 Simple disulfide: pdb=" SG CYS E 367 " - pdb=" SG CYS E 425 " distance=2.03 Simple disulfide: pdb=" SG CYS F 261 " - pdb=" SG CYS F 321 " distance=2.03 Simple disulfide: pdb=" SG CYS F 367 " - pdb=" SG CYS F 425 " distance=2.03 Simple disulfide: pdb=" SG CYS G 261 " - pdb=" SG CYS G 321 " distance=2.03 Simple disulfide: pdb=" SG CYS G 309 " - pdb=" SG CYS H 309 " distance=2.03 Simple disulfide: pdb=" SG CYS G 367 " - pdb=" SG CYS G 425 " distance=2.03 Simple disulfide: pdb=" SG CYS H 261 " - pdb=" SG CYS H 321 " distance=2.03 Simple disulfide: pdb=" SG CYS H 367 " - pdb=" SG CYS H 425 " distance=2.03 Simple disulfide: pdb=" SG CYS I 261 " - pdb=" SG CYS I 321 " distance=2.03 Simple disulfide: pdb=" SG CYS I 367 " - pdb=" SG CYS I 425 " distance=2.03 Simple disulfide: pdb=" SG CYS J 261 " - pdb=" SG CYS J 321 " distance=2.03 Simple disulfide: pdb=" SG CYS J 367 " - pdb=" SG CYS J 425 " distance=2.03 Simple disulfide: pdb=" SG CYS K 261 " - pdb=" SG CYS K 321 " distance=2.03 Simple disulfide: pdb=" SG CYS K 309 " - pdb=" SG CYS L 309 " distance=2.03 Simple disulfide: pdb=" SG CYS K 367 " - pdb=" SG CYS K 425 " distance=2.03 Simple disulfide: pdb=" SG CYS L 261 " - pdb=" SG CYS L 321 " distance=2.03 Simple disulfide: pdb=" SG CYS L 367 " - pdb=" SG CYS L 425 " distance=2.03 Simple disulfide: pdb=" SG CYS M 261 " - pdb=" SG CYS M 321 " distance=2.03 Simple disulfide: pdb=" SG CYS M 367 " - pdb=" SG CYS M 425 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 ALPHA1-6 " BMA N 3 " - " MAN N 4 " BETA1-2 " MAN N 4 " - " NAG N 5 " BETA1-4 " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " BETA1-6 " NAG N 1 " - " FUC N 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 132 " " NAG B 700 " - " ASN B 452 " " NAG C 700 " - " ASN C 452 " " NAG D 700 " - " ASN D 452 " " NAG E 700 " - " ASN E 452 " " NAG F 700 " - " ASN F 452 " " NAG G 700 " - " ASN G 452 " " NAG H 700 " - " ASN H 452 " " NAG I 700 " - " ASN I 452 " " NAG J 700 " - " ASN J 452 " " NAG K 700 " - " ASN K 452 " " NAG L 700 " - " ASN L 452 " " NAG M 700 " - " ASN M 452 " " NAG N 1 " - " ASN B 297 " Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.0 seconds 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5592 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 80 sheets defined 12.3% alpha, 42.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'B' and resid 246 through 251 removed outlier: 3.722A pdb=" N LEU B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 315 removed outlier: 3.668A pdb=" N TRP B 313 " --> pdb=" O CYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 432 through 436 removed outlier: 3.605A pdb=" N TYR B 436 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 446 No H-bonds generated for 'chain 'B' and resid 444 through 446' Processing helix chain 'C' and resid 309 through 315 removed outlier: 3.959A pdb=" N TRP C 313 " --> pdb=" O CYS C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 432 through 436 removed outlier: 3.509A pdb=" N TYR C 436 " --> pdb=" O HIS C 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 252 Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 354 through 358 removed outlier: 3.650A pdb=" N GLU D 357 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.797A pdb=" N LEU E 251 " --> pdb=" O PRO E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 315 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.851A pdb=" N THR E 359 " --> pdb=" O ASP E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 419 Processing helix chain 'E' and resid 432 through 436 removed outlier: 3.787A pdb=" N TYR E 436 " --> pdb=" O HIS E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 252 Processing helix chain 'F' and resid 309 through 315 Processing helix chain 'F' and resid 354 through 360 Processing helix chain 'F' and resid 414 through 419 removed outlier: 3.598A pdb=" N GLN F 419 " --> pdb=" O SER F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.740A pdb=" N MET G 252 " --> pdb=" O LYS G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 315 Processing helix chain 'G' and resid 354 through 360 removed outlier: 3.581A pdb=" N THR G 359 " --> pdb=" O ASP G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 419 Processing helix chain 'G' and resid 432 through 436 Processing helix chain 'H' and resid 246 through 252 Processing helix chain 'H' and resid 309 through 315 removed outlier: 3.668A pdb=" N TRP H 313 " --> pdb=" O CYS H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 356 through 360 removed outlier: 3.684A pdb=" N THR H 359 " --> pdb=" O ASP H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 419 Processing helix chain 'H' and resid 432 through 436 Processing helix chain 'I' and resid 246 through 252 Processing helix chain 'I' and resid 309 through 315 Processing helix chain 'I' and resid 356 through 360 Processing helix chain 'I' and resid 414 through 419 Processing helix chain 'I' and resid 432 through 436 Processing helix chain 'I' and resid 442 through 447 removed outlier: 4.316A pdb=" N GLY I 446 " --> pdb=" O ASP I 442 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS I 447 " --> pdb=" O LYS I 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 442 through 447' Processing helix chain 'J' and resid 246 through 252 Processing helix chain 'J' and resid 309 through 315 Processing helix chain 'J' and resid 356 through 360 Processing helix chain 'J' and resid 414 through 419 Processing helix chain 'J' and resid 432 through 436 Processing helix chain 'K' and resid 246 through 251 Processing helix chain 'K' and resid 309 through 316 Processing helix chain 'K' and resid 354 through 360 removed outlier: 3.923A pdb=" N THR K 359 " --> pdb=" O ASP K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 419 Processing helix chain 'K' and resid 432 through 436 removed outlier: 3.641A pdb=" N TYR K 436 " --> pdb=" O HIS K 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 252 Processing helix chain 'L' and resid 309 through 316 removed outlier: 3.611A pdb=" N GLY L 316 " --> pdb=" O ASP L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.559A pdb=" N THR L 359 " --> pdb=" O ASP L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 420 removed outlier: 3.985A pdb=" N GLY L 420 " --> pdb=" O ARG L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 432 through 436 removed outlier: 3.794A pdb=" N TYR L 436 " --> pdb=" O HIS L 433 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 252 removed outlier: 3.717A pdb=" N MET M 252 " --> pdb=" O LYS M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 309 through 315 removed outlier: 3.516A pdb=" N TRP M 313 " --> pdb=" O CYS M 309 " (cutoff:3.500A) Processing helix chain 'M' and resid 356 through 360 removed outlier: 3.919A pdb=" N THR M 359 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 414 through 419 removed outlier: 3.526A pdb=" N GLN M 419 " --> pdb=" O SER M 415 " (cutoff:3.500A) Processing helix chain 'M' and resid 432 through 436 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.547A pdb=" N THR A 55 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP A 57 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA6, first strand: chain 'A' and resid 113 through 114 removed outlier: 6.531A pdb=" N VAL A 113 " --> pdb=" O GLN A 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 140 through 145 removed outlier: 5.068A pdb=" N VAL A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS A 137 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 143 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASN A 132 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 169 " --> pdb=" O ASN A 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 140 through 145 removed outlier: 5.068A pdb=" N VAL A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N LYS A 137 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 143 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ASN A 132 " --> pdb=" O TYR A 169 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N TYR A 169 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 162 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AB1, first strand: chain 'A' and resid 225 through 229 Processing sheet with id=AB2, first strand: chain 'A' and resid 225 through 229 Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 243 Processing sheet with id=AB4, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.952A pdb=" N LYS B 274 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 293 through 294 Processing sheet with id=AB6, first strand: chain 'B' and resid 347 through 351 removed outlier: 3.626A pdb=" N LYS B 370 " --> pdb=" O GLN B 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 347 through 351 removed outlier: 3.626A pdb=" N LYS B 370 " --> pdb=" O GLN B 347 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LYS B 370 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 406 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 378 through 382 removed outlier: 3.577A pdb=" N LYS B 439 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 450 through 451 removed outlier: 6.848A pdb=" N LEU B 450 " --> pdb=" O TYR M 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 454 through 456 removed outlier: 6.150A pdb=" N LEU C 455 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU D 455 " --> pdb=" O ILE E 456 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.733A pdb=" N ASP C 265 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR C 300 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 239 through 243 removed outlier: 3.733A pdb=" N ASP C 265 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR C 300 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.838A pdb=" N LYS C 334 " --> pdb=" O CYS C 321 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 347 through 351 Processing sheet with id=AC6, first strand: chain 'C' and resid 347 through 351 removed outlier: 6.273A pdb=" N PHE C 404 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC8, first strand: chain 'D' and resid 239 through 240 removed outlier: 3.651A pdb=" N VAL D 264 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG D 301 " --> pdb=" O ARG D 292 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG D 292 " --> pdb=" O ARG D 301 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL D 303 " --> pdb=" O LYS D 290 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 274 through 279 removed outlier: 3.536A pdb=" N LYS D 320 " --> pdb=" O TYR D 278 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS D 334 " --> pdb=" O CYS D 321 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.512A pdb=" N THR D 366 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER D 408 " --> pdb=" O CYS D 367 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 347 through 351 removed outlier: 3.512A pdb=" N THR D 366 " --> pdb=" O LEU D 351 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N PHE D 404 " --> pdb=" O GLY D 371 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 386 through 388 removed outlier: 4.775A pdb=" N TRP D 381 " --> pdb=" O GLU D 388 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA D 378 " --> pdb=" O MET D 428 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 239 through 243 removed outlier: 3.841A pdb=" N THR E 260 " --> pdb=" O PHE E 243 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASP E 265 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR E 300 " --> pdb=" O ASP E 265 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 282 through 284 removed outlier: 4.369A pdb=" N TRP E 277 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 323 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E 332 " --> pdb=" O VAL E 323 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 347 through 351 removed outlier: 3.649A pdb=" N THR E 366 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE E 404 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 347 through 351 removed outlier: 3.649A pdb=" N THR E 366 " --> pdb=" O LEU E 351 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N PHE E 404 " --> pdb=" O GLY E 371 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 386 through 388 removed outlier: 4.386A pdb=" N TRP E 381 " --> pdb=" O GLU E 388 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 378 " --> pdb=" O MET E 428 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 380 " --> pdb=" O SER E 426 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS E 439 " --> pdb=" O CYS E 425 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 239 through 243 removed outlier: 3.717A pdb=" N SER F 239 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR F 260 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS F 261 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER F 304 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR F 300 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 239 through 243 removed outlier: 3.717A pdb=" N SER F 239 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR F 260 " --> pdb=" O PHE F 243 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS F 261 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER F 304 " --> pdb=" O CYS F 261 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N TYR F 300 " --> pdb=" O ASP F 265 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 273 through 279 removed outlier: 3.618A pdb=" N CYS F 321 " --> pdb=" O LYS F 334 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F 334 " --> pdb=" O CYS F 321 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 347 through 351 removed outlier: 3.617A pdb=" N LYS F 370 " --> pdb=" O GLN F 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR F 366 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER F 408 " --> pdb=" O CYS F 367 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 347 through 351 removed outlier: 3.617A pdb=" N LYS F 370 " --> pdb=" O GLN F 347 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR F 366 " --> pdb=" O LEU F 351 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N PHE F 404 " --> pdb=" O GLY F 371 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 386 through 387 removed outlier: 3.785A pdb=" N ALA F 378 " --> pdb=" O MET F 428 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 239 through 243 removed outlier: 3.503A pdb=" N VAL G 302 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL G 305 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 282 through 284 removed outlier: 3.668A pdb=" N VAL G 282 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TRP G 277 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER G 324 " --> pdb=" O LYS G 274 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 347 through 351 removed outlier: 3.511A pdb=" N THR G 366 " --> pdb=" O LEU G 351 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER G 408 " --> pdb=" O CYS G 367 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 347 through 351 removed outlier: 3.511A pdb=" N THR G 366 " --> pdb=" O LEU G 351 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE G 404 " --> pdb=" O GLY G 371 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AF2, first strand: chain 'G' and resid 454 through 455 removed outlier: 6.873A pdb=" N SER G 454 " --> pdb=" O LEU H 455 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER H 454 " --> pdb=" O LEU I 455 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N SER I 454 " --> pdb=" O LEU J 455 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N SER J 454 " --> pdb=" O LEU K 455 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'H' and resid 239 through 243 Processing sheet with id=AF4, first strand: chain 'H' and resid 239 through 243 removed outlier: 3.958A pdb=" N ASP H 265 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR H 300 " --> pdb=" O ASP H 265 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 282 through 283 removed outlier: 3.512A pdb=" N VAL H 323 " --> pdb=" O ILE H 332 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 347 through 351 removed outlier: 3.556A pdb=" N SER H 408 " --> pdb=" O CYS H 367 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 351 removed outlier: 6.036A pdb=" N PHE H 404 " --> pdb=" O GLY H 371 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 386 through 387 Processing sheet with id=AF9, first strand: chain 'I' and resid 239 through 243 removed outlier: 3.586A pdb=" N THR I 260 " --> pdb=" O PHE I 243 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 265 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR I 300 " --> pdb=" O ASP I 265 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL I 305 " --> pdb=" O LYS I 288 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 282 through 284 removed outlier: 3.553A pdb=" N TRP I 277 " --> pdb=" O VAL I 284 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 349 through 351 removed outlier: 3.533A pdb=" N VAL I 412 " --> pdb=" O VAL I 363 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU I 365 " --> pdb=" O LEU I 410 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 349 through 351 removed outlier: 5.932A pdb=" N PHE I 404 " --> pdb=" O GLY I 371 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 386 through 387 removed outlier: 3.819A pdb=" N ALA I 378 " --> pdb=" O MET I 428 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 239 through 243 removed outlier: 3.697A pdb=" N ASP J 265 " --> pdb=" O TYR J 300 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR J 300 " --> pdb=" O ASP J 265 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 239 through 243 removed outlier: 3.697A pdb=" N ASP J 265 " --> pdb=" O TYR J 300 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR J 300 " --> pdb=" O ASP J 265 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 282 through 284 removed outlier: 3.969A pdb=" N TRP J 277 " --> pdb=" O VAL J 284 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS J 334 " --> pdb=" O CYS J 321 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL J 323 " --> pdb=" O ILE J 332 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 347 through 351 removed outlier: 3.565A pdb=" N THR J 366 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER J 408 " --> pdb=" O CYS J 367 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 347 through 351 removed outlier: 3.565A pdb=" N THR J 366 " --> pdb=" O LEU J 351 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE J 404 " --> pdb=" O GLY J 371 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 386 through 388 removed outlier: 4.729A pdb=" N TRP J 381 " --> pdb=" O GLU J 388 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA J 378 " --> pdb=" O MET J 428 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET J 428 " --> pdb=" O ALA J 378 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 239 through 240 removed outlier: 3.687A pdb=" N VAL K 302 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL K 303 " --> pdb=" O LYS K 290 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 282 through 284 removed outlier: 4.279A pdb=" N TRP K 277 " --> pdb=" O VAL K 284 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 347 through 351 removed outlier: 3.524A pdb=" N THR K 366 " --> pdb=" O LEU K 351 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 347 through 351 removed outlier: 3.524A pdb=" N THR K 366 " --> pdb=" O LEU K 351 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE K 404 " --> pdb=" O GLY K 371 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 386 through 388 removed outlier: 4.478A pdb=" N TRP K 381 " --> pdb=" O GLU K 388 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA K 378 " --> pdb=" O MET K 428 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE K 423 " --> pdb=" O LEU K 441 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 239 through 240 removed outlier: 3.628A pdb=" N CYS L 261 " --> pdb=" O SER L 304 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER L 304 " --> pdb=" O CYS L 261 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR L 300 " --> pdb=" O ASP L 265 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 282 through 284 removed outlier: 4.573A pdb=" N TRP L 277 " --> pdb=" O VAL L 284 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS L 321 " --> pdb=" O LYS L 334 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS L 334 " --> pdb=" O CYS L 321 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 347 through 351 removed outlier: 3.749A pdb=" N LYS L 370 " --> pdb=" O GLN L 347 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER L 408 " --> pdb=" O CYS L 367 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 347 through 351 removed outlier: 3.749A pdb=" N LYS L 370 " --> pdb=" O GLN L 347 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N PHE L 404 " --> pdb=" O GLY L 371 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 386 through 387 Processing sheet with id=AI3, first strand: chain 'L' and resid 455 through 456 removed outlier: 5.975A pdb=" N LEU L 455 " --> pdb=" O ILE M 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'M' and resid 239 through 243 removed outlier: 3.559A pdb=" N ASP M 265 " --> pdb=" O TYR M 300 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR M 300 " --> pdb=" O ASP M 265 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG M 301 " --> pdb=" O ARG M 292 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG M 292 " --> pdb=" O ARG M 301 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL M 303 " --> pdb=" O LYS M 290 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 275 through 279 removed outlier: 3.898A pdb=" N ILE M 332 " --> pdb=" O VAL M 323 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 347 through 351 removed outlier: 3.561A pdb=" N SER M 408 " --> pdb=" O CYS M 367 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 347 through 351 removed outlier: 5.855A pdb=" N PHE M 404 " --> pdb=" O GLY M 371 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'M' and resid 386 through 387 932 hydrogen bonds defined for protein. 2241 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: 6.86 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7453 1.34 - 1.47: 5779 1.47 - 1.59: 10802 1.59 - 1.71: 0 1.71 - 1.84: 145 Bond restraints: 24179 Sorted by residual: bond pdb=" CA LYS E 443 " pdb=" C LYS E 443 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.27e-02 6.20e+03 1.15e+01 bond pdb=" CA GLN F 342 " pdb=" C GLN F 342 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.24e-02 6.50e+03 9.79e+00 bond pdb=" CG LEU I 410 " pdb=" CD1 LEU I 410 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.73e+00 bond pdb=" N SER E 444 " pdb=" CA SER E 444 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.23e-02 6.61e+03 4.23e+00 bond pdb=" CA ASP E 442 " pdb=" C ASP E 442 " ideal model delta sigma weight residual 1.525 1.503 0.022 1.25e-02 6.40e+03 3.12e+00 ... (remaining 24174 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 32519 2.74 - 5.47: 354 5.47 - 8.21: 43 8.21 - 10.94: 11 10.94 - 13.68: 1 Bond angle restraints: 32928 Sorted by residual: angle pdb=" C GLN F 342 " pdb=" N PRO F 343 " pdb=" CA PRO F 343 " ideal model delta sigma weight residual 120.13 114.05 6.08 1.13e+00 7.83e-01 2.90e+01 angle pdb=" CB MET G 457 " pdb=" CG MET G 457 " pdb=" SD MET G 457 " ideal model delta sigma weight residual 112.70 126.38 -13.68 3.00e+00 1.11e-01 2.08e+01 angle pdb=" CA MET B 252 " pdb=" CB MET B 252 " pdb=" CG MET B 252 " ideal model delta sigma weight residual 114.10 123.21 -9.11 2.00e+00 2.50e-01 2.08e+01 angle pdb=" CA VAL J 279 " pdb=" CB VAL J 279 " pdb=" CG1 VAL J 279 " ideal model delta sigma weight residual 110.40 116.62 -6.22 1.70e+00 3.46e-01 1.34e+01 angle pdb=" CA MET M 252 " pdb=" CB MET M 252 " pdb=" CG MET M 252 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.16e+01 ... (remaining 32923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 12940 18.00 - 36.01: 1613 36.01 - 54.01: 368 54.01 - 72.01: 78 72.01 - 90.01: 35 Dihedral angle restraints: 15034 sinusoidal: 6410 harmonic: 8624 Sorted by residual: dihedral pdb=" CB CYS B 309 " pdb=" SG CYS B 309 " pdb=" SG CYS M 309 " pdb=" CB CYS M 309 " ideal model delta sinusoidal sigma weight residual -86.00 2.98 -88.98 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS E 261 " pdb=" SG CYS E 261 " pdb=" SG CYS E 321 " pdb=" CB CYS E 321 " ideal model delta sinusoidal sigma weight residual -86.00 -173.34 87.34 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS C 309 " pdb=" SG CYS C 309 " pdb=" SG CYS D 309 " pdb=" CB CYS D 309 " ideal model delta sinusoidal sigma weight residual -86.00 -1.66 -84.34 1 1.00e+01 1.00e-02 8.65e+01 ... (remaining 15031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3159 0.072 - 0.143: 522 0.143 - 0.215: 12 0.215 - 0.286: 1 0.286 - 0.358: 1 Chirality restraints: 3695 Sorted by residual: chirality pdb=" C1 NAG L 700 " pdb=" ND2 ASN L 452 " pdb=" C2 NAG L 700 " pdb=" O5 NAG L 700 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C1 NAG F 700 " pdb=" ND2 ASN F 452 " pdb=" C2 NAG F 700 " pdb=" O5 NAG F 700 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C1 MAN N 4 " pdb=" O6 BMA N 3 " pdb=" C2 MAN N 4 " pdb=" O5 MAN N 4 " both_signs ideal model delta sigma weight residual False 2.40 2.42 -0.02 2.00e-02 2.50e+03 1.15e+00 ... (remaining 3692 not shown) Planarity restraints: 4216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 407 " -0.022 2.00e-02 2.50e+03 2.06e-02 8.45e+00 pdb=" CG TYR L 407 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR L 407 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR L 407 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR L 407 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR L 407 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 407 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 407 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN M 342 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO M 343 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO M 343 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 343 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 70 " 0.040 5.00e-02 4.00e+02 5.99e-02 5.74e+00 pdb=" N PRO A 71 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " 0.033 5.00e-02 4.00e+02 ... (remaining 4213 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 11275 2.97 - 3.45: 23236 3.45 - 3.94: 38353 3.94 - 4.42: 42800 4.42 - 4.90: 71347 Nonbonded interactions: 187011 Sorted by model distance: nonbonded pdb=" OH TYR F 407 " pdb=" CG2 THR G 366 " model vdw 2.489 3.460 nonbonded pdb=" O ILE H 456 " pdb=" CG2 ILE H 456 " model vdw 2.548 3.460 nonbonded pdb=" O5 NAG N 2 " pdb=" O6 NAG N 2 " model vdw 2.551 2.432 nonbonded pdb=" O GLU D 345 " pdb=" NE2 GLN D 347 " model vdw 2.562 3.120 nonbonded pdb=" O2 BMA N 3 " pdb=" O3 BMA N 3 " model vdw 2.563 2.432 ... (remaining 187006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.460 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 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 : 0.005 0.072 24230 Z= 0.212 Angle : 0.717 13.676 33049 Z= 0.360 Chirality : 0.048 0.358 3695 Planarity : 0.005 0.063 4202 Dihedral : 16.755 90.014 9346 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.85 % Allowed : 25.48 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.16), residues: 2890 helix: -1.65 (0.29), residues: 244 sheet: -0.41 (0.15), residues: 1213 loop : -0.03 (0.18), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 416 TYR 0.050 0.002 TYR L 407 PHE 0.016 0.001 PHE I 372 TRP 0.028 0.002 TRP F 417 HIS 0.007 0.001 HIS E 268 Details of bonding type rmsd covalent geometry : bond 0.00468 (24179) covalent geometry : angle 0.71059 (32928) SS BOND : bond 0.00325 ( 32) SS BOND : angle 0.96797 ( 64) hydrogen bonds : bond 0.23413 ( 810) hydrogen bonds : angle 10.54733 ( 2241) link_ALPHA1-6 : bond 0.00509 ( 1) link_ALPHA1-6 : angle 1.61110 ( 3) link_BETA1-2 : bond 0.00039 ( 1) link_BETA1-2 : angle 0.95326 ( 3) link_BETA1-4 : bond 0.00242 ( 2) link_BETA1-4 : angle 2.64507 ( 6) link_BETA1-6 : bond 0.00218 ( 1) link_BETA1-6 : angle 2.62841 ( 3) link_NAG-ASN : bond 0.00386 ( 14) link_NAG-ASN : angle 2.36087 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 253 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8745 (mmm-85) REVERT: A 117 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8661 (m-30) REVERT: A 250 MET cc_start: 0.8278 (tpp) cc_final: 0.8043 (tpp) REVERT: B 362 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8697 (mm-40) REVERT: B 368 LEU cc_start: 0.8946 (tt) cc_final: 0.8641 (tt) REVERT: D 249 ASP cc_start: 0.7878 (m-30) cc_final: 0.7407 (m-30) REVERT: E 443 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7878 (mtmt) REVERT: F 357 GLU cc_start: 0.7993 (tt0) cc_final: 0.7327 (tt0) REVERT: F 369 VAL cc_start: 0.9203 (t) cc_final: 0.8988 (m) REVERT: H 243 PHE cc_start: 0.8445 (m-80) cc_final: 0.8168 (m-80) REVERT: H 258 GLU cc_start: 0.8411 (pm20) cc_final: 0.8113 (mp0) REVERT: H 349 TYR cc_start: 0.8998 (m-80) cc_final: 0.8584 (m-80) REVERT: H 373 TYR cc_start: 0.8623 (t80) cc_final: 0.8279 (t80) REVERT: I 342 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8143 (tm-30) REVERT: J 252 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6353 (pmm) REVERT: K 252 MET cc_start: 0.7876 (mmp) cc_final: 0.7443 (mmm) REVERT: K 386 GLN cc_start: 0.8708 (pm20) cc_final: 0.8459 (pm20) REVERT: K 457 MET cc_start: 0.6663 (mmm) cc_final: 0.6189 (mmm) REVERT: M 309 CYS cc_start: 0.4818 (m) cc_final: 0.4507 (m) outliers start: 23 outliers final: 14 residues processed: 269 average time/residue: 0.1763 time to fit residues: 72.7915 Evaluate side-chains 236 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 218 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain E residue 443 LYS Chi-restraints excluded: chain F residue 457 MET Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 406 LEU Chi-restraints excluded: chain J residue 428 MET Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 428 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 ASN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 418 GLN I 285 HIS M 434 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.110197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082306 restraints weight = 67046.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.083653 restraints weight = 37185.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.084822 restraints weight = 25185.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.084983 restraints weight = 24253.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.085046 restraints weight = 20373.221| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24230 Z= 0.132 Angle : 0.591 11.219 33049 Z= 0.297 Chirality : 0.046 0.351 3695 Planarity : 0.004 0.066 4202 Dihedral : 6.101 59.158 3559 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.58 % Allowed : 23.19 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2890 helix: -1.02 (0.32), residues: 233 sheet: -0.16 (0.15), residues: 1244 loop : 0.13 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 255 TYR 0.016 0.001 TYR L 407 PHE 0.017 0.001 PHE A 47 TRP 0.014 0.001 TRP F 417 HIS 0.004 0.001 HIS I 429 Details of bonding type rmsd covalent geometry : bond 0.00300 (24179) covalent geometry : angle 0.58418 (32928) SS BOND : bond 0.00396 ( 32) SS BOND : angle 1.03072 ( 64) hydrogen bonds : bond 0.03828 ( 810) hydrogen bonds : angle 7.16966 ( 2241) link_ALPHA1-6 : bond 0.00213 ( 1) link_ALPHA1-6 : angle 1.33475 ( 3) link_BETA1-2 : bond 0.00052 ( 1) link_BETA1-2 : angle 0.83305 ( 3) link_BETA1-4 : bond 0.00376 ( 2) link_BETA1-4 : angle 2.26918 ( 6) link_BETA1-6 : bond 0.00050 ( 1) link_BETA1-6 : angle 2.13805 ( 3) link_NAG-ASN : bond 0.00346 ( 14) link_NAG-ASN : angle 2.19373 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 243 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 LEU cc_start: 0.8352 (tp) cc_final: 0.7961 (mp) REVERT: A 194 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9141 (tt) REVERT: B 362 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8731 (mm-40) REVERT: D 249 ASP cc_start: 0.7969 (m-30) cc_final: 0.7382 (m-30) REVERT: D 252 MET cc_start: 0.6712 (mpp) cc_final: 0.6481 (mpp) REVERT: D 309 CYS cc_start: 0.5059 (m) cc_final: 0.4780 (m) REVERT: D 368 LEU cc_start: 0.9101 (tp) cc_final: 0.8882 (tt) REVERT: D 390 ASN cc_start: 0.8682 (t0) cc_final: 0.8304 (t0) REVERT: F 357 GLU cc_start: 0.7829 (tt0) cc_final: 0.7389 (tt0) REVERT: G 355 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7511 (mtt180) REVERT: H 349 TYR cc_start: 0.9009 (m-80) cc_final: 0.8669 (m-80) REVERT: H 373 TYR cc_start: 0.8300 (t80) cc_final: 0.8076 (t80) REVERT: I 293 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6034 (tp30) REVERT: I 342 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8153 (tm-30) REVERT: J 252 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.5532 (pmm) REVERT: J 355 ARG cc_start: 0.8338 (mpp-170) cc_final: 0.8016 (mpp-170) REVERT: K 252 MET cc_start: 0.7691 (mmp) cc_final: 0.7304 (mmm) REVERT: L 419 GLN cc_start: 0.9212 (mt0) cc_final: 0.8769 (mp10) REVERT: M 309 CYS cc_start: 0.4018 (m) cc_final: 0.3732 (m) outliers start: 97 outliers final: 57 residues processed: 323 average time/residue: 0.1399 time to fit residues: 72.7158 Evaluate side-chains 277 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 216 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 356 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 412 VAL Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 285 HIS Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 285 HIS Chi-restraints excluded: chain L residue 412 VAL Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 140 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 18 optimal weight: 0.0000 chunk 170 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 214 optimal weight: 4.9990 chunk 284 optimal weight: 0.0270 chunk 97 optimal weight: 9.9990 overall best weight: 1.5646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 418 GLN G 435 HIS ** H 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 325 ASN K 311 GLN L 311 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.109532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.082467 restraints weight = 66078.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.083316 restraints weight = 35738.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.083846 restraints weight = 24610.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.084138 restraints weight = 23965.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.084246 restraints weight = 21090.899| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 24230 Z= 0.162 Angle : 0.583 9.744 33049 Z= 0.292 Chirality : 0.045 0.340 3695 Planarity : 0.004 0.054 4202 Dihedral : 5.545 59.636 3531 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.83 % Allowed : 23.97 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2890 helix: -0.93 (0.31), residues: 240 sheet: -0.09 (0.14), residues: 1250 loop : 0.14 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 292 TYR 0.029 0.001 TYR E 407 PHE 0.012 0.001 PHE I 372 TRP 0.014 0.001 TRP J 313 HIS 0.007 0.001 HIS I 285 Details of bonding type rmsd covalent geometry : bond 0.00367 (24179) covalent geometry : angle 0.57573 (32928) SS BOND : bond 0.00391 ( 32) SS BOND : angle 1.04353 ( 64) hydrogen bonds : bond 0.03645 ( 810) hydrogen bonds : angle 6.58829 ( 2241) link_ALPHA1-6 : bond 0.00332 ( 1) link_ALPHA1-6 : angle 1.58070 ( 3) link_BETA1-2 : bond 0.00292 ( 1) link_BETA1-2 : angle 0.96176 ( 3) link_BETA1-4 : bond 0.00254 ( 2) link_BETA1-4 : angle 2.37477 ( 6) link_BETA1-6 : bond 0.00033 ( 1) link_BETA1-6 : angle 2.22427 ( 3) link_NAG-ASN : bond 0.00319 ( 14) link_NAG-ASN : angle 2.19664 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 224 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8814 (mmm-85) REVERT: A 194 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9166 (tt) REVERT: B 362 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8744 (mm-40) REVERT: D 249 ASP cc_start: 0.8110 (m-30) cc_final: 0.7478 (m-30) REVERT: D 309 CYS cc_start: 0.4869 (m) cc_final: 0.4583 (m) REVERT: D 342 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8352 (pp30) REVERT: D 368 LEU cc_start: 0.9133 (tp) cc_final: 0.8907 (tt) REVERT: E 300 TYR cc_start: 0.6554 (m-80) cc_final: 0.6198 (m-80) REVERT: G 355 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7559 (mtt180) REVERT: H 373 TYR cc_start: 0.8332 (t80) cc_final: 0.8111 (t80) REVERT: I 293 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6106 (tp30) REVERT: I 342 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8161 (tm-30) REVERT: J 252 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.5342 (pmm) REVERT: J 355 ARG cc_start: 0.8383 (mpp-170) cc_final: 0.8048 (mpp-170) REVERT: K 252 MET cc_start: 0.7687 (mmp) cc_final: 0.7337 (mmm) REVERT: K 386 GLN cc_start: 0.8460 (pm20) cc_final: 0.8171 (pm20) REVERT: K 411 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8783 (p) REVERT: K 457 MET cc_start: 0.6688 (mmm) cc_final: 0.6169 (mmm) REVERT: L 419 GLN cc_start: 0.9231 (mt0) cc_final: 0.8858 (mp10) outliers start: 104 outliers final: 74 residues processed: 310 average time/residue: 0.1529 time to fit residues: 75.4989 Evaluate side-chains 298 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 217 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 309 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 256 THR Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 285 HIS Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain K residue 434 ASN Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Chi-restraints excluded: chain M residue 377 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 252 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 238 optimal weight: 6.9990 chunk 220 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 418 GLN H 295 GLN ** I 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.109389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.081454 restraints weight = 65688.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.083003 restraints weight = 34543.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.083633 restraints weight = 22830.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083904 restraints weight = 23359.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.084004 restraints weight = 19797.505| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24230 Z= 0.152 Angle : 0.576 8.287 33049 Z= 0.286 Chirality : 0.045 0.332 3695 Planarity : 0.004 0.053 4202 Dihedral : 5.452 52.478 3531 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.91 % Allowed : 24.26 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2890 helix: -0.82 (0.32), residues: 242 sheet: -0.01 (0.14), residues: 1249 loop : 0.21 (0.18), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 416 TYR 0.022 0.001 TYR E 407 PHE 0.011 0.001 PHE A 47 TRP 0.013 0.001 TRP J 313 HIS 0.008 0.001 HIS E 268 Details of bonding type rmsd covalent geometry : bond 0.00347 (24179) covalent geometry : angle 0.56912 (32928) SS BOND : bond 0.00366 ( 32) SS BOND : angle 0.94486 ( 64) hydrogen bonds : bond 0.03228 ( 810) hydrogen bonds : angle 6.16201 ( 2241) link_ALPHA1-6 : bond 0.00299 ( 1) link_ALPHA1-6 : angle 1.52436 ( 3) link_BETA1-2 : bond 0.00228 ( 1) link_BETA1-2 : angle 0.90390 ( 3) link_BETA1-4 : bond 0.00298 ( 2) link_BETA1-4 : angle 2.28765 ( 6) link_BETA1-6 : bond 0.00019 ( 1) link_BETA1-6 : angle 2.12243 ( 3) link_NAG-ASN : bond 0.00329 ( 14) link_NAG-ASN : angle 2.17344 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 230 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8807 (mmm-85) REVERT: A 104 SER cc_start: 0.8144 (OUTLIER) cc_final: 0.7860 (p) REVERT: A 194 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9159 (tt) REVERT: A 230 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8728 (mmm-85) REVERT: A 250 MET cc_start: 0.8128 (tpp) cc_final: 0.7820 (tpp) REVERT: B 362 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8717 (mm-40) REVERT: C 424 SER cc_start: 0.8196 (m) cc_final: 0.7846 (p) REVERT: D 249 ASP cc_start: 0.8143 (m-30) cc_final: 0.7562 (m-30) REVERT: D 309 CYS cc_start: 0.4709 (m) cc_final: 0.4487 (m) REVERT: D 342 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8344 (pp30) REVERT: G 355 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7574 (mtt180) REVERT: H 373 TYR cc_start: 0.8374 (t80) cc_final: 0.8127 (t80) REVERT: I 293 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6071 (tp30) REVERT: I 342 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8165 (tm-30) REVERT: J 355 ARG cc_start: 0.8402 (mpp-170) cc_final: 0.8067 (mpp-170) REVERT: K 252 MET cc_start: 0.7718 (mmp) cc_final: 0.7337 (mmm) REVERT: K 386 GLN cc_start: 0.8463 (pm20) cc_final: 0.8176 (pm20) REVERT: K 411 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8768 (p) REVERT: K 457 MET cc_start: 0.6811 (mmm) cc_final: 0.6105 (mmm) REVERT: L 249 ASP cc_start: 0.7938 (m-30) cc_final: 0.7563 (t0) REVERT: M 255 ARG cc_start: 0.8228 (mpp80) cc_final: 0.7843 (mpp80) outliers start: 106 outliers final: 80 residues processed: 318 average time/residue: 0.1430 time to fit residues: 72.3202 Evaluate side-chains 301 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 213 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 285 HIS Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 253 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain K residue 434 ASN Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 285 HIS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 412 VAL Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Chi-restraints excluded: chain M residue 377 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 212 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 244 optimal weight: 7.9990 chunk 272 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 260 optimal weight: 20.0000 chunk 215 optimal weight: 0.6980 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN F 419 GLN G 418 GLN I 285 HIS L 311 GLN M 276 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.108263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080542 restraints weight = 66577.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.081996 restraints weight = 36607.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.082137 restraints weight = 24789.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.082475 restraints weight = 25545.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.082563 restraints weight = 22381.144| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 24230 Z= 0.209 Angle : 0.608 7.869 33049 Z= 0.303 Chirality : 0.046 0.331 3695 Planarity : 0.004 0.055 4202 Dihedral : 5.500 54.098 3529 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.68 % Allowed : 24.04 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.16), residues: 2890 helix: -0.73 (0.32), residues: 234 sheet: -0.02 (0.14), residues: 1243 loop : 0.18 (0.18), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 255 TYR 0.026 0.002 TYR E 407 PHE 0.016 0.001 PHE I 372 TRP 0.024 0.001 TRP A 57 HIS 0.006 0.001 HIS I 429 Details of bonding type rmsd covalent geometry : bond 0.00467 (24179) covalent geometry : angle 0.60057 (32928) SS BOND : bond 0.00506 ( 32) SS BOND : angle 1.00430 ( 64) hydrogen bonds : bond 0.03289 ( 810) hydrogen bonds : angle 6.09829 ( 2241) link_ALPHA1-6 : bond 0.00235 ( 1) link_ALPHA1-6 : angle 1.58282 ( 3) link_BETA1-2 : bond 0.00149 ( 1) link_BETA1-2 : angle 0.91559 ( 3) link_BETA1-4 : bond 0.00129 ( 2) link_BETA1-4 : angle 2.48348 ( 6) link_BETA1-6 : bond 0.00168 ( 1) link_BETA1-6 : angle 2.52789 ( 3) link_NAG-ASN : bond 0.00346 ( 14) link_NAG-ASN : angle 2.26964 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 216 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8818 (mmm-85) REVERT: A 194 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9157 (tt) REVERT: A 230 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8749 (mmm-85) REVERT: A 250 MET cc_start: 0.8214 (tpp) cc_final: 0.7867 (tpp) REVERT: B 362 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8754 (mm-40) REVERT: B 440 SER cc_start: 0.8678 (m) cc_final: 0.8473 (p) REVERT: D 249 ASP cc_start: 0.8167 (m-30) cc_final: 0.7640 (m-30) REVERT: D 342 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8328 (pp30) REVERT: G 355 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7573 (mtt180) REVERT: G 360 LYS cc_start: 0.8629 (tppt) cc_final: 0.7738 (mtmt) REVERT: H 373 TYR cc_start: 0.8319 (t80) cc_final: 0.8108 (t80) REVERT: I 293 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6074 (tp30) REVERT: J 242 LEU cc_start: 0.5156 (OUTLIER) cc_final: 0.4680 (tt) REVERT: K 252 MET cc_start: 0.7706 (mmp) cc_final: 0.7357 (mmm) REVERT: K 386 GLN cc_start: 0.8538 (pm20) cc_final: 0.8241 (pm20) REVERT: K 411 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8871 (p) REVERT: K 457 MET cc_start: 0.6928 (mmm) cc_final: 0.6218 (mmm) REVERT: L 249 ASP cc_start: 0.8001 (m-30) cc_final: 0.7636 (t0) REVERT: L 311 GLN cc_start: 0.8303 (tp-100) cc_final: 0.8098 (tp-100) outliers start: 127 outliers final: 95 residues processed: 321 average time/residue: 0.1512 time to fit residues: 76.7065 Evaluate side-chains 311 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 208 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain H residue 457 MET Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 285 HIS Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 253 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain J residue 428 MET Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain K residue 434 ASN Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 393 THR Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 406 LEU Chi-restraints excluded: chain L residue 412 VAL Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 428 MET Chi-restraints excluded: chain M residue 430 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 173 optimal weight: 5.9990 chunk 288 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN B 285 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.106756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.078228 restraints weight = 68158.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.079576 restraints weight = 40777.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.080415 restraints weight = 26450.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.080759 restraints weight = 24175.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.080819 restraints weight = 21459.921| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24230 Z= 0.280 Angle : 0.657 7.451 33049 Z= 0.331 Chirality : 0.047 0.334 3695 Planarity : 0.004 0.054 4202 Dihedral : 5.699 57.447 3527 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 5.13 % Allowed : 24.08 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2890 helix: -0.85 (0.32), residues: 235 sheet: -0.09 (0.15), residues: 1230 loop : 0.01 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 292 TYR 0.029 0.002 TYR E 407 PHE 0.022 0.002 PHE I 372 TRP 0.015 0.002 TRP B 313 HIS 0.006 0.001 HIS I 429 Details of bonding type rmsd covalent geometry : bond 0.00622 (24179) covalent geometry : angle 0.64848 (32928) SS BOND : bond 0.00483 ( 32) SS BOND : angle 1.32963 ( 64) hydrogen bonds : bond 0.03477 ( 810) hydrogen bonds : angle 6.21908 ( 2241) link_ALPHA1-6 : bond 0.00295 ( 1) link_ALPHA1-6 : angle 1.69340 ( 3) link_BETA1-2 : bond 0.00040 ( 1) link_BETA1-2 : angle 0.83966 ( 3) link_BETA1-4 : bond 0.00389 ( 2) link_BETA1-4 : angle 2.65587 ( 6) link_BETA1-6 : bond 0.00364 ( 1) link_BETA1-6 : angle 2.76021 ( 3) link_NAG-ASN : bond 0.00387 ( 14) link_NAG-ASN : angle 2.40630 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 199 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8819 (mmm-85) REVERT: A 194 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9199 (tt) REVERT: A 230 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8746 (mmm-85) REVERT: B 318 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: B 362 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8768 (mm-40) REVERT: D 249 ASP cc_start: 0.8350 (m-30) cc_final: 0.7802 (m-30) REVERT: D 342 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8310 (pp30) REVERT: D 347 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8125 (mm110) REVERT: E 407 TYR cc_start: 0.8805 (m-80) cc_final: 0.8472 (m-10) REVERT: G 355 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7535 (mtt180) REVERT: G 362 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8304 (mm110) REVERT: H 338 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8250 (tppt) REVERT: I 293 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6277 (tp30) REVERT: J 242 LEU cc_start: 0.5333 (OUTLIER) cc_final: 0.4858 (tt) REVERT: K 252 MET cc_start: 0.7791 (mmp) cc_final: 0.7440 (mmm) REVERT: K 386 GLN cc_start: 0.8523 (pm20) cc_final: 0.8224 (pm20) REVERT: K 411 THR cc_start: 0.9192 (OUTLIER) cc_final: 0.8836 (p) REVERT: K 457 MET cc_start: 0.7086 (mmm) cc_final: 0.6264 (mmm) REVERT: L 249 ASP cc_start: 0.7991 (m-30) cc_final: 0.7614 (t0) REVERT: L 301 ARG cc_start: 0.7395 (ttt-90) cc_final: 0.6672 (ttt-90) outliers start: 139 outliers final: 106 residues processed: 315 average time/residue: 0.1652 time to fit residues: 81.8750 Evaluate side-chains 312 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 195 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 438 GLN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 342 GLN Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 427 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 362 GLN Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 440 SER Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 264 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain H residue 457 MET Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 284 VAL Chi-restraints excluded: chain I residue 285 HIS Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 253 ILE Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 336 ILE Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain J residue 425 CYS Chi-restraints excluded: chain J residue 428 MET Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 411 THR Chi-restraints excluded: chain K residue 412 VAL Chi-restraints excluded: chain K residue 434 ASN Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 253 ILE Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 393 THR Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 406 LEU Chi-restraints excluded: chain L residue 412 VAL Chi-restraints excluded: chain L residue 425 CYS Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 312 ASP Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 428 MET Chi-restraints excluded: chain M residue 430 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 190 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 244 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 239 optimal weight: 0.0770 chunk 26 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN D 419 GLN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 419 GLN G 418 GLN I 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.112164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.084652 restraints weight = 67758.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.086234 restraints weight = 35514.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.087526 restraints weight = 23725.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.087713 restraints weight = 21453.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.087381 restraints weight = 18798.836| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24230 Z= 0.115 Angle : 0.584 8.089 33049 Z= 0.288 Chirality : 0.045 0.327 3695 Planarity : 0.004 0.053 4202 Dihedral : 5.374 54.323 3527 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.43 % Allowed : 25.74 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2890 helix: -0.69 (0.33), residues: 236 sheet: 0.06 (0.15), residues: 1231 loop : 0.22 (0.18), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 255 TYR 0.019 0.001 TYR E 349 PHE 0.016 0.001 PHE A 47 TRP 0.017 0.001 TRP K 417 HIS 0.004 0.001 HIS I 429 Details of bonding type rmsd covalent geometry : bond 0.00267 (24179) covalent geometry : angle 0.57655 (32928) SS BOND : bond 0.00297 ( 32) SS BOND : angle 1.03503 ( 64) hydrogen bonds : bond 0.02998 ( 810) hydrogen bonds : angle 5.70942 ( 2241) link_ALPHA1-6 : bond 0.00560 ( 1) link_ALPHA1-6 : angle 1.49169 ( 3) link_BETA1-2 : bond 0.00341 ( 1) link_BETA1-2 : angle 0.82711 ( 3) link_BETA1-4 : bond 0.00573 ( 2) link_BETA1-4 : angle 2.16104 ( 6) link_BETA1-6 : bond 0.00055 ( 1) link_BETA1-6 : angle 2.05901 ( 3) link_NAG-ASN : bond 0.00325 ( 14) link_NAG-ASN : angle 2.13273 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 234 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8764 (mmm-85) REVERT: A 169 TYR cc_start: 0.7318 (t80) cc_final: 0.6993 (t80) REVERT: A 194 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9149 (tt) REVERT: A 250 MET cc_start: 0.7948 (tpp) cc_final: 0.7706 (tpp) REVERT: D 249 ASP cc_start: 0.8063 (m-30) cc_final: 0.7560 (m-30) REVERT: G 360 LYS cc_start: 0.8644 (tppt) cc_final: 0.7779 (mtmt) REVERT: H 338 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8284 (tppt) REVERT: I 293 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.5980 (tp30) REVERT: J 242 LEU cc_start: 0.5190 (OUTLIER) cc_final: 0.4695 (tt) REVERT: K 252 MET cc_start: 0.7640 (mmp) cc_final: 0.7282 (mmm) REVERT: K 386 GLN cc_start: 0.8569 (pm20) cc_final: 0.8273 (pm20) REVERT: L 249 ASP cc_start: 0.7823 (m-30) cc_final: 0.7517 (t0) REVERT: L 301 ARG cc_start: 0.7480 (ttt-90) cc_final: 0.7269 (ttt-90) outliers start: 93 outliers final: 72 residues processed: 315 average time/residue: 0.1615 time to fit residues: 79.5006 Evaluate side-chains 296 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain H residue 457 MET Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 285 HIS Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 259 VAL Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 336 ILE Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 285 HIS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 428 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 89 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS C 347 GLN ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 418 GLN I 285 HIS M 276 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.112341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.084438 restraints weight = 67970.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.085958 restraints weight = 37432.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.087515 restraints weight = 24623.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.087461 restraints weight = 22732.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087385 restraints weight = 20216.359| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24230 Z= 0.131 Angle : 0.591 10.414 33049 Z= 0.293 Chirality : 0.045 0.322 3695 Planarity : 0.004 0.061 4202 Dihedral : 5.260 55.316 3527 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.61 % Allowed : 25.92 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2890 helix: -0.65 (0.33), residues: 235 sheet: 0.09 (0.15), residues: 1218 loop : 0.29 (0.18), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 292 TYR 0.033 0.001 TYR L 407 PHE 0.014 0.001 PHE A 47 TRP 0.046 0.001 TRP E 381 HIS 0.005 0.001 HIS I 429 Details of bonding type rmsd covalent geometry : bond 0.00307 (24179) covalent geometry : angle 0.58468 (32928) SS BOND : bond 0.00290 ( 32) SS BOND : angle 0.99551 ( 64) hydrogen bonds : bond 0.02937 ( 810) hydrogen bonds : angle 5.56744 ( 2241) link_ALPHA1-6 : bond 0.00371 ( 1) link_ALPHA1-6 : angle 1.50090 ( 3) link_BETA1-2 : bond 0.00239 ( 1) link_BETA1-2 : angle 0.89256 ( 3) link_BETA1-4 : bond 0.00305 ( 2) link_BETA1-4 : angle 2.18151 ( 6) link_BETA1-6 : bond 0.00010 ( 1) link_BETA1-6 : angle 2.08981 ( 3) link_NAG-ASN : bond 0.00314 ( 14) link_NAG-ASN : angle 2.09091 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 232 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8806 (mmm-85) REVERT: A 169 TYR cc_start: 0.7295 (t80) cc_final: 0.7004 (t80) REVERT: A 194 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9123 (tt) REVERT: A 250 MET cc_start: 0.7907 (tpp) cc_final: 0.7691 (tpp) REVERT: D 249 ASP cc_start: 0.8098 (m-30) cc_final: 0.7592 (m-30) REVERT: F 300 TYR cc_start: 0.4444 (OUTLIER) cc_final: 0.4111 (t80) REVERT: G 355 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7293 (mtt180) REVERT: G 360 LYS cc_start: 0.8667 (tppt) cc_final: 0.7815 (mtmt) REVERT: H 338 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8239 (tppt) REVERT: I 293 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6031 (tp30) REVERT: I 342 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8312 (tm-30) REVERT: J 242 LEU cc_start: 0.5537 (OUTLIER) cc_final: 0.5033 (tt) REVERT: K 252 MET cc_start: 0.7639 (mmp) cc_final: 0.7296 (mmm) REVERT: K 386 GLN cc_start: 0.8553 (pm20) cc_final: 0.8260 (pm20) REVERT: K 457 MET cc_start: 0.6976 (mmm) cc_final: 0.6355 (mmm) REVERT: L 249 ASP cc_start: 0.7916 (m-30) cc_final: 0.7594 (t0) REVERT: L 301 ARG cc_start: 0.7439 (ttt-90) cc_final: 0.7196 (ttt-90) REVERT: M 419 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8259 (pm20) outliers start: 98 outliers final: 81 residues processed: 314 average time/residue: 0.1648 time to fit residues: 81.0232 Evaluate side-chains 310 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 221 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain G residue 456 ILE Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 285 HIS Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 428 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 285 HIS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 406 LEU Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 419 GLN Chi-restraints excluded: chain M residue 428 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 152 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 280 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 418 GLN K 419 GLN L 311 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.115577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.084445 restraints weight = 70087.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.085762 restraints weight = 39329.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.086699 restraints weight = 24241.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.087063 restraints weight = 22653.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.087091 restraints weight = 20441.546| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24230 Z= 0.141 Angle : 0.597 11.624 33049 Z= 0.296 Chirality : 0.045 0.320 3695 Planarity : 0.004 0.052 4202 Dihedral : 5.258 56.115 3527 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.50 % Allowed : 26.25 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.16), residues: 2890 helix: -0.66 (0.32), residues: 245 sheet: 0.12 (0.15), residues: 1220 loop : 0.26 (0.18), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 292 TYR 0.029 0.001 TYR L 407 PHE 0.015 0.001 PHE M 275 TRP 0.036 0.001 TRP E 381 HIS 0.004 0.001 HIS I 429 Details of bonding type rmsd covalent geometry : bond 0.00327 (24179) covalent geometry : angle 0.59027 (32928) SS BOND : bond 0.00315 ( 32) SS BOND : angle 0.98856 ( 64) hydrogen bonds : bond 0.02920 ( 810) hydrogen bonds : angle 5.49779 ( 2241) link_ALPHA1-6 : bond 0.00379 ( 1) link_ALPHA1-6 : angle 1.48939 ( 3) link_BETA1-2 : bond 0.00199 ( 1) link_BETA1-2 : angle 0.88257 ( 3) link_BETA1-4 : bond 0.00263 ( 2) link_BETA1-4 : angle 2.12142 ( 6) link_BETA1-6 : bond 0.00076 ( 1) link_BETA1-6 : angle 2.03720 ( 3) link_NAG-ASN : bond 0.00315 ( 14) link_NAG-ASN : angle 2.08425 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 221 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8780 (mmm-85) REVERT: A 169 TYR cc_start: 0.7503 (t80) cc_final: 0.7174 (t80) REVERT: A 194 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9157 (tt) REVERT: A 250 MET cc_start: 0.8083 (tpp) cc_final: 0.7803 (tpp) REVERT: B 318 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7867 (tp30) REVERT: D 249 ASP cc_start: 0.8228 (m-30) cc_final: 0.7674 (m-30) REVERT: F 300 TYR cc_start: 0.4444 (OUTLIER) cc_final: 0.4110 (t80) REVERT: G 355 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7471 (mtt180) REVERT: G 360 LYS cc_start: 0.8663 (tppt) cc_final: 0.7791 (mtmt) REVERT: H 338 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8264 (tppt) REVERT: I 293 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6276 (tp30) REVERT: I 342 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8263 (tm-30) REVERT: J 242 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5132 (tt) REVERT: K 252 MET cc_start: 0.7694 (mmp) cc_final: 0.7320 (mmm) REVERT: K 386 GLN cc_start: 0.8508 (pm20) cc_final: 0.8193 (pm20) REVERT: K 457 MET cc_start: 0.6997 (mmm) cc_final: 0.6370 (mmm) REVERT: L 249 ASP cc_start: 0.8006 (m-30) cc_final: 0.7640 (t0) REVERT: L 301 ARG cc_start: 0.7290 (ttt-90) cc_final: 0.7062 (ttt-90) REVERT: M 419 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8436 (pm20) outliers start: 95 outliers final: 80 residues processed: 300 average time/residue: 0.1735 time to fit residues: 81.2889 Evaluate side-chains 299 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 210 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 369 VAL Chi-restraints excluded: chain J residue 428 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 434 ASN Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 285 HIS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 406 LEU Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 419 GLN Chi-restraints excluded: chain M residue 428 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 276 optimal weight: 20.0000 chunk 176 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 221 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 418 GLN M 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.112801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082196 restraints weight = 71091.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.083584 restraints weight = 38508.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.083689 restraints weight = 25758.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.084395 restraints weight = 25965.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.084368 restraints weight = 22242.426| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24230 Z= 0.285 Angle : 0.688 9.701 33049 Z= 0.345 Chirality : 0.047 0.323 3695 Planarity : 0.005 0.058 4202 Dihedral : 5.702 59.820 3527 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.36 % Allowed : 26.44 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.16), residues: 2890 helix: -0.92 (0.31), residues: 248 sheet: -0.03 (0.15), residues: 1210 loop : -0.01 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 416 TYR 0.047 0.002 TYR E 407 PHE 0.025 0.002 PHE I 372 TRP 0.030 0.002 TRP E 381 HIS 0.007 0.001 HIS H 429 Details of bonding type rmsd covalent geometry : bond 0.00633 (24179) covalent geometry : angle 0.67994 (32928) SS BOND : bond 0.00539 ( 32) SS BOND : angle 1.20916 ( 64) hydrogen bonds : bond 0.03396 ( 810) hydrogen bonds : angle 5.95382 ( 2241) link_ALPHA1-6 : bond 0.00203 ( 1) link_ALPHA1-6 : angle 1.65729 ( 3) link_BETA1-2 : bond 0.00086 ( 1) link_BETA1-2 : angle 0.91694 ( 3) link_BETA1-4 : bond 0.00125 ( 2) link_BETA1-4 : angle 2.65423 ( 6) link_BETA1-6 : bond 0.00309 ( 1) link_BETA1-6 : angle 2.82631 ( 3) link_NAG-ASN : bond 0.00447 ( 14) link_NAG-ASN : angle 2.39114 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5780 Ramachandran restraints generated. 2890 Oldfield, 0 Emsley, 2890 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 199 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8855 (mmm-85) REVERT: A 194 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9177 (tt) REVERT: A 250 MET cc_start: 0.8052 (tpp) cc_final: 0.7785 (tpp) REVERT: B 318 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7989 (tp30) REVERT: D 249 ASP cc_start: 0.8308 (m-30) cc_final: 0.7770 (m-30) REVERT: F 300 TYR cc_start: 0.4401 (OUTLIER) cc_final: 0.4065 (t80) REVERT: G 355 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7521 (mtt180) REVERT: G 360 LYS cc_start: 0.8673 (tppt) cc_final: 0.8034 (tppt) REVERT: H 338 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8237 (tppt) REVERT: I 293 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6215 (tp30) REVERT: J 242 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.4910 (tt) REVERT: K 252 MET cc_start: 0.7709 (mmp) cc_final: 0.7391 (mmm) REVERT: K 386 GLN cc_start: 0.8544 (pm20) cc_final: 0.8272 (pm20) REVERT: K 457 MET cc_start: 0.6871 (mmm) cc_final: 0.6184 (mmm) REVERT: L 249 ASP cc_start: 0.8064 (m-30) cc_final: 0.7652 (t0) REVERT: L 301 ARG cc_start: 0.7358 (ttt-90) cc_final: 0.6652 (ttt-90) outliers start: 91 outliers final: 78 residues processed: 279 average time/residue: 0.1597 time to fit residues: 69.9364 Evaluate side-chains 284 residues out of total 2712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 198 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 318 GLU Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 TYR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 359 THR Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 249 ASP Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 427 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 262 VAL Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 300 TYR Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 369 VAL Chi-restraints excluded: chain F residue 377 ILE Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 350 THR Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 425 CYS Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 453 VAL Chi-restraints excluded: chain H residue 312 ASP Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 338 LYS Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain H residue 451 TYR Chi-restraints excluded: chain I residue 252 MET Chi-restraints excluded: chain I residue 260 THR Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 303 VAL Chi-restraints excluded: chain I residue 358 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 456 ILE Chi-restraints excluded: chain J residue 242 LEU Chi-restraints excluded: chain J residue 252 MET Chi-restraints excluded: chain J residue 263 VAL Chi-restraints excluded: chain J residue 314 LEU Chi-restraints excluded: chain J residue 428 MET Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain K residue 268 HIS Chi-restraints excluded: chain K residue 273 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 393 THR Chi-restraints excluded: chain K residue 434 ASN Chi-restraints excluded: chain K residue 447 LYS Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 398 LEU Chi-restraints excluded: chain L residue 450 LEU Chi-restraints excluded: chain M residue 276 ASN Chi-restraints excluded: chain M residue 314 LEU Chi-restraints excluded: chain M residue 365 LEU Chi-restraints excluded: chain M residue 377 ILE Chi-restraints excluded: chain M residue 428 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 187 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 231 optimal weight: 0.2980 chunk 76 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 177 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 HIS ** E 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 419 GLN G 418 GLN M 276 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.113215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.082134 restraints weight = 70212.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.083604 restraints weight = 36387.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.083612 restraints weight = 25572.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.083988 restraints weight = 25277.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.084187 restraints weight = 22833.440| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 24230 Z= 0.231 Angle : 0.797 59.199 33049 Z= 0.432 Chirality : 0.047 0.746 3695 Planarity : 0.005 0.056 4202 Dihedral : 5.728 59.999 3527 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.54 % Allowed : 26.29 % Favored : 70.17 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.16), residues: 2890 helix: -0.92 (0.31), residues: 248 sheet: -0.05 (0.15), residues: 1210 loop : -0.02 (0.18), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 355 TYR 0.039 0.002 TYR E 407 PHE 0.022 0.002 PHE I 372 TRP 0.025 0.002 TRP E 381 HIS 0.005 0.001 HIS H 429 Details of bonding type rmsd covalent geometry : bond 0.00511 (24179) covalent geometry : angle 0.79044 (32928) SS BOND : bond 0.00450 ( 32) SS BOND : angle 1.28647 ( 64) hydrogen bonds : bond 0.03610 ( 810) hydrogen bonds : angle 6.00586 ( 2241) link_ALPHA1-6 : bond 0.00171 ( 1) link_ALPHA1-6 : angle 1.60562 ( 3) link_BETA1-2 : bond 0.00114 ( 1) link_BETA1-2 : angle 0.93188 ( 3) link_BETA1-4 : bond 0.00086 ( 2) link_BETA1-4 : angle 2.68342 ( 6) link_BETA1-6 : bond 0.00425 ( 1) link_BETA1-6 : angle 2.80656 ( 3) link_NAG-ASN : bond 0.00437 ( 14) link_NAG-ASN : angle 2.38389 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3865.42 seconds wall clock time: 68 minutes 6.43 seconds (4086.43 seconds total)