Starting phenix.real_space_refine on Sat Sep 12 21:09:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.map" model { file = "/net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ue9_20751/09_2026/6ue9_20751.cif" } resolution = 2.9 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= -0.013 sd= 0.420 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 98 5.16 5 C 11488 2.51 5 N 3151 2.21 5 O 3490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18227 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1616 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1686 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 6, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "C" Number of atoms: 4150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4150 Classifications: {'peptide': 537} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 511} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1038 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1656 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1666 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 1570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1570 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 17, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 11, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 107 Chain: "H" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1556 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 18, 'TRANS': 205} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 11, 'ASP:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 103 Chain: "K" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1581 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 18, 'TRANS': 202} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 8, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "L" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1543 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 18, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 139 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 10, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 98 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 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 chiralities: 1 Time building chain proxies: 3.66, per 1000 atoms: 0.20 Number of scatterers: 18227 At special positions: 0 Unit cell: (173.196, 148.745, 174.215, 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 98 16.00 O 3490 8.00 N 3151 7.00 C 11488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.04 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.05 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.04 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 526 " distance=2.04 Simple disulfide: pdb=" SG CYS C 468 " - pdb=" SG CYS F 311 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.04 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.04 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.02 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.05 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.04 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.04 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 471 " - pdb=" SG CYS E 471 " distance=2.03 Simple disulfide: pdb=" SG CYS E 242 " - pdb=" SG CYS H 299 " distance=2.04 Simple disulfide: pdb=" SG CYS E 299 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 369 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 323 " distance=2.04 Simple disulfide: pdb=" SG CYS H 369 " - pdb=" SG CYS H 432 " distance=2.03 Simple disulfide: pdb=" SG CYS K 242 " - pdb=" SG CYS L 299 " distance=2.04 Simple disulfide: pdb=" SG CYS K 266 " - pdb=" SG CYS K 323 " distance=2.04 Simple disulfide: pdb=" SG CYS K 299 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 369 " - pdb=" SG CYS K 432 " distance=2.03 Simple disulfide: pdb=" SG CYS L 266 " - pdb=" SG CYS L 323 " distance=2.04 Simple disulfide: pdb=" SG CYS L 369 " - pdb=" SG CYS L 432 " distance=2.04 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 BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 501 " - " ASN A 337 " " NAG B 501 " - " ASN B 337 " " NAG C 601 " - " ASN C 403 " " NAG C 604 " - " ASN C 65 " " NAG C 605 " - " ASN C 451 " " NAG F 501 " - " ASN F 337 " " NAG G 501 " - " ASN G 337 " " NAG I 1 " - " ASN C 72 " " NAG J 1 " - " ASN D 49 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 564.2 milliseconds 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4598 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 55 sheets defined 9.7% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.616A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.828A pdb=" N ASN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.759A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.611A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.608A pdb=" N LEU B 256 " --> pdb=" O ALA B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.603A pdb=" N GLU B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 359' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.741A pdb=" N LYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.652A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.777A pdb=" N VAL C 245 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 242 through 246' Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.691A pdb=" N PHE C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.775A pdb=" N ASP C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 302 " --> pdb=" O LYS C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.631A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.535A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.637A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 252 through 258 removed outlier: 3.661A pdb=" N LEU F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.587A pdb=" N GLY F 318 " --> pdb=" O PRO F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 421 through 427 removed outlier: 3.698A pdb=" N LYS F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 258 removed outlier: 3.548A pdb=" N LEU G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 removed outlier: 4.320A pdb=" N GLY G 300 " --> pdb=" O ASP G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'G' and resid 420 through 427 removed outlier: 3.615A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 317 removed outlier: 3.697A pdb=" N ASN E 316 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.522A pdb=" N ALA E 360 " --> pdb=" O GLU E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.763A pdb=" N LEU H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 312 through 317 removed outlier: 3.552A pdb=" N ASN H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.828A pdb=" N LEU H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN H 362 " --> pdb=" O GLU H 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 357 through 362' Processing helix chain 'H' and resid 421 through 427 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 297 through 301 removed outlier: 4.539A pdb=" N GLY K 300 " --> pdb=" O ASP K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 312 through 318 Processing helix chain 'K' and resid 356 through 360 Processing helix chain 'K' and resid 421 through 427 Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.713A pdb=" N ALA L 360 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 426 removed outlier: 3.931A pdb=" N TRP L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 248 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.835A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA6, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.304A pdb=" N ILE K 458 " --> pdb=" O ASN L 459 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER L 461 " --> pdb=" O ILE K 458 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL K 460 " --> pdb=" O SER L 461 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL L 463 " --> pdb=" O VAL K 460 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 462 " --> pdb=" O VAL L 463 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.759A pdb=" N SER B 247 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 267 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR B 265 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 308 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR B 267 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 306 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR B 269 " --> pdb=" O VAL B 304 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL B 304 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 320 through 325 removed outlier: 3.517A pdb=" N ALA B 325 " --> pdb=" O LEU B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.747A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N TYR B 411 " --> pdb=" O GLY B 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.453A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.575A pdb=" N ILE C 79 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 122 through 125 removed outlier: 6.571A pdb=" N TYR C 122 " --> pdb=" O GLN C 218 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU C 220 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 124 " --> pdb=" O LEU C 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB7, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.559A pdb=" N LEU C 201 " --> pdb=" O TYR C 148 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 225 through 229 removed outlier: 6.123A pdb=" N GLU C 225 " --> pdb=" O GLN C 325 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE C 327 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 227 " --> pdb=" O PHE C 327 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 239 Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.260A pdb=" N VAL C 341 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 440 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLY C 343 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 381 " --> pdb=" O TRP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 349 through 354 removed outlier: 3.517A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 408 " --> pdb=" O VAL C 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 460 through 461 Processing sheet with id=AC4, first strand: chain 'C' and resid 474 through 479 removed outlier: 3.775A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRP C 525 " --> pdb=" O CYS C 478 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE C 533 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 6 through 11 removed outlier: 5.460A pdb=" N VAL D 7 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER D 20 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN E 459 " --> pdb=" O VAL H 460 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N VAL H 462 " --> pdb=" O ASN E 459 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER E 461 " --> pdb=" O VAL H 462 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AC7, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AC8, first strand: chain 'F' and resid 245 through 249 removed outlier: 3.651A pdb=" N ARG F 245 " --> pdb=" O THR F 269 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR F 269 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY F 270 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR F 302 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 324 through 325 Processing sheet with id=AD1, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.726A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N TYR F 411 " --> pdb=" O GLY F 373 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 388 through 389 Processing sheet with id=AD4, first strand: chain 'G' and resid 245 through 249 removed outlier: 3.744A pdb=" N ARG G 245 " --> pdb=" O THR G 269 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS G 249 " --> pdb=" O THR G 265 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR G 265 " --> pdb=" O HIS G 249 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 264 " --> pdb=" O LEU G 308 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 278 through 281 Processing sheet with id=AD6, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 348 through 352 removed outlier: 3.855A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD9, first strand: chain 'E' and resid 245 through 248 removed outlier: 4.240A pdb=" N ARG E 245 " --> pdb=" O THR E 269 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR E 269 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 268 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLY E 270 " --> pdb=" O TYR E 302 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR E 302 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 290 through 291 removed outlier: 4.622A pdb=" N VAL E 290 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL E 307 " --> pdb=" O VAL E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 396 " --> pdb=" O ILE E 416 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.706A pdb=" N ARG E 372 " --> pdb=" O GLU E 348 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 380 through 382 Processing sheet with id=AE5, first strand: chain 'E' and resid 384 through 385 Processing sheet with id=AE6, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.505A pdb=" N ARG H 245 " --> pdb=" O THR H 269 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 269 " --> pdb=" O ARG H 245 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'H' and resid 280 through 281 Processing sheet with id=AE8, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AE9, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.592A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 388 through 389 Processing sheet with id=AF3, first strand: chain 'K' and resid 246 through 248 removed outlier: 4.076A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL K 290 " --> pdb=" O VAL K 307 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 278 through 281 removed outlier: 3.642A pdb=" N THR K 278 " --> pdb=" O ALA K 326 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU K 396 " --> pdb=" O ILE K 416 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.043A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 365 " --> pdb=" O VAL K 419 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR K 410 " --> pdb=" O GLU K 403 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.526A pdb=" N SER K 431 " --> pdb=" O LEU K 384 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.951A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU L 370 " --> pdb=" O HIS L 350 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU L 352 " --> pdb=" O THR L 368 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU L 396 " --> pdb=" O ILE L 416 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 388 through 389 removed outlier: 3.637A pdb=" N GLN L 388 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN L 385 " --> pdb=" O GLN L 388 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG L 382 " --> pdb=" O MET L 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 401 through 403 removed outlier: 3.692A pdb=" N ARG L 401 " --> pdb=" O ALA L 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA L 412 " --> pdb=" O ARG L 401 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR L 410 " --> pdb=" O GLU L 403 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1452 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: 3.14 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5888 1.34 - 1.46: 4375 1.46 - 1.59: 8280 1.59 - 1.71: 0 1.71 - 1.84: 115 Bond restraints: 18658 Sorted by residual: bond pdb=" C1 NAG C 605 " pdb=" O5 NAG C 605 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" C THR D 54 " pdb=" N SER D 55 " ideal model delta sigma weight residual 1.327 1.300 0.027 1.05e-02 9.07e+03 6.40e+00 bond pdb=" C1 NAG C 601 " pdb=" O5 NAG C 601 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 18653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 25127 3.22 - 6.45: 389 6.45 - 9.67: 62 9.67 - 12.89: 7 12.89 - 16.11: 1 Bond angle restraints: 25586 Sorted by residual: angle pdb=" N SER D 55 " pdb=" CA SER D 55 " pdb=" C SER D 55 " ideal model delta sigma weight residual 108.13 99.01 9.12 9.00e-01 1.23e+00 1.03e+02 angle pdb=" C ASN C 329 " pdb=" N GLU C 330 " pdb=" CA GLU C 330 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C GLY A 453 " pdb=" N LYS A 454 " pdb=" CA LYS A 454 " ideal model delta sigma weight residual 120.39 127.45 -7.06 1.39e+00 5.18e-01 2.58e+01 angle pdb=" N VAL C 158 " pdb=" CA VAL C 158 " pdb=" C VAL C 158 " ideal model delta sigma weight residual 113.20 108.46 4.74 9.60e-01 1.09e+00 2.43e+01 angle pdb=" CA SER A 260 " pdb=" C SER A 260 " pdb=" N GLU A 261 " ideal model delta sigma weight residual 116.84 125.20 -8.36 1.71e+00 3.42e-01 2.39e+01 ... (remaining 25581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10004 17.96 - 35.93: 893 35.93 - 53.89: 159 53.89 - 71.85: 19 71.85 - 89.81: 9 Dihedral angle restraints: 11084 sinusoidal: 3980 harmonic: 7104 Sorted by residual: dihedral pdb=" CB CYS K 299 " pdb=" SG CYS K 299 " pdb=" SG CYS L 242 " pdb=" CB CYS L 242 " ideal model delta sinusoidal sigma weight residual 93.00 -177.19 -89.81 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" CB CYS H 266 " pdb=" SG CYS H 266 " pdb=" SG CYS H 323 " pdb=" CB CYS H 323 " ideal model delta sinusoidal sigma weight residual 93.00 3.83 89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS D 109 " pdb=" SG CYS D 109 " pdb=" SG CYS D 134 " pdb=" CB CYS D 134 " ideal model delta sinusoidal sigma weight residual -86.00 -158.33 72.33 1 1.00e+01 1.00e-02 6.69e+01 ... (remaining 11081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2647 0.085 - 0.170: 391 0.170 - 0.254: 32 0.254 - 0.339: 5 0.339 - 0.424: 5 Chirality restraints: 3080 Sorted by residual: chirality pdb=" C1 NAG C 605 " pdb=" ND2 ASN C 451 " pdb=" C2 NAG C 605 " pdb=" O5 NAG C 605 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" C2 NAG J 2 " pdb=" C1 NAG J 2 " pdb=" C3 NAG J 2 " pdb=" N2 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.08 -0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" CB ILE E 448 " pdb=" CA ILE E 448 " pdb=" CG1 ILE E 448 " pdb=" CG2 ILE E 448 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 3077 not shown) Planarity restraints: 3287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 403 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO F 404 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 404 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 404 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 327 " -0.046 5.00e-02 4.00e+02 7.06e-02 7.97e+00 pdb=" N PRO B 328 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 328 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 328 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 375 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO L 376 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO L 376 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 376 " 0.039 5.00e-02 4.00e+02 ... (remaining 3284 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3153 2.77 - 3.30: 14380 3.30 - 3.84: 26867 3.84 - 4.37: 28681 4.37 - 4.90: 54365 Nonbonded interactions: 127446 Sorted by model distance: nonbonded pdb=" OG1 THR H 282 " pdb=" OG1 THR H 322 " model vdw 2.241 3.040 nonbonded pdb=" O THR H 280 " pdb=" OG1 THR H 324 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR L 320 " pdb=" OD1 ASN L 337 " model vdw 2.281 3.040 nonbonded pdb=" OH TYR C 122 " pdb=" OD1 ASN C 133 " model vdw 2.292 3.040 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.318 3.120 ... (remaining 127441 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 'A' and (resid 242 through 244 or (resid 245 and (name N or name CA or na \ me C or name O or name CB )) or resid 246 through 253 or (resid 254 through 255 \ and (name N or name CA or name C or name O or name CB )) or resid 256 through 25 \ 9 or (resid 260 through 262 and (name N or name CA or name C or name O or name C \ B )) or resid 263 through 270 or (resid 271 through 272 and (name N or name CA o \ r name C or name O or name CB )) or resid 276 through 286 or (resid 287 and (nam \ e N or name CA or name C or name O or name CB )) or resid 288 through 312 or (re \ sid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 th \ rough 318 or (resid 319 and (name N or name CA or name C or name O or name CB )) \ or resid 320 through 340 or (resid 341 and (name N or name CA or name C or name \ O or name CB )) or resid 342 through 345 or (resid 346 and (name N or name CA o \ r name C or name O or name CB )) or resid 347 through 356 or (resid 357 through \ 363 and (name N or name CA or name C or name O or name CB )) or resid 364 throug \ h 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) or \ resid 378 through 387 or (resid 388 and (name N or name CA or name C or name O o \ r name CB )) or resid 389 through 391 or (resid 392 through 394 and (name N or n \ ame CA or name C or name O or name CB )) or resid 395 through 404 or (resid 405 \ through 406 and (name N or name CA or name C or name O or name CB )) or resid 40 \ 7 through 424 or (resid 425 through 426 and (name N or name CA or name C or name \ O or name CB )) or resid 427 or (resid 428 and (name N or name CA or name C or \ name O or name CB )) or resid 429 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 449 or (resid 450 and \ (name N or name CA or name C or name O or name CB )) or resid 456 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 295 or (resid 296 through 298 and (name N or name CA or n \ ame C or name O or name CB )) or resid 299 through 312 or (resid 313 and (name N \ or name CA or name C or name O or name CB )) or resid 314 through 340 or (resid \ 341 and (name N or name CA or name C or name O or name CB )) or resid 342 throu \ gh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) or \ resid 347 through 356 or (resid 357 through 363 and (name N or name CA or name \ C or name O or name CB )) or resid 364 through 376 or (resid 377 and (name N or \ name CA or name C or name O or name CB )) or resid 378 through 387 or (resid 388 \ and (name N or name CA or name C or name O or name CB )) or resid 389 through 3 \ 91 or (resid 392 through 394 and (name N or name CA or name C or name O or name \ CB )) or resid 395 through 404 or (resid 405 through 406 and (name N or name CA \ or name C or name O or name CB )) or resid 407 through 424 or (resid 425 through \ 426 and (name N or name CA or name C or name O or name CB )) or resid 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB )) or resid 429 t \ hrough 445 or (resid 446 and (name N or name CA or name C or name O or name CB ) \ ) or resid 447 through 449 or (resid 450 and (name N or name CA or name C or nam \ e O or name CB )) or resid 456 through 464)) selection = (chain 'E' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 450 o \ r resid 456 through 464)) selection = (chain 'F' and (resid 242 through 259 or (resid 260 through 262 and (name N or n \ ame CA or name C or name O or name CB )) or resid 263 through 272 or resid 276 t \ hrough 310 or (resid 311 through 313 and (name N or name CA or name C or name O \ or name CB )) or resid 314 through 340 or (resid 341 and (name N or name CA or n \ ame C or name O or name CB )) or resid 342 through 345 or (resid 346 and (name N \ or name CA or name C or name O or name CB )) or resid 347 through 356 or (resid \ 357 through 363 and (name N or name CA or name C or name O or name CB )) or res \ id 364 through 376 or (resid 377 and (name N or name CA or name C or name O or n \ ame CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or name \ C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 and \ (name N or name CA or name C or name O or name CB )) or resid 395 through 404 o \ r (resid 405 through 406 and (name N or name CA or name C or name O or name CB ) \ ) or resid 407 through 424 or (resid 425 through 426 and (name N or name CA or n \ ame C or name O or name CB )) or resid 427 through 445 or (resid 446 and (name N \ or name CA or name C or name O or name CB )) or resid 447 through 449 or (resid \ 450 and (name N or name CA or name C or name O or name CB )) or resid 456 throu \ gh 464)) selection = (chain 'G' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 316 or (resid 317 and (name N or name CA or name C or nam \ e O or name CB )) or resid 318 through 340 or (resid 341 and (name N or name CA \ or name C or name O or name CB )) or resid 342 through 345 or (resid 346 and (na \ me N or name CA or name C or name O or name CB )) or resid 347 through 356 or (r \ esid 357 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 376 or (resid 377 and (name N or name CA or name C or name O \ or name CB )) or resid 378 through 387 or (resid 388 and (name N or name CA or n \ ame C or name O or name CB )) or resid 389 through 391 or (resid 392 through 394 \ and (name N or name CA or name C or name O or name CB )) or resid 395 through 4 \ 04 or (resid 405 through 406 and (name N or name CA or name C or name O or name \ CB )) or resid 407 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 424 or (resid 425 through 426 and (na \ me N or name CA or name C or name O or name CB )) or resid 427 through 445 or (r \ esid 446 and (name N or name CA or name C or name O or name CB )) or resid 447 t \ hrough 449 or (resid 450 and (name N or name CA or name C or name O or name CB ) \ ) or resid 456 through 464)) selection = (chain 'H' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 272 or resid 276 through 312 o \ r (resid 313 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 14 through 424 or (resid 425 through 426 and (name N or name CA or name C or nam \ e O or name CB )) or resid 427 through 450 or resid 456 through 464)) selection = (chain 'K' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 312 or (resid 313 and (name N or name CA or name C or nam \ e O or name CB )) or resid 314 through 316 or (resid 317 and (name N or name CA \ or name C or name O or name CB )) or resid 318 through 340 or (resid 341 and (na \ me N or name CA or name C or name O or name CB )) or resid 342 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB )) or resid 347 t \ hrough 356 or (resid 357 through 363 and (name N or name CA or name C or name O \ or name CB )) or resid 364 through 376 or (resid 377 and (name N or name CA or n \ ame C or name O or name CB )) or resid 378 through 387 or (resid 388 and (name N \ or name CA or name C or name O or name CB )) or resid 389 through 392 or (resid \ 393 through 394 and (name N or name CA or name C or name O or name CB )) or res \ id 395 through 404 or (resid 405 through 406 and (name N or name CA or name C or \ name O or name CB )) or resid 407 through 445 or (resid 446 and (name N or name \ CA or name C or name O or name CB )) or resid 447 through 450 or resid 456 thro \ ugh 464)) selection = (chain 'L' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB )) or resid 256 through 259 or (resid 260 through 262 \ and (name N or name CA or name C or name O or name CB )) or resid 263 through 27 \ 2 or resid 276 through 345 or (resid 346 and (name N or name CA or name C or nam \ e O or name CB )) or resid 347 through 358 or (resid 359 through 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 376 or (resid \ 377 and (name N or name CA or name C or name O or name CB )) or resid 378 throu \ gh 392 or (resid 393 through 394 and (name N or name CA or name C or name O or n \ ame CB )) or resid 395 through 425 or (resid 426 and (name N or name CA or name \ C or name O or name CB )) or resid 427 through 450 or resid 456 through 464)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 14.670 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 18707 Z= 0.298 Angle : 1.068 16.113 25696 Z= 0.562 Chirality : 0.062 0.424 3080 Planarity : 0.008 0.075 3278 Dihedral : 13.690 86.726 6375 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.23 % Favored : 88.77 % Rotamer: Outliers : 0.32 % Allowed : 9.85 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.09 % 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: -3.87 (0.14), residues: 2439 helix: -4.23 (0.21), residues: 143 sheet: -1.61 (0.16), residues: 863 loop : -3.14 (0.13), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 43 TYR 0.019 0.003 TYR G 395 PHE 0.031 0.003 PHE C 136 TRP 0.016 0.002 TRP L 315 HIS 0.007 0.001 HIS K 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.30 (18658) covalent geometry : angle 1.04921 / 0.56 (25586) SS BOND : bond 0.00659 / 0.46 ( 37) SS BOND : angle 1.77700 / 1.12 ( 74) hydrogen bonds : bond 0.29066 / 20.13 ( 485) hydrogen bonds : angle 8.89482 / 6.14 ( 1452) link_BETA1-4 : bond 0.01737 / 0.83 ( 3) link_BETA1-4 : angle 3.29532 / 1.63 ( 9) link_NAG-ASN : bond 0.01075 / 0.57 ( 9) link_NAG-ASN : angle 5.41490 / 3.56 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 539 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 327 HIS cc_start: 0.4382 (p90) cc_final: 0.4129 (p90) REVERT: K 365 VAL cc_start: 0.4065 (m) cc_final: 0.3552 (m) outliers start: 6 outliers final: 3 residues processed: 544 average time/residue: 0.4311 time to fit residues: 269.9995 Evaluate side-chains 262 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 259 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 363 ILE Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 393 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 291 GLN ** A 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 HIS B 406 GLN C 209 ASN D 11 ASN D 30 ASN D 37 ASN D 90 ASN F 362 ASN F 459 ASN G 263 ASN G 291 GLN ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN E 327 HIS E 459 ASN H 243 HIS H 249 HIS ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 316 ASN ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS H 459 ASN K 243 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 457 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.123236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.090626 restraints weight = 46355.986| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 4.25 r_work: 0.3332 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 18707 Z= 0.264 Angle : 1.086 16.389 25696 Z= 0.516 Chirality : 0.054 0.375 3080 Planarity : 0.008 0.089 3278 Dihedral : 6.543 34.706 2605 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 8.36 % Allowed : 19.01 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -3.12 (0.15), residues: 2439 helix: -3.23 (0.29), residues: 131 sheet: -0.98 (0.17), residues: 809 loop : -2.73 (0.14), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 250 TYR 0.026 0.003 TYR D 110 PHE 0.033 0.003 PHE H 443 TRP 0.032 0.003 TRP C 431 HIS 0.008 0.002 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (18658) covalent geometry : angle 1.07250 / 0.51 (25586) SS BOND : bond 0.01661 / 1.34 ( 37) SS BOND : angle 1.71437 / 1.00 ( 74) hydrogen bonds : bond 0.04777 / 3.32 ( 485) hydrogen bonds : angle 6.24288 / 4.30 ( 1452) link_BETA1-4 : bond 0.02081 / 1.04 ( 3) link_BETA1-4 : angle 4.42089 / 2.20 ( 9) link_NAG-ASN : bond 0.01271 / 0.66 ( 9) link_NAG-ASN : angle 4.26077 / 2.58 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 399 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 ASN cc_start: 0.8910 (p0) cc_final: 0.8710 (p0) REVERT: A 433 MET cc_start: 0.7701 (tpp) cc_final: 0.7500 (tmm) REVERT: C 32 HIS cc_start: 0.6198 (OUTLIER) cc_final: 0.5179 (t-90) REVERT: C 310 HIS cc_start: 0.6666 (OUTLIER) cc_final: 0.6321 (m170) REVERT: D 12 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7261 (tppp) REVERT: D 110 TYR cc_start: 0.7744 (m-80) cc_final: 0.7399 (m-80) REVERT: F 269 THR cc_start: 0.6394 (p) cc_final: 0.6113 (t) REVERT: F 433 MET cc_start: 0.4073 (tpt) cc_final: 0.3813 (tpt) REVERT: G 380 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7462 (tp) REVERT: G 389 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7272 (tm-30) REVERT: G 401 ARG cc_start: 0.6025 (OUTLIER) cc_final: 0.5566 (ptp-170) REVERT: E 291 GLN cc_start: 0.6558 (pp30) cc_final: 0.6096 (tm130) REVERT: E 418 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7216 (tpp80) REVERT: H 316 ASN cc_start: 0.8965 (OUTLIER) cc_final: 0.8661 (p0) REVERT: H 382 ARG cc_start: 0.8237 (mmt180) cc_final: 0.7950 (mmp80) REVERT: K 357 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8247 (pm20) REVERT: L 393 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7060 (pp20) REVERT: L 411 TYR cc_start: 0.4740 (m-10) cc_final: 0.3966 (m-80) outliers start: 157 outliers final: 58 residues processed: 507 average time/residue: 0.3663 time to fit residues: 219.0223 Evaluate side-chains 360 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 294 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 345 PHE Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 310 HIS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 338 ILE Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 380 LEU Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 401 ARG Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 374 PHE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 418 ARG Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 316 ASN Chi-restraints excluded: chain H residue 424 TRP Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 357 GLU Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 456 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 19 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 168 optimal weight: 0.0060 chunk 67 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 200 optimal weight: 0.0470 chunk 156 optimal weight: 1.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 HIS A 385 GLN C 78 ASN C 530 GLN D 88 GLN D 107 ASN F 316 ASN F 327 HIS ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 445 GLN H 457 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.123545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091262 restraints weight = 47087.782| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.30 r_work: 0.3367 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.6958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18707 Z= 0.181 Angle : 0.889 13.191 25696 Z= 0.423 Chirality : 0.049 0.376 3080 Planarity : 0.006 0.062 3278 Dihedral : 5.674 34.297 2598 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 7.51 % Allowed : 23.54 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -2.52 (0.16), residues: 2439 helix: -2.52 (0.33), residues: 156 sheet: -0.51 (0.18), residues: 808 loop : -2.38 (0.14), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 392 TYR 0.018 0.002 TYR C 90 PHE 0.024 0.002 PHE A 279 TRP 0.054 0.002 TRP C 37 HIS 0.013 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (18658) covalent geometry : angle 0.87696 / 0.42 (25586) SS BOND : bond 0.01153 / 0.97 ( 37) SS BOND : angle 1.62371 / 1.08 ( 74) hydrogen bonds : bond 0.04633 / 3.21 ( 485) hydrogen bonds : angle 5.52310 / 3.79 ( 1452) link_BETA1-4 : bond 0.00721 / 0.36 ( 3) link_BETA1-4 : angle 2.25823 / 1.18 ( 9) link_NAG-ASN : bond 0.01248 / 0.61 ( 9) link_NAG-ASN : angle 3.80521 / 2.37 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 380 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.7118 (mmp80) REVERT: C 32 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.5757 (t-90) REVERT: C 89 ARG cc_start: 0.7023 (pmm-80) cc_final: 0.6776 (ptt90) REVERT: C 229 GLU cc_start: 0.6354 (mm-30) cc_final: 0.5884 (mt-10) REVERT: C 330 GLU cc_start: 0.5525 (OUTLIER) cc_final: 0.5299 (pp20) REVERT: C 421 TYR cc_start: 0.7123 (m-80) cc_final: 0.6628 (m-80) REVERT: D 110 TYR cc_start: 0.7886 (m-80) cc_final: 0.7659 (m-80) REVERT: F 316 ASN cc_start: 0.7297 (t0) cc_final: 0.6304 (p0) REVERT: F 464 MET cc_start: 0.7855 (ttm) cc_final: 0.7410 (tmm) REVERT: G 377 LYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5394 (tmmm) REVERT: G 401 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6530 (mtt180) REVERT: E 378 ASP cc_start: 0.8022 (t0) cc_final: 0.7670 (t0) REVERT: E 402 GLN cc_start: 0.7987 (tp40) cc_final: 0.7777 (tp40) REVERT: H 380 LEU cc_start: 0.8301 (tm) cc_final: 0.7767 (tm) REVERT: H 415 SER cc_start: 0.8226 (m) cc_final: 0.8017 (p) REVERT: K 253 LEU cc_start: 0.7666 (mm) cc_final: 0.7455 (tp) REVERT: K 291 GLN cc_start: 0.6732 (pp30) cc_final: 0.6218 (mp-120) REVERT: L 393 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7268 (pp20) REVERT: L 411 TYR cc_start: 0.4677 (m-10) cc_final: 0.3333 (m-80) outliers start: 141 outliers final: 55 residues processed: 473 average time/residue: 0.3998 time to fit residues: 221.7221 Evaluate side-chains 381 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 321 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 299 CYS Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain G residue 368 THR Chi-restraints excluded: chain G residue 377 LYS Chi-restraints excluded: chain G residue 401 ARG Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 225 optimal weight: 6.9990 chunk 215 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 236 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 104 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN A 445 GLN C 78 ASN D 107 ASN E 459 ASN H 243 HIS ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.124163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.091739 restraints weight = 47538.874| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 4.27 r_work: 0.3380 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.8643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 18707 Z= 0.174 Angle : 0.884 15.365 25696 Z= 0.414 Chirality : 0.048 0.352 3080 Planarity : 0.005 0.052 3278 Dihedral : 5.425 36.723 2598 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 7.19 % Allowed : 26.52 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -2.19 (0.16), residues: 2439 helix: -1.74 (0.40), residues: 146 sheet: -0.29 (0.18), residues: 803 loop : -2.21 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 382 TYR 0.019 0.002 TYR B 395 PHE 0.021 0.002 PHE H 321 TRP 0.022 0.002 TRP F 315 HIS 0.018 0.001 HIS L 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 (18658) covalent geometry : angle 0.87363 / 0.41 (25586) SS BOND : bond 0.00473 / 0.34 ( 37) SS BOND : angle 1.32576 / 0.88 ( 74) hydrogen bonds : bond 0.03694 / 2.55 ( 485) hydrogen bonds : angle 5.40390 / 3.70 ( 1452) link_BETA1-4 : bond 0.00706 / 0.36 ( 3) link_BETA1-4 : angle 1.92676 / 1.06 ( 9) link_NAG-ASN : bond 0.00780 / 0.40 ( 9) link_NAG-ASN : angle 3.76668 / 2.39 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 393 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8013 (pp) REVERT: B 313 GLN cc_start: 0.8364 (pm20) cc_final: 0.7903 (tp-100) REVERT: B 441 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8126 (tm) REVERT: C 89 ARG cc_start: 0.7472 (pmm-80) cc_final: 0.7224 (ptp-110) REVERT: C 221 LYS cc_start: 0.7242 (pmtt) cc_final: 0.6698 (ptmt) REVERT: C 349 VAL cc_start: 0.7128 (OUTLIER) cc_final: 0.6789 (t) REVERT: C 465 HIS cc_start: 0.6856 (m-70) cc_final: 0.5981 (m-70) REVERT: C 500 VAL cc_start: 0.3939 (m) cc_final: 0.3710 (p) REVERT: D 108 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8239 (ttmt) REVERT: D 126 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8079 (pm20) REVERT: F 316 ASN cc_start: 0.7330 (t0) cc_final: 0.6505 (p0) REVERT: F 346 ARG cc_start: 0.6422 (pmm150) cc_final: 0.5442 (pmm-80) REVERT: F 364 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8210 (tm) REVERT: F 449 ASP cc_start: 0.7741 (p0) cc_final: 0.7497 (p0) REVERT: F 464 MET cc_start: 0.8199 (ttm) cc_final: 0.7730 (tmm) REVERT: E 378 ASP cc_start: 0.8004 (t0) cc_final: 0.7545 (t0) REVERT: E 402 GLN cc_start: 0.8001 (tp40) cc_final: 0.7706 (tp40) REVERT: H 382 ARG cc_start: 0.8688 (mmp80) cc_final: 0.8392 (mmp80) REVERT: K 291 GLN cc_start: 0.6924 (pp30) cc_final: 0.6317 (pp30) REVERT: K 350 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7718 (m-70) REVERT: K 396 LEU cc_start: 0.5865 (OUTLIER) cc_final: 0.5646 (tm) REVERT: L 393 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7321 (pp20) REVERT: L 411 TYR cc_start: 0.5208 (m-80) cc_final: 0.4142 (m-80) REVERT: L 415 SER cc_start: 0.7988 (t) cc_final: 0.7485 (p) REVERT: L 430 PHE cc_start: 0.5118 (m-10) cc_final: 0.4388 (m-80) REVERT: L 433 MET cc_start: 0.4936 (ptm) cc_final: 0.4672 (ptp) outliers start: 135 outliers final: 69 residues processed: 481 average time/residue: 0.4056 time to fit residues: 227.7019 Evaluate side-chains 403 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 328 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 445 GLN Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 364 LEU Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 382 ARG Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 441 LEU Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 268 LEU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 350 HIS Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 27 optimal weight: 0.0030 chunk 166 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 226 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN C 32 HIS C 78 ASN ** C 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 HIS G 291 GLN G 445 GLN H 243 HIS ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS K 249 HIS ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 362 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.122948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090119 restraints weight = 47464.789| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 4.30 r_work: 0.3362 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 1.0166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 18707 Z= 0.184 Angle : 0.889 15.990 25696 Z= 0.419 Chirality : 0.048 0.361 3080 Planarity : 0.006 0.060 3278 Dihedral : 5.313 32.775 2598 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 7.45 % Allowed : 29.55 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.03 (0.16), residues: 2439 helix: -1.46 (0.40), residues: 156 sheet: -0.18 (0.18), residues: 801 loop : -2.11 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 392 TYR 0.022 0.002 TYR C 169 PHE 0.022 0.001 PHE L 374 TRP 0.018 0.002 TRP F 398 HIS 0.036 0.001 HIS K 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (18658) covalent geometry : angle 0.88033 / 0.42 (25586) SS BOND : bond 0.00507 / 0.35 ( 37) SS BOND : angle 1.30264 / 0.89 ( 74) hydrogen bonds : bond 0.03923 / 2.70 ( 485) hydrogen bonds : angle 5.38778 / 3.71 ( 1452) link_BETA1-4 : bond 0.00851 / 0.43 ( 3) link_BETA1-4 : angle 1.50897 / 0.83 ( 9) link_NAG-ASN : bond 0.00755 / 0.40 ( 9) link_NAG-ASN : angle 3.50475 / 2.27 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 373 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8439 (pp) REVERT: A 346 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8328 (ptp90) REVERT: A 410 THR cc_start: 0.7946 (p) cc_final: 0.7652 (p) REVERT: B 253 LEU cc_start: 0.7183 (pt) cc_final: 0.6616 (tt) REVERT: B 313 GLN cc_start: 0.8459 (pm20) cc_final: 0.8092 (tp-100) REVERT: C 221 LYS cc_start: 0.7900 (pmtt) cc_final: 0.7394 (ptmt) REVERT: C 465 HIS cc_start: 0.7079 (m-70) cc_final: 0.6228 (m-70) REVERT: D 7 VAL cc_start: 0.8403 (t) cc_final: 0.8181 (p) REVERT: D 36 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7712 (ttt180) REVERT: D 65 LEU cc_start: 0.7970 (tt) cc_final: 0.7641 (tt) REVERT: D 81 ASN cc_start: 0.7544 (m110) cc_final: 0.7307 (m110) REVERT: F 316 ASN cc_start: 0.7829 (t0) cc_final: 0.7127 (p0) REVERT: F 335 THR cc_start: 0.5596 (OUTLIER) cc_final: 0.5032 (p) REVERT: F 346 ARG cc_start: 0.7197 (pmm150) cc_final: 0.6114 (pmm-80) REVERT: F 425 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8220 (mptm) REVERT: F 449 ASP cc_start: 0.8585 (p0) cc_final: 0.8340 (p0) REVERT: E 378 ASP cc_start: 0.7933 (t0) cc_final: 0.7316 (t0) REVERT: K 291 GLN cc_start: 0.7219 (pp30) cc_final: 0.6514 (pp30) REVERT: K 321 PHE cc_start: 0.5912 (m-80) cc_final: 0.5683 (m-10) REVERT: K 348 GLU cc_start: 0.7694 (pt0) cc_final: 0.6768 (pp20) REVERT: K 350 HIS cc_start: 0.8652 (m-70) cc_final: 0.8176 (m-70) REVERT: L 393 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7276 (pp20) REVERT: L 404 PRO cc_start: 0.4851 (Cg_exo) cc_final: 0.4650 (Cg_endo) REVERT: L 411 TYR cc_start: 0.5307 (m-80) cc_final: 0.3984 (m-80) REVERT: L 433 MET cc_start: 0.5114 (ptm) cc_final: 0.4814 (ptp) outliers start: 140 outliers final: 78 residues processed: 473 average time/residue: 0.4097 time to fit residues: 225.2838 Evaluate side-chains 410 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 327 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 339 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 32 HIS Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 398 LEU Chi-restraints excluded: chain C residue 405 THR Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 425 LYS Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 372 ARG Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 339 THR Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 456 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 31 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 82 optimal weight: 0.0570 chunk 14 optimal weight: 1.9990 chunk 193 optimal weight: 0.0980 chunk 84 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 GLN C 78 ASN C 310 HIS ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN F 457 HIS ** G 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 GLN E 263 ASN E 459 ASN H 243 HIS ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 HIS K 457 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.123333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090453 restraints weight = 47207.827| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 4.26 r_work: 0.3362 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 1.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18707 Z= 0.145 Angle : 0.881 18.169 25696 Z= 0.403 Chirality : 0.047 0.348 3080 Planarity : 0.005 0.059 3278 Dihedral : 5.090 30.975 2598 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.96 % Allowed : 32.11 % Favored : 61.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -1.87 (0.16), residues: 2439 helix: -1.37 (0.39), residues: 159 sheet: -0.07 (0.18), residues: 810 loop : -2.02 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 58 TYR 0.012 0.001 TYR C 90 PHE 0.019 0.001 PHE H 321 TRP 0.025 0.001 TRP E 424 HIS 0.005 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (18658) covalent geometry : angle 0.86642 / 0.40 (25586) SS BOND : bond 0.00425 / 0.29 ( 37) SS BOND : angle 1.12953 / 0.82 ( 74) hydrogen bonds : bond 0.03397 / 2.37 ( 485) hydrogen bonds : angle 5.24444 / 3.61 ( 1452) link_BETA1-4 : bond 0.01889 / 0.90 ( 3) link_BETA1-4 : angle 3.12495 / 1.65 ( 9) link_NAG-ASN : bond 0.01033 / 0.57 ( 9) link_NAG-ASN : angle 4.48873 / 2.66 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 341 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8746 (pp) REVERT: A 389 GLU cc_start: 0.7304 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 410 THR cc_start: 0.8068 (p) cc_final: 0.7780 (p) REVERT: A 428 GLU cc_start: 0.8811 (tp30) cc_final: 0.8606 (mm-30) REVERT: A 449 ASP cc_start: 0.9131 (p0) cc_final: 0.8816 (p0) REVERT: B 313 GLN cc_start: 0.8443 (pm20) cc_final: 0.8192 (tp-100) REVERT: C 221 LYS cc_start: 0.8122 (pmtt) cc_final: 0.7633 (ptmt) REVERT: C 447 LYS cc_start: 0.6726 (mptp) cc_final: 0.6443 (mptt) REVERT: C 465 HIS cc_start: 0.7153 (m-70) cc_final: 0.6376 (m-70) REVERT: D 36 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7605 (ttt180) REVERT: D 65 LEU cc_start: 0.8223 (tt) cc_final: 0.7813 (tt) REVERT: D 78 GLU cc_start: 0.6723 (tt0) cc_final: 0.6247 (tm-30) REVERT: F 316 ASN cc_start: 0.7820 (t0) cc_final: 0.7113 (p0) REVERT: F 346 ARG cc_start: 0.7339 (pmm150) cc_final: 0.6502 (pmm-80) REVERT: F 348 GLU cc_start: 0.8139 (mp0) cc_final: 0.7817 (mp0) REVERT: F 449 ASP cc_start: 0.8679 (p0) cc_final: 0.8463 (p0) REVERT: E 378 ASP cc_start: 0.7800 (t0) cc_final: 0.7170 (t0) REVERT: K 291 GLN cc_start: 0.7361 (pp30) cc_final: 0.6637 (pp30) REVERT: K 321 PHE cc_start: 0.5870 (m-80) cc_final: 0.5600 (m-10) REVERT: L 367 LEU cc_start: 0.7860 (mm) cc_final: 0.7166 (OUTLIER) REVERT: L 393 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7344 (pp20) REVERT: L 398 TRP cc_start: 0.5039 (OUTLIER) cc_final: 0.4832 (m-90) REVERT: L 411 TYR cc_start: 0.5345 (m-80) cc_final: 0.4031 (m-80) REVERT: L 415 SER cc_start: 0.8587 (m) cc_final: 0.7951 (p) REVERT: L 433 MET cc_start: 0.4981 (ptm) cc_final: 0.4475 (ptm) outliers start: 112 outliers final: 71 residues processed: 421 average time/residue: 0.4125 time to fit residues: 202.4431 Evaluate side-chains 378 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 305 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 458 ILE Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 372 ARG Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 339 THR Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 441 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 398 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 237 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 211 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN A 445 GLN B 459 ASN C 32 HIS C 78 ASN C 310 HIS F 457 HIS G 445 GLN H 243 HIS K 350 HIS K 457 HIS L 249 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.124129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.090613 restraints weight = 48156.989| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 4.44 r_work: 0.3369 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 1.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18707 Z= 0.175 Angle : 0.905 18.126 25696 Z= 0.424 Chirality : 0.048 0.348 3080 Planarity : 0.006 0.093 3278 Dihedral : 5.107 27.663 2598 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 7.08 % Allowed : 31.15 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -1.82 (0.16), residues: 2439 helix: -1.18 (0.40), residues: 165 sheet: -0.06 (0.18), residues: 826 loop : -2.01 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 392 TYR 0.015 0.002 TYR D 63 PHE 0.027 0.002 PHE E 430 TRP 0.039 0.002 TRP E 424 HIS 0.007 0.001 HIS E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (18658) covalent geometry : angle 0.89721 / 0.42 (25586) SS BOND : bond 0.00458 / 0.33 ( 37) SS BOND : angle 1.13063 / 0.80 ( 74) hydrogen bonds : bond 0.03812 / 2.65 ( 485) hydrogen bonds : angle 5.31750 / 3.67 ( 1452) link_BETA1-4 : bond 0.00674 / 0.32 ( 3) link_BETA1-4 : angle 2.15766 / 1.06 ( 9) link_NAG-ASN : bond 0.00660 / 0.35 ( 9) link_NAG-ASN : angle 3.33224 / 2.06 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 337 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8926 (pp) REVERT: A 346 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8559 (ptp90) REVERT: A 403 GLU cc_start: 0.7453 (pt0) cc_final: 0.7194 (pt0) REVERT: A 410 THR cc_start: 0.8378 (p) cc_final: 0.7638 (p) REVERT: A 449 ASP cc_start: 0.9246 (p0) cc_final: 0.8979 (p0) REVERT: B 313 GLN cc_start: 0.8551 (pm20) cc_final: 0.8328 (tp-100) REVERT: B 426 LYS cc_start: 0.8841 (mptm) cc_final: 0.8365 (ttmm) REVERT: B 428 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7471 (mp0) REVERT: B 449 ASP cc_start: 0.7466 (p0) cc_final: 0.7162 (p0) REVERT: C 106 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9078 (t) REVERT: C 191 GLN cc_start: 0.6560 (mm-40) cc_final: 0.5908 (tm-30) REVERT: C 221 LYS cc_start: 0.8781 (pmtt) cc_final: 0.8380 (ptmt) REVERT: C 381 VAL cc_start: 0.8862 (OUTLIER) cc_final: 0.8633 (t) REVERT: C 447 LYS cc_start: 0.7257 (mptp) cc_final: 0.6785 (mptt) REVERT: D 78 GLU cc_start: 0.7463 (tt0) cc_final: 0.6876 (tm-30) REVERT: D 82 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8102 (tp40) REVERT: F 249 HIS cc_start: 0.6115 (OUTLIER) cc_final: 0.5842 (m-70) REVERT: F 316 ASN cc_start: 0.8015 (t0) cc_final: 0.7119 (p0) REVERT: F 335 THR cc_start: 0.5630 (OUTLIER) cc_final: 0.5128 (p) REVERT: F 346 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7270 (pmm-80) REVERT: F 357 GLU cc_start: 0.8626 (pm20) cc_final: 0.8393 (pm20) REVERT: G 372 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7633 (ptm-80) REVERT: G 389 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: G 466 GLU cc_start: 0.8963 (mp0) cc_final: 0.8741 (mp0) REVERT: E 249 HIS cc_start: 0.7245 (m90) cc_final: 0.6570 (p-80) REVERT: E 378 ASP cc_start: 0.7620 (t0) cc_final: 0.7161 (t0) REVERT: E 449 ASP cc_start: 0.8188 (m-30) cc_final: 0.6989 (p0) REVERT: H 423 ASP cc_start: 0.8792 (p0) cc_final: 0.8555 (p0) REVERT: K 250 ARG cc_start: 0.8168 (tmm-80) cc_final: 0.7801 (ttp80) REVERT: K 291 GLN cc_start: 0.7679 (pp30) cc_final: 0.7074 (pp30) REVERT: K 321 PHE cc_start: 0.5951 (m-80) cc_final: 0.5690 (m-10) REVERT: K 348 GLU cc_start: 0.8394 (pt0) cc_final: 0.7332 (pp20) REVERT: K 350 HIS cc_start: 0.8471 (OUTLIER) cc_final: 0.8031 (m-70) REVERT: K 372 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7398 (ttt180) REVERT: L 367 LEU cc_start: 0.7817 (mm) cc_final: 0.7140 (pp) REVERT: L 393 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7451 (pp20) REVERT: L 411 TYR cc_start: 0.5455 (m-80) cc_final: 0.4063 (m-80) REVERT: L 430 PHE cc_start: 0.5216 (OUTLIER) cc_final: 0.4755 (m-80) REVERT: L 433 MET cc_start: 0.4865 (ptm) cc_final: 0.4502 (ptm) outliers start: 133 outliers final: 70 residues processed: 434 average time/residue: 0.4275 time to fit residues: 214.3321 Evaluate side-chains 371 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 289 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 355 TYR Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain F residue 246 LEU Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 378 ASP Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 372 ARG Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain G residue 462 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 350 HIS Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 430 PHE Chi-restraints excluded: chain L residue 441 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 48 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 87 optimal weight: 0.0060 chunk 70 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 385 GLN A 445 GLN C 78 ASN F 343 ASN F 457 HIS ** G 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 459 ASN H 243 HIS K 350 HIS K 457 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.123134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089156 restraints weight = 48100.096| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 4.39 r_work: 0.3341 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 1.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18707 Z= 0.160 Angle : 0.891 20.499 25696 Z= 0.415 Chirality : 0.047 0.341 3080 Planarity : 0.005 0.063 3278 Dihedral : 4.976 28.621 2598 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 5.59 % Allowed : 34.08 % Favored : 60.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -1.74 (0.16), residues: 2439 helix: -1.15 (0.40), residues: 160 sheet: -0.03 (0.18), residues: 821 loop : -1.92 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 392 TYR 0.058 0.002 TYR C 355 PHE 0.021 0.001 PHE H 321 TRP 0.035 0.002 TRP E 424 HIS 0.022 0.001 HIS K 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.16 (18658) covalent geometry : angle 0.88151 / 0.41 (25586) SS BOND : bond 0.00488 / 0.34 ( 37) SS BOND : angle 1.49161 / 1.04 ( 74) hydrogen bonds : bond 0.03645 / 2.55 ( 485) hydrogen bonds : angle 5.26132 / 3.64 ( 1452) link_BETA1-4 : bond 0.00442 / 0.22 ( 3) link_BETA1-4 : angle 1.60016 / 0.86 ( 9) link_NAG-ASN : bond 0.00648 / 0.36 ( 9) link_NAG-ASN : angle 3.42469 / 2.11 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 310 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8985 (pp) REVERT: A 348 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8257 (mp0) REVERT: A 449 ASP cc_start: 0.9266 (p0) cc_final: 0.9037 (p0) REVERT: B 403 GLU cc_start: 0.8730 (pt0) cc_final: 0.8354 (pm20) REVERT: C 191 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6300 (tm-30) REVERT: C 221 LYS cc_start: 0.8891 (pmtt) cc_final: 0.8525 (ptmt) REVERT: C 447 LYS cc_start: 0.7415 (mptp) cc_final: 0.6900 (mptt) REVERT: C 465 HIS cc_start: 0.7440 (m-70) cc_final: 0.7157 (m-70) REVERT: C 536 GLU cc_start: 0.8406 (mp0) cc_final: 0.7613 (mt-10) REVERT: D 76 GLU cc_start: 0.9282 (mp0) cc_final: 0.9073 (mm-30) REVERT: D 78 GLU cc_start: 0.7403 (tt0) cc_final: 0.6967 (tm-30) REVERT: D 82 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8214 (tp40) REVERT: D 91 ILE cc_start: 0.8499 (tp) cc_final: 0.8156 (pp) REVERT: D 108 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8647 (ttmt) REVERT: F 316 ASN cc_start: 0.8160 (t0) cc_final: 0.7240 (p0) REVERT: F 335 THR cc_start: 0.5903 (OUTLIER) cc_final: 0.5460 (p) REVERT: F 357 GLU cc_start: 0.8568 (pm20) cc_final: 0.8336 (pm20) REVERT: F 358 GLU cc_start: 0.8745 (tt0) cc_final: 0.8468 (tt0) REVERT: F 464 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8782 (mtm) REVERT: G 389 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8351 (tm-30) REVERT: G 466 GLU cc_start: 0.8978 (mp0) cc_final: 0.8724 (mp0) REVERT: E 249 HIS cc_start: 0.7306 (m90) cc_final: 0.6627 (p-80) REVERT: E 378 ASP cc_start: 0.7432 (t0) cc_final: 0.6769 (t0) REVERT: E 424 TRP cc_start: 0.7952 (t60) cc_final: 0.7357 (t-100) REVERT: E 449 ASP cc_start: 0.8133 (m-30) cc_final: 0.6859 (p0) REVERT: K 250 ARG cc_start: 0.8309 (tmm-80) cc_final: 0.7911 (ttp80) REVERT: K 291 GLN cc_start: 0.7660 (pp30) cc_final: 0.6958 (pp30) REVERT: K 321 PHE cc_start: 0.5958 (m-80) cc_final: 0.5705 (m-10) REVERT: K 348 GLU cc_start: 0.8355 (pt0) cc_final: 0.7919 (pm20) REVERT: K 372 ARG cc_start: 0.7671 (ttt180) cc_final: 0.6464 (ptm-80) REVERT: K 433 MET cc_start: 0.8373 (ptp) cc_final: 0.7874 (ppp) REVERT: L 393 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7473 (pp20) REVERT: L 433 MET cc_start: 0.4931 (ptm) cc_final: 0.4582 (ptm) outliers start: 105 outliers final: 62 residues processed: 393 average time/residue: 0.4547 time to fit residues: 205.9131 Evaluate side-chains 355 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 289 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain D residue 10 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 393 GLU Chi-restraints excluded: chain G residue 400 SER Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 400 SER Chi-restraints excluded: chain K residue 439 LEU Chi-restraints excluded: chain K residue 444 THR Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 384 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 151 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 179 optimal weight: 0.0470 chunk 105 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 160 optimal weight: 0.9980 overall best weight: 0.9882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 GLN C 78 ASN F 343 ASN G 402 GLN ** G 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 HIS K 350 HIS K 457 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.122100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.087920 restraints weight = 47848.035| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.67 r_work: 0.3302 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 1.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18707 Z= 0.166 Angle : 0.910 20.526 25696 Z= 0.424 Chirality : 0.047 0.344 3080 Planarity : 0.006 0.106 3278 Dihedral : 5.007 26.727 2598 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.81 % Favored : 93.15 % Rotamer: Outliers : 4.95 % Allowed : 35.04 % Favored : 60.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -1.69 (0.16), residues: 2439 helix: -1.01 (0.40), residues: 162 sheet: -0.04 (0.18), residues: 822 loop : -1.88 (0.15), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 392 TYR 0.031 0.002 TYR B 472 PHE 0.028 0.001 PHE K 345 TRP 0.035 0.002 TRP H 315 HIS 0.006 0.001 HIS K 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.16 (18658) covalent geometry : angle 0.90088 / 0.42 (25586) SS BOND : bond 0.00721 / 0.59 ( 37) SS BOND : angle 1.50776 / 1.05 ( 74) hydrogen bonds : bond 0.03643 / 2.57 ( 485) hydrogen bonds : angle 5.25251 / 3.64 ( 1452) link_BETA1-4 : bond 0.00811 / 0.39 ( 3) link_BETA1-4 : angle 1.57168 / 0.85 ( 9) link_NAG-ASN : bond 0.00639 / 0.35 ( 9) link_NAG-ASN : angle 3.36070 / 2.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8864 (mpt-90) cc_final: 0.8548 (ptp90) REVERT: A 367 LEU cc_start: 0.8778 (tt) cc_final: 0.8471 (pp) REVERT: A 449 ASP cc_start: 0.9288 (p0) cc_final: 0.9078 (p0) REVERT: B 358 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8462 (tt0) REVERT: B 375 SER cc_start: 0.9028 (t) cc_final: 0.8786 (p) REVERT: B 388 GLN cc_start: 0.8163 (tt0) cc_final: 0.7819 (pp30) REVERT: B 403 GLU cc_start: 0.8801 (pt0) cc_final: 0.8415 (pm20) REVERT: C 191 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6460 (tm-30) REVERT: C 221 LYS cc_start: 0.8977 (pmtt) cc_final: 0.8652 (ptmt) REVERT: C 447 LYS cc_start: 0.7576 (mptp) cc_final: 0.7063 (mptt) REVERT: C 536 GLU cc_start: 0.8513 (mp0) cc_final: 0.7700 (mt-10) REVERT: D 8 LEU cc_start: 0.9199 (tp) cc_final: 0.8984 (mt) REVERT: D 76 GLU cc_start: 0.9302 (mp0) cc_final: 0.9028 (mm-30) REVERT: D 78 GLU cc_start: 0.7389 (tt0) cc_final: 0.6946 (tm-30) REVERT: D 91 ILE cc_start: 0.8579 (tp) cc_final: 0.8273 (pp) REVERT: D 126 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8625 (pm20) REVERT: F 249 HIS cc_start: 0.6208 (OUTLIER) cc_final: 0.5881 (m-70) REVERT: F 335 THR cc_start: 0.6052 (OUTLIER) cc_final: 0.5644 (p) REVERT: F 357 GLU cc_start: 0.8557 (pm20) cc_final: 0.8320 (pm20) REVERT: F 358 GLU cc_start: 0.8816 (tt0) cc_final: 0.8522 (tt0) REVERT: F 464 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8940 (mtm) REVERT: G 466 GLU cc_start: 0.9033 (mp0) cc_final: 0.8781 (mp0) REVERT: E 249 HIS cc_start: 0.7227 (m90) cc_final: 0.6478 (p-80) REVERT: E 378 ASP cc_start: 0.7371 (t0) cc_final: 0.6673 (t0) REVERT: E 385 GLN cc_start: 0.7819 (pp30) cc_final: 0.7527 (pp30) REVERT: E 449 ASP cc_start: 0.8036 (m-30) cc_final: 0.7144 (p0) REVERT: H 389 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7739 (tm-30) REVERT: H 423 ASP cc_start: 0.8786 (p0) cc_final: 0.7918 (p0) REVERT: K 250 ARG cc_start: 0.8375 (tmm-80) cc_final: 0.7866 (ttp80) REVERT: K 291 GLN cc_start: 0.7706 (pp30) cc_final: 0.7076 (pp30) REVERT: K 321 PHE cc_start: 0.6049 (m-80) cc_final: 0.5766 (m-10) REVERT: K 348 GLU cc_start: 0.8451 (pt0) cc_final: 0.7065 (pp20) REVERT: K 350 HIS cc_start: 0.8462 (m90) cc_final: 0.7869 (m-70) REVERT: K 372 ARG cc_start: 0.7716 (ttt180) cc_final: 0.7121 (ttp-110) REVERT: K 433 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7995 (ppp) REVERT: L 367 LEU cc_start: 0.7622 (mm) cc_final: 0.7119 (pp) REVERT: L 393 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7564 (pp20) REVERT: L 416 ILE cc_start: 0.9106 (mp) cc_final: 0.8858 (tp) REVERT: L 433 MET cc_start: 0.5121 (ptm) cc_final: 0.4787 (ptm) outliers start: 93 outliers final: 63 residues processed: 373 average time/residue: 0.4741 time to fit residues: 202.8725 Evaluate side-chains 349 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 282 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 400 SER Chi-restraints excluded: chain G residue 408 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 414 THR Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain K residue 433 MET Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 8 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 177 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 231 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 445 GLN C 78 ASN D 81 ASN G 445 GLN E 459 ASN H 243 HIS K 457 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.120539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085862 restraints weight = 47691.017| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 4.35 r_work: 0.3297 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 1.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 18707 Z= 0.182 Angle : 0.941 21.522 25696 Z= 0.444 Chirality : 0.048 0.342 3080 Planarity : 0.006 0.110 3278 Dihedral : 5.086 34.079 2598 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 4.31 % Allowed : 36.05 % Favored : 59.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -1.72 (0.17), residues: 2439 helix: -1.14 (0.40), residues: 162 sheet: -0.23 (0.18), residues: 848 loop : -1.77 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 89 TYR 0.023 0.002 TYR B 472 PHE 0.024 0.001 PHE H 321 TRP 0.039 0.002 TRP H 315 HIS 0.004 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (18658) covalent geometry : angle 0.93329 / 0.44 (25586) SS BOND : bond 0.00479 / 0.32 ( 37) SS BOND : angle 1.41027 / 1.01 ( 74) hydrogen bonds : bond 0.03947 / 2.81 ( 485) hydrogen bonds : angle 5.33328 / 3.68 ( 1452) link_BETA1-4 : bond 0.00365 / 0.18 ( 3) link_BETA1-4 : angle 1.73337 / 0.94 ( 9) link_NAG-ASN : bond 0.00585 / 0.33 ( 9) link_NAG-ASN : angle 3.38282 / 2.09 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4878 Ramachandran restraints generated. 2439 Oldfield, 0 Emsley, 2439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 308 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 LEU cc_start: 0.8745 (tt) cc_final: 0.8452 (pp) REVERT: A 389 GLU cc_start: 0.8933 (tt0) cc_final: 0.8632 (tm-30) REVERT: A 428 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8373 (tp30) REVERT: B 358 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8564 (tt0) REVERT: B 375 SER cc_start: 0.8917 (t) cc_final: 0.8674 (p) REVERT: B 403 GLU cc_start: 0.8862 (pt0) cc_final: 0.8513 (pm20) REVERT: C 43 ARG cc_start: 0.7268 (ptm-80) cc_final: 0.7025 (tmm160) REVERT: C 191 GLN cc_start: 0.6981 (mm-40) cc_final: 0.6589 (tm-30) REVERT: C 221 LYS cc_start: 0.9103 (pmtt) cc_final: 0.8853 (ptpt) REVERT: C 447 LYS cc_start: 0.7986 (mptp) cc_final: 0.7522 (mptt) REVERT: C 536 GLU cc_start: 0.8549 (mp0) cc_final: 0.7740 (mt-10) REVERT: D 76 GLU cc_start: 0.9244 (mp0) cc_final: 0.9012 (mm-30) REVERT: D 78 GLU cc_start: 0.7637 (tt0) cc_final: 0.7239 (tp30) REVERT: D 91 ILE cc_start: 0.8774 (tp) cc_final: 0.8551 (pp) REVERT: D 108 LYS cc_start: 0.8984 (ttmm) cc_final: 0.8746 (ttmm) REVERT: D 126 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8514 (pm20) REVERT: F 249 HIS cc_start: 0.6369 (OUTLIER) cc_final: 0.6071 (m-70) REVERT: F 335 THR cc_start: 0.6438 (OUTLIER) cc_final: 0.6059 (p) REVERT: F 358 GLU cc_start: 0.8946 (tt0) cc_final: 0.8596 (tt0) REVERT: G 393 GLU cc_start: 0.8115 (pm20) cc_final: 0.7868 (pp20) REVERT: G 426 LYS cc_start: 0.8643 (mmmt) cc_final: 0.8383 (mmpt) REVERT: E 378 ASP cc_start: 0.7303 (t0) cc_final: 0.6746 (t0) REVERT: E 385 GLN cc_start: 0.7954 (pp30) cc_final: 0.7682 (pp30) REVERT: E 433 MET cc_start: 0.6415 (tpp) cc_final: 0.5073 (tpt) REVERT: E 449 ASP cc_start: 0.8199 (m-30) cc_final: 0.7385 (p0) REVERT: H 389 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7806 (tm-30) REVERT: K 250 ARG cc_start: 0.8454 (tmm-80) cc_final: 0.7982 (ttp80) REVERT: K 291 GLN cc_start: 0.7921 (pp30) cc_final: 0.7429 (pp30) REVERT: K 321 PHE cc_start: 0.6144 (m-80) cc_final: 0.5750 (m-10) REVERT: K 348 GLU cc_start: 0.8429 (pt0) cc_final: 0.7250 (pp20) REVERT: K 350 HIS cc_start: 0.8426 (m90) cc_final: 0.7860 (m-70) REVERT: K 372 ARG cc_start: 0.7881 (ttt180) cc_final: 0.7410 (ttp-110) REVERT: K 433 MET cc_start: 0.8731 (ptp) cc_final: 0.8102 (ppp) REVERT: L 393 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7678 (pp20) REVERT: L 416 ILE cc_start: 0.9176 (mp) cc_final: 0.8915 (tp) REVERT: L 433 MET cc_start: 0.5238 (ptm) cc_final: 0.4842 (ptm) outliers start: 81 outliers final: 51 residues processed: 367 average time/residue: 0.5035 time to fit residues: 210.3415 Evaluate side-chains 327 residues out of total 2115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 381 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 455 VAL Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain F residue 249 HIS Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 410 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 361 LEU Chi-restraints excluded: chain G residue 400 SER Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 460 VAL Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 381 VAL Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain H residue 339 THR Chi-restraints excluded: chain H residue 349 VAL Chi-restraints excluded: chain H residue 380 LEU Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 458 ILE Chi-restraints excluded: chain H residue 460 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 367 LEU Chi-restraints excluded: chain K residue 384 LEU Chi-restraints excluded: chain K residue 429 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 384 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 111 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 205 optimal weight: 10.0000 chunk 11 optimal weight: 0.0470 chunk 83 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 26 optimal weight: 0.0770 chunk 41 optimal weight: 5.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 ASN A 445 GLN C 78 ASN D 45 ASN F 445 GLN H 243 HIS K 457 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.121482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.087115 restraints weight = 48004.817| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 4.63 r_work: 0.3306 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 1.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18707 Z= 0.148 Angle : 0.915 20.666 25696 Z= 0.425 Chirality : 0.047 0.336 3080 Planarity : 0.006 0.111 3278 Dihedral : 4.877 26.963 2598 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.19 % Allowed : 37.97 % Favored : 58.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % 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: -1.61 (0.17), residues: 2439 helix: -1.05 (0.41), residues: 157 sheet: -0.12 (0.18), residues: 832 loop : -1.72 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 392 TYR 0.015 0.001 TYR E 411 PHE 0.028 0.001 PHE K 345 TRP 0.038 0.002 TRP H 315 HIS 0.005 0.001 HIS A 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (18658) covalent geometry : angle 0.90841 / 0.42 (25586) SS BOND : bond 0.00417 / 0.28 ( 37) SS BOND : angle 1.19019 / 0.85 ( 74) hydrogen bonds : bond 0.03516 / 2.50 ( 485) hydrogen bonds : angle 5.23922 / 3.63 ( 1452) link_BETA1-4 : bond 0.00616 / 0.30 ( 3) link_BETA1-4 : angle 1.64681 / 0.83 ( 9) link_NAG-ASN : bond 0.00580 / 0.33 ( 9) link_NAG-ASN : angle 3.19122 / 2.01 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7534.75 seconds wall clock time: 128 minutes 32.30 seconds (7712.30 seconds total)