Starting phenix.real_space_refine on Sat Sep 12 21:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ue8_20750/09_2026/6ue8_20750.map" } resolution = 3.0 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= -0.012 sd= 0.434 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 11463 2.51 5 N 3144 2.21 5 O 3478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 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: 18183 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: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4130 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 509} 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: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1042 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 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: "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: 4.59, per 1000 atoms: 0.25 Number of scatterers: 18183 At special positions: 0 Unit cell: (173.196, 147.726, 180.328, 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 3478 8.00 N 3144 7.00 C 11463 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 13 " - pdb=" SG CYS D 101 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS F 471 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.03 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.03 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.04 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=2.03 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=2.02 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=2.03 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=2.03 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=2.03 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 603 " - " ASN C 65 " " 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: 1.64 Conformation dependent library (CDL) restraints added in 884.7 milliseconds 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4594 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 53 sheets defined 10.0% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 removed outlier: 3.606A pdb=" N LEU A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 317 removed outlier: 3.672A pdb=" N ASN A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.537A pdb=" N LYS A 394 " --> pdb=" O PRO A 391 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 421 through 427 removed outlier: 3.953A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 357 through 362 removed outlier: 4.205A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 357 through 362' 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 422 through 427 Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.681A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 272 through 276 removed outlier: 3.849A pdb=" N PHE C 275 " --> pdb=" O ALA C 272 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU C 276 " --> pdb=" O PRO C 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 272 through 276' Processing helix chain 'C' and resid 298 through 302 removed outlier: 3.596A pdb=" N ASP C 301 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.054A 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: 3.690A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 removed outlier: 3.717A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER C 472 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 removed outlier: 4.292A pdb=" N ASP C 520 " --> pdb=" O THR C 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 312 through 318 removed outlier: 4.175A pdb=" N ASN F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS F 317 " --> pdb=" O GLN F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 removed outlier: 3.730A pdb=" N LEU F 359 " --> pdb=" O PRO F 355 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 360' 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: 3.895A pdb=" N LYS F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 355 through 360 removed outlier: 3.679A pdb=" N LEU G 359 " --> pdb=" O PRO G 355 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA G 360 " --> pdb=" O SER G 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 355 through 360' Processing helix chain 'G' and resid 421 through 427 removed outlier: 3.709A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 removed outlier: 3.628A pdb=" N TRP E 315 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 362 removed outlier: 4.439A pdb=" N LEU E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN E 362 " --> pdb=" O GLU E 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 357 through 362' Processing helix chain 'E' and resid 391 through 395 removed outlier: 4.264A pdb=" N TYR E 395 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 258 removed outlier: 3.850A pdb=" N LEU H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 311 through 316 removed outlier: 3.522A pdb=" N TRP H 315 " --> pdb=" O CYS H 311 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 311 through 316' Processing helix chain 'H' and resid 357 through 362 removed outlier: 3.716A pdb=" N LEU H 361 " --> pdb=" O GLU H 357 " (cutoff:3.500A) removed outlier: 3.745A 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 391 through 395 removed outlier: 4.133A pdb=" N TYR H 395 " --> pdb=" O ARG H 392 " (cutoff:3.500A) Processing helix chain 'H' and resid 421 through 427 Processing helix chain 'K' and resid 252 through 258 Processing helix chain 'K' and resid 312 through 318 removed outlier: 3.610A pdb=" N GLY K 318 " --> pdb=" O PRO K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 356 through 362 removed outlier: 3.652A pdb=" N LEU K 361 " --> pdb=" O GLU K 357 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN K 362 " --> pdb=" O GLU K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 420 through 427 removed outlier: 3.905A pdb=" N TRP K 424 " --> pdb=" O ALA K 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 256 removed outlier: 3.869A pdb=" N ASP L 255 " --> pdb=" O ALA L 252 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU L 256 " --> pdb=" O LEU L 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 252 through 256' Processing helix chain 'L' and resid 356 through 360 removed outlier: 3.884A pdb=" N ALA L 360 " --> pdb=" O GLU L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 421 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 246 through 247 removed outlier: 3.620A pdb=" N SER A 247 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 267 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 290 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.540A pdb=" N ALA A 336 " --> pdb=" O CYS A 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.907A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.845A 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: 3.907A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR A 410 " --> pdb=" O GLU A 403 " (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: 8.198A pdb=" N PHE D 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER B 461 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N TYR D 63 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 463 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE K 458 " --> pdb=" O HIS L 457 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL K 460 " --> pdb=" O ASN L 459 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.754A pdb=" N ARG B 245 " --> pdb=" O THR B 269 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY B 270 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 302 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 280 through 281 removed outlier: 3.595A pdb=" N PHE B 321 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 338 " --> pdb=" O PHE B 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.812A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.812A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 5.757A 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: 6.269A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 removed outlier: 3.749A pdb=" N ASN C 65 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 125 removed outlier: 7.068A 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 removed outlier: 3.569A pdb=" N VAL C 130 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 189 " --> pdb=" O VAL C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 149 through 151 removed outlier: 3.580A pdb=" N LYS C 149 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE C 151 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR C 154 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 225 through 229 removed outlier: 3.565A pdb=" N GLU C 225 " --> pdb=" O ALA C 323 " (cutoff:3.500A) removed outlier: 7.270A 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 removed outlier: 3.642A pdb=" N VAL C 292 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 340 through 343 removed outlier: 3.527A pdb=" N GLY C 343 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR C 433 " --> pdb=" O CYS C 423 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 419 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 424 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL C 381 " --> pdb=" O TRP C 366 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 348 through 354 removed outlier: 3.607A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 351 " --> pdb=" O VAL C 408 " (cutoff:3.500A) removed outlier: 3.856A 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 462 removed outlier: 4.015A pdb=" N LEU C 460 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 513 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 511 " --> pdb=" O VAL C 462 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 484 through 487 removed outlier: 3.950A pdb=" N GLN C 486 " --> pdb=" O LYS C 479 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS C 479 " --> pdb=" O GLN C 486 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS C 478 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRP C 523 " --> pdb=" O TRP C 480 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR C 524 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA C 539 " --> pdb=" O TYR C 524 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N CYS C 526 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR C 537 " --> pdb=" O CYS C 526 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 528 " --> pdb=" O GLY C 535 " (cutoff:3.500A) removed outlier: 4.026A 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: 6.772A pdb=" N ILE D 18 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP D 10 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA D 16 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE D 33 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL D 34 " --> pdb=" O HIS F 457 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ASN F 459 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG D 36 " --> pdb=" O ASN F 459 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER F 461 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE D 38 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL F 463 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE D 40 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ALA F 465 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL D 42 " --> pdb=" O ALA F 465 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE G 458 " --> pdb=" O ASN H 459 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N SER H 461 " --> pdb=" O ILE G 458 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL G 460 " --> pdb=" O SER H 461 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL H 463 " --> pdb=" O VAL G 460 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL G 462 " --> pdb=" O VAL H 463 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 75 through 78 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 247 removed outlier: 3.526A pdb=" N CYS F 266 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 268 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL F 304 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY F 270 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR F 302 " --> pdb=" O GLY F 270 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 279 through 280 removed outlier: 3.661A pdb=" N ALA F 325 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU F 334 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.804A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.575A 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: 3.804A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) removed outlier: 5.575A 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 322 through 323 Processing sheet with id=AD5, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.016A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU G 396 " --> pdb=" O ILE G 416 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.016A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AD8, first strand: chain 'E' and resid 245 through 249 Processing sheet with id=AD9, first strand: chain 'E' and resid 295 through 297 removed outlier: 3.678A pdb=" N SER E 303 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP E 297 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.381A pdb=" N THR E 368 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.381A pdb=" N THR E 368 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 412 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG E 401 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 388 through 389 removed outlier: 3.737A pdb=" N GLN E 388 " --> pdb=" O GLN E 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN E 385 " --> pdb=" O GLN E 388 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 380 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 384 " --> pdb=" O SER E 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 245 through 249 removed outlier: 3.522A pdb=" N THR H 269 " --> pdb=" O ARG H 245 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER H 247 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR H 267 " --> pdb=" O SER H 247 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N HIS H 249 " --> pdb=" O THR H 265 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR H 265 " --> pdb=" O HIS H 249 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 320 through 322 removed outlier: 3.516A pdb=" N PHE H 321 " --> pdb=" O ILE H 338 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 348 through 352 removed outlier: 4.135A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 348 through 352 removed outlier: 4.135A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N TYR H 411 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR H 410 " --> pdb=" O GLU H 403 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 388 through 389 removed outlier: 3.685A pdb=" N PHE H 430 " --> pdb=" O ILE H 448 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 247 through 248 removed outlier: 4.487A pdb=" N SER K 247 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR K 267 " --> pdb=" O SER K 247 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU K 268 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL K 304 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 247 through 248 removed outlier: 4.487A pdb=" N SER K 247 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR K 267 " --> pdb=" O SER K 247 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU K 268 " --> pdb=" O VAL K 304 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL K 304 " --> pdb=" O LEU K 268 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 278 through 281 removed outlier: 3.501A pdb=" N LEU K 334 " --> pdb=" O ALA K 325 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.058A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU K 396 " --> pdb=" O ILE K 416 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 348 through 352 removed outlier: 4.058A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.958A pdb=" N PHE K 430 " --> pdb=" O ILE K 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE K 448 " --> pdb=" O PHE K 430 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 350 through 351 removed outlier: 3.723A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU L 396 " --> pdb=" O ILE L 416 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 350 through 351 removed outlier: 3.723A pdb=" N HIS L 350 " --> pdb=" O LEU L 370 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 388 through 389 removed outlier: 4.111A pdb=" N GLN L 388 " --> pdb=" O GLN L 385 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN L 385 " --> pdb=" O GLN L 388 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU L 380 " --> pdb=" O GLY L 435 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY L 435 " --> pdb=" O LEU L 380 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG L 382 " --> pdb=" O MET L 433 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1398 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: 3.72 Time building geometry restraints manager: 2.21 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: 5827 1.34 - 1.46: 4438 1.46 - 1.59: 8234 1.59 - 1.72: 0 1.72 - 1.84: 115 Bond restraints: 18614 Sorted by residual: bond pdb=" C GLU K 389 " pdb=" N LEU K 390 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 8.79e+00 bond pdb=" C GLU A 389 " pdb=" N LEU A 390 " ideal model delta sigma weight residual 1.331 1.255 0.076 2.83e-02 1.25e+03 7.21e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N LEU G 359 " pdb=" CA LEU G 359 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 6.11e+00 bond pdb=" N GLU D 35 " pdb=" CA GLU D 35 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.89e+00 ... (remaining 18609 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 24400 2.42 - 4.83: 951 4.83 - 7.25: 136 7.25 - 9.67: 31 9.67 - 12.08: 9 Bond angle restraints: 25527 Sorted by residual: angle pdb=" C ALA L 438 " pdb=" N LEU L 439 " pdb=" CA LEU L 439 " ideal model delta sigma weight residual 120.68 131.71 -11.03 1.52e+00 4.33e-01 5.27e+01 angle pdb=" C HIS E 249 " pdb=" N ARG E 250 " pdb=" CA ARG E 250 " ideal model delta sigma weight residual 121.03 131.25 -10.22 1.60e+00 3.91e-01 4.08e+01 angle pdb=" C VAL E 307 " pdb=" N LEU E 308 " pdb=" CA LEU E 308 " ideal model delta sigma weight residual 122.65 132.54 -9.89 1.66e+00 3.63e-01 3.55e+01 angle pdb=" N GLY C 527 " pdb=" CA GLY C 527 " pdb=" C GLY C 527 " ideal model delta sigma weight residual 111.42 119.49 -8.07 1.42e+00 4.96e-01 3.23e+01 angle pdb=" C TRP L 281 " pdb=" N THR L 282 " pdb=" CA THR L 282 " ideal model delta sigma weight residual 120.26 127.47 -7.21 1.34e+00 5.57e-01 2.89e+01 ... (remaining 25522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 9987 17.91 - 35.82: 940 35.82 - 53.73: 122 53.73 - 71.64: 18 71.64 - 89.55: 6 Dihedral angle restraints: 11073 sinusoidal: 3975 harmonic: 7098 Sorted by residual: 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 93.00 164.04 -71.04 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CB CYS A 242 " pdb=" SG CYS A 242 " pdb=" SG CYS B 299 " pdb=" CB CYS B 299 " ideal model delta sinusoidal sigma weight residual 93.00 159.61 -66.61 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS C 253 " pdb=" SG CYS C 253 " pdb=" SG CYS C 261 " pdb=" CB CYS C 261 " ideal model delta sinusoidal sigma weight residual -86.00 -149.92 63.92 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 11070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2532 0.080 - 0.160: 479 0.160 - 0.239: 49 0.239 - 0.319: 5 0.319 - 0.399: 3 Chirality restraints: 3068 Sorted by residual: 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 -2.09 -0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CG LEU L 264 " pdb=" CB LEU L 264 " pdb=" CD1 LEU L 264 " pdb=" CD2 LEU L 264 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C2 NAG A 501 " pdb=" C1 NAG A 501 " pdb=" C3 NAG A 501 " pdb=" N2 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.15 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 3065 not shown) Planarity restraints: 3280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 55 " 0.057 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO D 56 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 56 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO D 56 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 327 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO G 328 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 328 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 328 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 282 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO G 283 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO G 283 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 283 " 0.037 5.00e-02 4.00e+02 ... (remaining 3277 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 707 2.70 - 3.25: 14778 3.25 - 3.80: 25886 3.80 - 4.35: 30411 4.35 - 4.90: 54662 Nonbonded interactions: 126444 Sorted by model distance: nonbonded pdb=" NH2 ARG D 21 " pdb=" OE1 GLU D 35 " model vdw 2.144 3.120 nonbonded pdb=" O LEU C 460 " pdb=" OG1 THR C 512 " model vdw 2.248 3.040 nonbonded pdb=" O SER C 506 " pdb=" OG SER C 506 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR H 282 " pdb=" OG1 THR H 322 " model vdw 2.275 3.040 nonbonded pdb=" O LEU L 396 " pdb=" OG SER L 415 " model vdw 2.277 3.040 ... (remaining 126439 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: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.830 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.008 0.083 18661 Z= 0.369 Angle : 1.159 12.575 25631 Z= 0.626 Chirality : 0.062 0.399 3068 Planarity : 0.009 0.085 3273 Dihedral : 13.382 89.552 6368 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.65 % Favored : 88.35 % Rotamer: Outliers : 0.48 % Allowed : 9.91 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % Twisted General : 0.18 % 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: -3.88 (0.14), residues: 2437 helix: -4.46 (0.19), residues: 136 sheet: -1.55 (0.17), residues: 783 loop : -3.14 (0.13), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 250 TYR 0.024 0.003 TYR A 395 PHE 0.024 0.003 PHE C 136 TRP 0.018 0.003 TRP A 383 HIS 0.009 0.002 HIS E 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00835 / 0.37 (18614) covalent geometry : angle 1.14268 / 0.62 (25527) SS BOND : bond 0.00591 / 0.42 ( 37) SS BOND : angle 2.11049 / 1.41 ( 74) hydrogen bonds : bond 0.28877 / 19.53 ( 450) hydrogen bonds : angle 8.92201 / 6.01 ( 1398) link_BETA1-4 : bond 0.01107 / 0.54 ( 3) link_BETA1-4 : angle 5.53441 / 2.39 ( 9) link_NAG-ASN : bond 0.00809 / 0.41 ( 7) link_NAG-ASN : angle 4.91219 / 3.77 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 450 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 468 ASP cc_start: 0.8127 (p0) cc_final: 0.7843 (p0) REVERT: K 378 ASP cc_start: 0.7088 (m-30) cc_final: 0.6848 (m-30) REVERT: L 411 TYR cc_start: 0.4961 (m-80) cc_final: 0.4416 (m-80) outliers start: 9 outliers final: 1 residues processed: 457 average time/residue: 0.6459 time to fit residues: 328.2402 Evaluate side-chains 241 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 434 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 291 GLN A 457 HIS B 343 ASN C 68 ASN C 247 ASN D 81 ASN F 343 ASN G 263 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 459 ASN E 459 ASN ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN K 249 HIS K 313 GLN K 385 GLN L 249 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.137932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.100389 restraints weight = 46235.244| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 4.46 r_work: 0.3453 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 18661 Z= 0.152 Angle : 0.819 11.865 25631 Z= 0.405 Chirality : 0.045 0.289 3068 Planarity : 0.007 0.069 3273 Dihedral : 6.392 33.088 2596 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.74 % Allowed : 18.59 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.58 % Cis-general : 0.00 % Twisted Proline : 1.16 % 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: -2.98 (0.15), residues: 2437 helix: -3.44 (0.29), residues: 134 sheet: -0.82 (0.18), residues: 811 loop : -2.66 (0.14), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 336 TYR 0.015 0.001 TYR C 148 PHE 0.022 0.002 PHE K 345 TRP 0.022 0.001 TRP B 281 HIS 0.006 0.001 HIS K 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (18614) covalent geometry : angle 0.80797 / 0.40 (25527) SS BOND : bond 0.00421 / 0.31 ( 37) SS BOND : angle 1.72272 / 1.14 ( 74) hydrogen bonds : bond 0.04271 / 2.86 ( 450) hydrogen bonds : angle 5.81894 / 3.95 ( 1398) link_BETA1-4 : bond 0.00593 / 0.30 ( 3) link_BETA1-4 : angle 3.17325 / 1.49 ( 9) link_NAG-ASN : bond 0.00505 / 0.24 ( 7) link_NAG-ASN : angle 3.22265 / 2.41 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 284 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 LEU cc_start: 0.8894 (tt) cc_final: 0.8425 (mt) REVERT: A 403 GLU cc_start: 0.9121 (pt0) cc_final: 0.8750 (pt0) REVERT: B 385 GLN cc_start: 0.9030 (tp40) cc_final: 0.8733 (tp40) REVERT: B 392 ARG cc_start: 0.9287 (mmm-85) cc_final: 0.8954 (ttp-110) REVERT: B 423 ASP cc_start: 0.8917 (m-30) cc_final: 0.8626 (m-30) REVERT: B 428 GLU cc_start: 0.8194 (mp0) cc_final: 0.7562 (mp0) REVERT: B 464 MET cc_start: 0.7337 (ppp) cc_final: 0.6957 (ppp) REVERT: C 483 THR cc_start: 0.7462 (OUTLIER) cc_final: 0.7062 (t) REVERT: F 340 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7748 (ttmt) REVERT: F 389 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8408 (tm-30) REVERT: E 414 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8228 (p) REVERT: E 430 PHE cc_start: 0.7189 (m-80) cc_final: 0.6960 (m-80) REVERT: E 448 ILE cc_start: 0.6559 (OUTLIER) cc_final: 0.6097 (pp) REVERT: H 403 GLU cc_start: 0.8013 (pt0) cc_final: 0.6986 (pm20) REVERT: H 433 MET cc_start: 0.8415 (tpp) cc_final: 0.7302 (mmm) REVERT: K 317 HIS cc_start: 0.7865 (p-80) cc_final: 0.7616 (p-80) REVERT: K 338 ILE cc_start: 0.5444 (OUTLIER) cc_final: 0.5115 (mt) REVERT: K 378 ASP cc_start: 0.7437 (m-30) cc_final: 0.7208 (m-30) REVERT: K 403 GLU cc_start: 0.7502 (pt0) cc_final: 0.7038 (pt0) REVERT: K 418 ARG cc_start: 0.6143 (mtt180) cc_final: 0.5851 (mmt180) REVERT: K 433 MET cc_start: 0.8788 (mmm) cc_final: 0.8578 (mmm) REVERT: L 372 ARG cc_start: 0.6916 (ptm-80) cc_final: 0.6675 (ppp80) REVERT: L 385 GLN cc_start: 0.6038 (OUTLIER) cc_final: 0.5838 (tp40) REVERT: L 403 GLU cc_start: 0.8808 (pt0) cc_final: 0.8591 (pt0) outliers start: 89 outliers final: 28 residues processed: 342 average time/residue: 0.5794 time to fit residues: 223.1272 Evaluate side-chains 253 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 344 THR Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 278 THR Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 385 GLN Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 121 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 163 optimal weight: 0.0020 chunk 102 optimal weight: 2.9990 chunk 37 optimal weight: 0.0370 chunk 137 optimal weight: 0.0970 chunk 235 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.8268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 343 ASN G 362 ASN ** G 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 445 GLN E 350 HIS H 291 GLN K 385 GLN L 459 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.135683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.100122 restraints weight = 46158.606| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 4.36 r_work: 0.3474 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18661 Z= 0.137 Angle : 0.751 11.855 25631 Z= 0.364 Chirality : 0.044 0.290 3068 Planarity : 0.006 0.057 3273 Dihedral : 5.616 29.993 2596 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.85 % Allowed : 19.98 % Favored : 75.17 % 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: -2.46 (0.16), residues: 2437 helix: -2.80 (0.35), residues: 142 sheet: -0.30 (0.18), residues: 793 loop : -2.40 (0.14), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 336 TYR 0.012 0.001 TYR L 411 PHE 0.019 0.001 PHE K 345 TRP 0.031 0.001 TRP B 281 HIS 0.008 0.001 HIS F 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (18614) covalent geometry : angle 0.74282 / 0.36 (25527) SS BOND : bond 0.00431 / 0.35 ( 37) SS BOND : angle 1.32031 / 0.85 ( 74) hydrogen bonds : bond 0.03661 / 2.42 ( 450) hydrogen bonds : angle 5.18274 / 3.54 ( 1398) link_BETA1-4 : bond 0.00413 / 0.21 ( 3) link_BETA1-4 : angle 2.70434 / 1.28 ( 9) link_NAG-ASN : bond 0.00438 / 0.20 ( 7) link_NAG-ASN : angle 2.94769 / 2.30 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 254 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ARG cc_start: 0.8918 (ttp80) cc_final: 0.8613 (ttm110) REVERT: A 403 GLU cc_start: 0.9138 (pt0) cc_final: 0.8795 (pt0) REVERT: B 255 ASP cc_start: 0.8950 (m-30) cc_final: 0.8748 (m-30) REVERT: B 265 THR cc_start: 0.7958 (OUTLIER) cc_final: 0.7728 (t) REVERT: B 296 ARG cc_start: 0.8367 (mmt180) cc_final: 0.8132 (tpp80) REVERT: B 385 GLN cc_start: 0.9083 (tp40) cc_final: 0.8823 (tp40) REVERT: B 423 ASP cc_start: 0.8956 (m-30) cc_final: 0.8590 (m-30) REVERT: B 428 GLU cc_start: 0.8284 (mp0) cc_final: 0.7415 (mp0) REVERT: B 464 MET cc_start: 0.7196 (ppp) cc_final: 0.6897 (ppp) REVERT: C 330 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8823 (pp20) REVERT: C 459 THR cc_start: 0.7568 (OUTLIER) cc_final: 0.6728 (t) REVERT: C 461 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7983 (mmtm) REVERT: C 483 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.7004 (t) REVERT: F 340 LYS cc_start: 0.8072 (ttmt) cc_final: 0.7777 (ttmt) REVERT: G 394 LYS cc_start: 0.8659 (mmmm) cc_final: 0.8321 (mmmt) REVERT: E 402 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8280 (tm-30) REVERT: E 430 PHE cc_start: 0.7312 (m-80) cc_final: 0.6997 (m-80) REVERT: E 448 ILE cc_start: 0.6473 (OUTLIER) cc_final: 0.6005 (pp) REVERT: H 403 GLU cc_start: 0.8151 (pt0) cc_final: 0.7167 (pm20) REVERT: H 433 MET cc_start: 0.8568 (tpp) cc_final: 0.8023 (mmt) REVERT: K 317 HIS cc_start: 0.7720 (p-80) cc_final: 0.7415 (p-80) REVERT: K 378 ASP cc_start: 0.7756 (m-30) cc_final: 0.7407 (m-30) REVERT: K 403 GLU cc_start: 0.7445 (pt0) cc_final: 0.7097 (pt0) REVERT: K 418 ARG cc_start: 0.6398 (mtt180) cc_final: 0.6082 (mmt180) REVERT: K 433 MET cc_start: 0.8736 (mmm) cc_final: 0.8489 (mmm) REVERT: L 369 CYS cc_start: 0.6647 (OUTLIER) cc_final: 0.6217 (p) REVERT: L 372 ARG cc_start: 0.6999 (ptm-80) cc_final: 0.6790 (ptm-80) REVERT: L 403 GLU cc_start: 0.8877 (pt0) cc_final: 0.8500 (pm20) REVERT: L 443 PHE cc_start: 0.8081 (m-80) cc_final: 0.7044 (t80) outliers start: 91 outliers final: 40 residues processed: 314 average time/residue: 0.5802 time to fit residues: 205.2881 Evaluate side-chains 264 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 218 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 323 CYS Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain K residue 282 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 393 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 369 CYS Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 151 optimal weight: 3.9990 chunk 117 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 173 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 chunk 16 optimal weight: 0.0270 overall best weight: 1.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN G 362 ASN G 436 HIS H 385 GLN K 385 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.132142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.096857 restraints weight = 46112.772| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 4.35 r_work: 0.3424 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18661 Z= 0.200 Angle : 0.801 12.306 25631 Z= 0.391 Chirality : 0.046 0.269 3068 Planarity : 0.006 0.053 3273 Dihedral : 5.567 30.360 2596 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 5.38 % Allowed : 21.42 % Favored : 73.20 % 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: -2.23 (0.16), residues: 2437 helix: -2.01 (0.43), residues: 129 sheet: -0.16 (0.18), residues: 806 loop : -2.32 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 336 TYR 0.013 0.001 TYR B 472 PHE 0.023 0.002 PHE K 345 TRP 0.031 0.002 TRP B 281 HIS 0.008 0.001 HIS F 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (18614) covalent geometry : angle 0.79245 / 0.39 (25527) SS BOND : bond 0.00613 / 0.48 ( 37) SS BOND : angle 1.64783 / 1.11 ( 74) hydrogen bonds : bond 0.04000 / 2.66 ( 450) hydrogen bonds : angle 5.23743 / 3.60 ( 1398) link_BETA1-4 : bond 0.00411 / 0.20 ( 3) link_BETA1-4 : angle 2.48075 / 1.23 ( 9) link_NAG-ASN : bond 0.00582 / 0.28 ( 7) link_NAG-ASN : angle 2.87034 / 2.12 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 227 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.9238 (pt0) cc_final: 0.8800 (pt0) REVERT: B 327 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6524 (t70) REVERT: B 385 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8791 (tp40) REVERT: B 392 ARG cc_start: 0.9134 (mmm-85) cc_final: 0.8826 (ttp-110) REVERT: B 428 GLU cc_start: 0.8469 (mp0) cc_final: 0.8018 (mp0) REVERT: C 330 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8801 (pp20) REVERT: C 424 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7001 (pp) REVERT: C 459 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.6957 (t) REVERT: C 483 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.6815 (t) REVERT: D 76 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9093 (mm-30) REVERT: F 340 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7971 (ttmt) REVERT: F 346 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8197 (ptt-90) REVERT: F 403 GLU cc_start: 0.9137 (pt0) cc_final: 0.8914 (pt0) REVERT: G 394 LYS cc_start: 0.8819 (mmmm) cc_final: 0.8611 (mmmt) REVERT: E 430 PHE cc_start: 0.7281 (m-80) cc_final: 0.6938 (m-80) REVERT: E 448 ILE cc_start: 0.6697 (OUTLIER) cc_final: 0.6178 (pp) REVERT: E 458 ILE cc_start: 0.9183 (mt) cc_final: 0.8975 (mp) REVERT: H 315 TRP cc_start: 0.8496 (OUTLIER) cc_final: 0.8105 (t60) REVERT: H 403 GLU cc_start: 0.8231 (pt0) cc_final: 0.7297 (pm20) REVERT: H 433 MET cc_start: 0.8754 (tpp) cc_final: 0.8258 (mmm) REVERT: K 317 HIS cc_start: 0.7870 (p-80) cc_final: 0.7645 (p-80) REVERT: K 338 ILE cc_start: 0.5700 (OUTLIER) cc_final: 0.5347 (mt) REVERT: K 358 GLU cc_start: 0.8266 (pt0) cc_final: 0.8010 (pt0) REVERT: K 378 ASP cc_start: 0.7925 (m-30) cc_final: 0.7593 (m-30) REVERT: K 403 GLU cc_start: 0.7439 (pt0) cc_final: 0.7067 (pt0) REVERT: K 418 ARG cc_start: 0.6661 (mtt180) cc_final: 0.6294 (mmt180) REVERT: K 433 MET cc_start: 0.8817 (mmm) cc_final: 0.8227 (mmm) REVERT: L 369 CYS cc_start: 0.6286 (OUTLIER) cc_final: 0.5990 (p) REVERT: L 382 ARG cc_start: 0.5782 (OUTLIER) cc_final: 0.4628 (mtm180) REVERT: L 403 GLU cc_start: 0.8983 (pt0) cc_final: 0.8594 (pm20) REVERT: L 433 MET cc_start: 0.6260 (mpm) cc_final: 0.5246 (tmm) REVERT: L 443 PHE cc_start: 0.7559 (m-80) cc_final: 0.6769 (t80) outliers start: 101 outliers final: 47 residues processed: 294 average time/residue: 0.5977 time to fit residues: 197.5207 Evaluate side-chains 261 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 202 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 483 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 323 CYS Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 264 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain L residue 369 CYS Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 382 ARG Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 85 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 223 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 203 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 11 optimal weight: 0.0870 chunk 191 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 ASN ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 ASN G 249 HIS K 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.133853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.098760 restraints weight = 46023.076| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.31 r_work: 0.3450 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18661 Z= 0.129 Angle : 0.738 11.430 25631 Z= 0.354 Chirality : 0.044 0.283 3068 Planarity : 0.005 0.054 3273 Dihedral : 5.122 27.109 2596 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.06 % Allowed : 22.27 % Favored : 72.67 % 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: -1.96 (0.16), residues: 2437 helix: -1.48 (0.47), residues: 123 sheet: 0.03 (0.18), residues: 798 loop : -2.16 (0.15), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 336 TYR 0.011 0.001 TYR C 148 PHE 0.021 0.001 PHE K 345 TRP 0.022 0.001 TRP B 281 HIS 0.008 0.001 HIS F 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (18614) covalent geometry : angle 0.73134 / 0.35 (25527) SS BOND : bond 0.00351 / 0.29 ( 37) SS BOND : angle 1.24022 / 0.83 ( 74) hydrogen bonds : bond 0.03135 / 2.06 ( 450) hydrogen bonds : angle 4.86487 / 3.34 ( 1398) link_BETA1-4 : bond 0.00330 / 0.17 ( 3) link_BETA1-4 : angle 2.27153 / 1.07 ( 9) link_NAG-ASN : bond 0.00450 / 0.20 ( 7) link_NAG-ASN : angle 2.60517 / 2.03 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 236 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.9212 (pt0) cc_final: 0.8810 (pt0) REVERT: A 425 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9242 (ttmt) REVERT: B 255 ASP cc_start: 0.9041 (m-30) cc_final: 0.8752 (m-30) REVERT: B 265 THR cc_start: 0.7755 (OUTLIER) cc_final: 0.7501 (t) REVERT: B 327 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6492 (t70) REVERT: B 385 GLN cc_start: 0.9078 (tp40) cc_final: 0.8802 (tp40) REVERT: B 403 GLU cc_start: 0.8650 (pt0) cc_final: 0.8199 (pm20) REVERT: B 428 GLU cc_start: 0.8478 (mp0) cc_final: 0.7969 (mp0) REVERT: B 464 MET cc_start: 0.6774 (ppp) cc_final: 0.6446 (ppp) REVERT: C 43 ARG cc_start: 0.6912 (mmp80) cc_final: 0.6652 (mmp-170) REVERT: C 330 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8829 (pp20) REVERT: C 357 ARG cc_start: 0.8564 (mtp-110) cc_final: 0.8187 (mtp180) REVERT: F 340 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7940 (ttmt) REVERT: F 346 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8080 (ptt-90) REVERT: F 358 GLU cc_start: 0.9101 (tt0) cc_final: 0.8805 (tt0) REVERT: G 348 GLU cc_start: 0.8178 (mp0) cc_final: 0.7764 (mp0) REVERT: G 393 GLU cc_start: 0.8907 (pm20) cc_final: 0.8673 (pm20) REVERT: G 394 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8555 (mmmt) REVERT: E 445 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6597 (tm-30) REVERT: E 448 ILE cc_start: 0.6448 (OUTLIER) cc_final: 0.5994 (pp) REVERT: H 315 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.8185 (t60) REVERT: H 385 GLN cc_start: 0.9396 (tt0) cc_final: 0.9134 (tp-100) REVERT: H 403 GLU cc_start: 0.8298 (pt0) cc_final: 0.7422 (pm20) REVERT: H 433 MET cc_start: 0.8664 (tpp) cc_final: 0.8150 (mmm) REVERT: K 338 ILE cc_start: 0.5606 (OUTLIER) cc_final: 0.5278 (mt) REVERT: K 348 GLU cc_start: 0.7172 (mp0) cc_final: 0.6744 (mp0) REVERT: K 358 GLU cc_start: 0.8246 (pt0) cc_final: 0.7894 (pt0) REVERT: K 378 ASP cc_start: 0.7902 (m-30) cc_final: 0.7573 (m-30) REVERT: K 403 GLU cc_start: 0.7376 (pt0) cc_final: 0.7029 (pt0) REVERT: K 418 ARG cc_start: 0.6646 (mtt180) cc_final: 0.6338 (mmt180) REVERT: K 433 MET cc_start: 0.8791 (mmm) cc_final: 0.8146 (mmm) REVERT: L 369 CYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6347 (p) REVERT: L 403 GLU cc_start: 0.8810 (pt0) cc_final: 0.8472 (pm20) REVERT: L 433 MET cc_start: 0.6185 (mpm) cc_final: 0.5306 (mtp) outliers start: 95 outliers final: 44 residues processed: 298 average time/residue: 0.5738 time to fit residues: 193.3238 Evaluate side-chains 263 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 209 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 458 ILE Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 445 GLN Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 315 TRP Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 396 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 335 THR Chi-restraints excluded: chain L residue 369 CYS Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 105 optimal weight: 0.0050 chunk 82 optimal weight: 0.4980 chunk 84 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 187 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 201 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS G 249 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.133353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098393 restraints weight = 46221.799| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 4.34 r_work: 0.3451 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18661 Z= 0.132 Angle : 0.728 11.391 25631 Z= 0.351 Chirality : 0.043 0.273 3068 Planarity : 0.005 0.068 3273 Dihedral : 4.965 25.400 2596 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.58 % Allowed : 23.60 % Favored : 71.82 % 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: -1.80 (0.17), residues: 2437 helix: -1.32 (0.48), residues: 123 sheet: 0.13 (0.18), residues: 799 loop : -2.05 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 336 TYR 0.010 0.001 TYR C 148 PHE 0.019 0.001 PHE K 345 TRP 0.021 0.001 TRP B 281 HIS 0.023 0.001 HIS G 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (18614) covalent geometry : angle 0.72188 / 0.35 (25527) SS BOND : bond 0.00336 / 0.26 ( 37) SS BOND : angle 1.14115 / 0.72 ( 74) hydrogen bonds : bond 0.03128 / 2.06 ( 450) hydrogen bonds : angle 4.79291 / 3.29 ( 1398) link_BETA1-4 : bond 0.00289 / 0.15 ( 3) link_BETA1-4 : angle 2.11959 / 1.01 ( 9) link_NAG-ASN : bond 0.00448 / 0.20 ( 7) link_NAG-ASN : angle 2.52344 / 1.97 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 218 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.9201 (pt0) cc_final: 0.8793 (pt0) REVERT: A 425 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.9269 (ttmt) REVERT: B 255 ASP cc_start: 0.9036 (m-30) cc_final: 0.8741 (m-30) REVERT: B 265 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7550 (t) REVERT: B 327 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6528 (t70) REVERT: B 385 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8793 (tp40) REVERT: B 403 GLU cc_start: 0.8660 (pt0) cc_final: 0.8205 (pm20) REVERT: B 423 ASP cc_start: 0.9011 (m-30) cc_final: 0.8796 (m-30) REVERT: B 428 GLU cc_start: 0.8491 (mp0) cc_final: 0.7754 (mp0) REVERT: C 43 ARG cc_start: 0.6895 (mmp80) cc_final: 0.6675 (mmp-170) REVERT: C 330 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8839 (pp20) REVERT: C 424 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6809 (pp) REVERT: D 76 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9033 (mm-30) REVERT: F 340 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7977 (ttmt) REVERT: F 346 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8117 (ptt-90) REVERT: F 403 GLU cc_start: 0.9057 (pt0) cc_final: 0.8847 (pt0) REVERT: G 348 GLU cc_start: 0.8227 (mp0) cc_final: 0.7788 (mp0) REVERT: G 394 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8552 (mmtp) REVERT: E 448 ILE cc_start: 0.6479 (OUTLIER) cc_final: 0.5722 (mp) REVERT: H 368 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.8001 (t) REVERT: H 403 GLU cc_start: 0.8295 (pt0) cc_final: 0.7461 (pm20) REVERT: H 433 MET cc_start: 0.8616 (tpp) cc_final: 0.8327 (mmm) REVERT: K 317 HIS cc_start: 0.7868 (p-80) cc_final: 0.7651 (p-80) REVERT: K 338 ILE cc_start: 0.5700 (OUTLIER) cc_final: 0.5358 (mt) REVERT: K 358 GLU cc_start: 0.8270 (pt0) cc_final: 0.7912 (pt0) REVERT: K 378 ASP cc_start: 0.7943 (m-30) cc_final: 0.7634 (m-30) REVERT: K 403 GLU cc_start: 0.7413 (pt0) cc_final: 0.7084 (pt0) REVERT: K 418 ARG cc_start: 0.6748 (mtt180) cc_final: 0.6441 (mmt180) REVERT: K 433 MET cc_start: 0.8730 (mmm) cc_final: 0.8119 (mmm) REVERT: L 369 CYS cc_start: 0.6563 (OUTLIER) cc_final: 0.6341 (p) REVERT: L 401 ARG cc_start: 0.7356 (mmt-90) cc_final: 0.6990 (mmt180) REVERT: L 403 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8437 (pm20) REVERT: L 433 MET cc_start: 0.6288 (mpm) cc_final: 0.5833 (mmt) outliers start: 86 outliers final: 49 residues processed: 278 average time/residue: 0.5799 time to fit residues: 182.1425 Evaluate side-chains 264 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain G residue 249 HIS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain K residue 290 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 369 CYS Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 403 GLU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 230 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 227 optimal weight: 0.0170 chunk 167 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 143 optimal weight: 4.9990 chunk 1 optimal weight: 0.0040 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 overall best weight: 0.7770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS H 291 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.133480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.098610 restraints weight = 46489.410| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 4.36 r_work: 0.3457 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18661 Z= 0.128 Angle : 0.738 11.382 25631 Z= 0.356 Chirality : 0.043 0.273 3068 Planarity : 0.005 0.069 3273 Dihedral : 4.843 23.197 2596 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 4.42 % Allowed : 24.24 % Favored : 71.34 % 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: -1.70 (0.17), residues: 2437 helix: -1.19 (0.48), residues: 124 sheet: 0.20 (0.18), residues: 785 loop : -1.98 (0.15), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 336 TYR 0.010 0.001 TYR C 148 PHE 0.018 0.001 PHE K 345 TRP 0.020 0.001 TRP B 281 HIS 0.010 0.001 HIS H 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (18614) covalent geometry : angle 0.73152 / 0.35 (25527) SS BOND : bond 0.00326 / 0.24 ( 37) SS BOND : angle 1.28679 / 0.70 ( 74) hydrogen bonds : bond 0.02992 / 1.98 ( 450) hydrogen bonds : angle 4.70228 / 3.24 ( 1398) link_BETA1-4 : bond 0.00326 / 0.16 ( 3) link_BETA1-4 : angle 2.02752 / 0.96 ( 9) link_NAG-ASN : bond 0.00447 / 0.20 ( 7) link_NAG-ASN : angle 2.44363 / 1.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 224 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 403 GLU cc_start: 0.9188 (pt0) cc_final: 0.8790 (pt0) REVERT: A 425 LYS cc_start: 0.9543 (OUTLIER) cc_final: 0.9269 (ttmt) REVERT: B 255 ASP cc_start: 0.9027 (m-30) cc_final: 0.8737 (m-30) REVERT: B 265 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7564 (t) REVERT: B 327 HIS cc_start: 0.7318 (OUTLIER) cc_final: 0.6496 (t70) REVERT: B 385 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8792 (tp40) REVERT: B 403 GLU cc_start: 0.8602 (pt0) cc_final: 0.8165 (pm20) REVERT: B 428 GLU cc_start: 0.8497 (mp0) cc_final: 0.7781 (mp0) REVERT: B 464 MET cc_start: 0.6679 (ppp) cc_final: 0.6294 (ppp) REVERT: C 43 ARG cc_start: 0.6879 (mmp80) cc_final: 0.6673 (mmp-170) REVERT: C 217 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5603 (tp) REVERT: C 330 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8813 (pp20) REVERT: C 424 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6628 (pp) REVERT: D 76 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9045 (mm-30) REVERT: F 340 LYS cc_start: 0.8254 (ttmt) cc_final: 0.7996 (ttmt) REVERT: F 403 GLU cc_start: 0.9061 (pt0) cc_final: 0.8861 (pt0) REVERT: G 348 GLU cc_start: 0.8250 (mp0) cc_final: 0.7834 (mp0) REVERT: E 352 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8341 (mm) REVERT: E 448 ILE cc_start: 0.6573 (OUTLIER) cc_final: 0.5822 (mp) REVERT: H 368 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8038 (t) REVERT: H 385 GLN cc_start: 0.9376 (tt0) cc_final: 0.9036 (tp-100) REVERT: H 403 GLU cc_start: 0.8302 (pt0) cc_final: 0.7451 (pm20) REVERT: H 433 MET cc_start: 0.8556 (tpp) cc_final: 0.8251 (mmm) REVERT: K 338 ILE cc_start: 0.5733 (OUTLIER) cc_final: 0.5393 (mt) REVERT: K 358 GLU cc_start: 0.8282 (pt0) cc_final: 0.7960 (pt0) REVERT: K 378 ASP cc_start: 0.7961 (m-30) cc_final: 0.7665 (m-30) REVERT: K 403 GLU cc_start: 0.7433 (pt0) cc_final: 0.7091 (pt0) REVERT: K 418 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6528 (mmt180) REVERT: K 433 MET cc_start: 0.8724 (mmm) cc_final: 0.8133 (mmm) REVERT: L 401 ARG cc_start: 0.7428 (mmt-90) cc_final: 0.7055 (mmt90) REVERT: L 403 GLU cc_start: 0.8727 (pt0) cc_final: 0.8456 (pm20) REVERT: L 433 MET cc_start: 0.6262 (mpm) cc_final: 0.5822 (mmt) outliers start: 83 outliers final: 47 residues processed: 281 average time/residue: 0.5975 time to fit residues: 188.5294 Evaluate side-chains 270 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 212 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 359 LEU Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 378 ASP Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 172 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 212 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 208 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 291 GLN B 343 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.131591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.096959 restraints weight = 45943.366| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 4.28 r_work: 0.3407 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18661 Z= 0.166 Angle : 0.768 10.343 25631 Z= 0.374 Chirality : 0.044 0.264 3068 Planarity : 0.005 0.074 3273 Dihedral : 4.984 31.848 2596 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.94 % Allowed : 25.79 % Favored : 70.27 % 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: -1.76 (0.17), residues: 2437 helix: -1.19 (0.46), residues: 129 sheet: 0.15 (0.18), residues: 812 loop : -2.05 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 336 TYR 0.012 0.001 TYR C 148 PHE 0.019 0.002 PHE K 345 TRP 0.018 0.001 TRP B 281 HIS 0.014 0.001 HIS K 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (18614) covalent geometry : angle 0.76102 / 0.37 (25527) SS BOND : bond 0.00401 / 0.31 ( 37) SS BOND : angle 1.43975 / 0.84 ( 74) hydrogen bonds : bond 0.03431 / 2.29 ( 450) hydrogen bonds : angle 4.79458 / 3.31 ( 1398) link_BETA1-4 : bond 0.00336 / 0.17 ( 3) link_BETA1-4 : angle 1.98068 / 0.97 ( 9) link_NAG-ASN : bond 0.00522 / 0.24 ( 7) link_NAG-ASN : angle 2.49583 / 1.93 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8198 (tm-30) REVERT: A 403 GLU cc_start: 0.9202 (pt0) cc_final: 0.8737 (pt0) REVERT: A 425 LYS cc_start: 0.9557 (OUTLIER) cc_final: 0.9303 (ttmt) REVERT: A 457 HIS cc_start: 0.7506 (OUTLIER) cc_final: 0.7268 (p90) REVERT: B 255 ASP cc_start: 0.9060 (m-30) cc_final: 0.8782 (m-30) REVERT: B 265 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7620 (t) REVERT: B 385 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8784 (tp40) REVERT: B 392 ARG cc_start: 0.9093 (mmm-85) cc_final: 0.8683 (ttp-110) REVERT: B 403 GLU cc_start: 0.8671 (pt0) cc_final: 0.8212 (pm20) REVERT: B 428 GLU cc_start: 0.8493 (mp0) cc_final: 0.7694 (mp0) REVERT: B 464 MET cc_start: 0.7238 (ppp) cc_final: 0.6830 (ppp) REVERT: C 191 GLN cc_start: 0.5525 (mt0) cc_final: 0.5307 (mp10) REVERT: C 330 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8829 (pp20) REVERT: C 424 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6744 (pp) REVERT: D 71 LYS cc_start: 0.8383 (mtmm) cc_final: 0.7949 (ptmm) REVERT: D 76 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9098 (mm-30) REVERT: F 340 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7998 (ttmt) REVERT: G 348 GLU cc_start: 0.8332 (mp0) cc_final: 0.7894 (mp0) REVERT: E 352 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8421 (mm) REVERT: E 448 ILE cc_start: 0.6758 (OUTLIER) cc_final: 0.6037 (mp) REVERT: H 368 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8112 (t) REVERT: H 385 GLN cc_start: 0.9377 (tt0) cc_final: 0.9005 (tp-100) REVERT: H 433 MET cc_start: 0.8607 (tpp) cc_final: 0.8229 (mmm) REVERT: K 338 ILE cc_start: 0.5834 (OUTLIER) cc_final: 0.5493 (mt) REVERT: K 340 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7791 (ttmm) REVERT: K 358 GLU cc_start: 0.8372 (pt0) cc_final: 0.8000 (pt0) REVERT: K 378 ASP cc_start: 0.8022 (m-30) cc_final: 0.7718 (m-30) REVERT: K 403 GLU cc_start: 0.7596 (pt0) cc_final: 0.7280 (pt0) REVERT: K 418 ARG cc_start: 0.7055 (mtt180) cc_final: 0.6730 (mmt180) REVERT: K 433 MET cc_start: 0.8707 (mmm) cc_final: 0.8099 (mmm) REVERT: L 401 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.7228 (mmt180) REVERT: L 403 GLU cc_start: 0.8776 (pt0) cc_final: 0.8461 (pm20) REVERT: L 433 MET cc_start: 0.6245 (mpm) cc_final: 0.5951 (mmt) outliers start: 74 outliers final: 44 residues processed: 272 average time/residue: 0.6299 time to fit residues: 192.0519 Evaluate side-chains 260 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 425 LYS Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 461 SER Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 284 SER Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 136 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 95 optimal weight: 0.0370 chunk 73 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 GLN H 291 GLN ** K 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.132714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.098114 restraints weight = 45966.943| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 4.32 r_work: 0.3428 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18661 Z= 0.132 Angle : 0.755 10.753 25631 Z= 0.367 Chirality : 0.044 0.272 3068 Planarity : 0.005 0.073 3273 Dihedral : 4.760 29.802 2596 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.36 % Allowed : 26.90 % Favored : 69.74 % 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: -1.63 (0.17), residues: 2437 helix: -1.02 (0.47), residues: 129 sheet: 0.20 (0.18), residues: 795 loop : -1.91 (0.16), residues: 1513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 336 TYR 0.010 0.001 TYR G 395 PHE 0.019 0.001 PHE K 345 TRP 0.021 0.001 TRP B 281 HIS 0.020 0.001 HIS K 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.13 (18614) covalent geometry : angle 0.75026 / 0.37 (25527) SS BOND : bond 0.00282 / 0.22 ( 37) SS BOND : angle 1.20393 / 0.72 ( 74) hydrogen bonds : bond 0.02998 / 1.98 ( 450) hydrogen bonds : angle 4.63894 / 3.20 ( 1398) link_BETA1-4 : bond 0.00373 / 0.19 ( 3) link_BETA1-4 : angle 1.87974 / 0.89 ( 9) link_NAG-ASN : bond 0.00433 / 0.18 ( 7) link_NAG-ASN : angle 2.33517 / 1.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8174 (tm-30) REVERT: A 403 GLU cc_start: 0.9194 (pt0) cc_final: 0.8760 (pt0) REVERT: A 457 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7209 (p90) REVERT: B 255 ASP cc_start: 0.9045 (m-30) cc_final: 0.8763 (m-30) REVERT: B 265 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7567 (t) REVERT: B 327 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6535 (t70) REVERT: B 385 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8768 (tp40) REVERT: B 392 ARG cc_start: 0.9073 (mmm-85) cc_final: 0.8790 (ttp-110) REVERT: B 403 GLU cc_start: 0.8696 (pt0) cc_final: 0.8241 (pm20) REVERT: B 428 GLU cc_start: 0.8451 (mp0) cc_final: 0.8024 (mp0) REVERT: C 330 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8795 (pp20) REVERT: C 424 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6801 (pp) REVERT: D 71 LYS cc_start: 0.8344 (mtmm) cc_final: 0.8102 (ptmm) REVERT: D 76 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9098 (mm-30) REVERT: D 89 SER cc_start: 0.9482 (OUTLIER) cc_final: 0.9151 (t) REVERT: F 340 LYS cc_start: 0.8261 (ttmt) cc_final: 0.8011 (ttmt) REVERT: F 358 GLU cc_start: 0.9092 (tt0) cc_final: 0.8671 (tt0) REVERT: F 402 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: G 348 GLU cc_start: 0.8320 (mp0) cc_final: 0.7876 (mp0) REVERT: E 352 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8340 (mm) REVERT: E 448 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6331 (mp) REVERT: H 368 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8156 (t) REVERT: H 385 GLN cc_start: 0.9381 (tt0) cc_final: 0.8952 (tp40) REVERT: H 433 MET cc_start: 0.8514 (tpp) cc_final: 0.8236 (mmm) REVERT: K 338 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5509 (mt) REVERT: K 358 GLU cc_start: 0.8360 (pt0) cc_final: 0.8112 (pt0) REVERT: K 378 ASP cc_start: 0.7996 (m-30) cc_final: 0.7713 (m-30) REVERT: K 401 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7072 (mtt90) REVERT: K 403 GLU cc_start: 0.7560 (pt0) cc_final: 0.7303 (pt0) REVERT: K 418 ARG cc_start: 0.7076 (mtt180) cc_final: 0.6834 (mmt180) REVERT: K 433 MET cc_start: 0.8696 (mmm) cc_final: 0.8056 (mmm) REVERT: L 401 ARG cc_start: 0.7445 (mmt-90) cc_final: 0.7174 (mmt180) REVERT: L 403 GLU cc_start: 0.8741 (pt0) cc_final: 0.8444 (pm20) REVERT: L 433 MET cc_start: 0.6494 (mpm) cc_final: 0.5986 (mmt) outliers start: 63 outliers final: 42 residues processed: 261 average time/residue: 0.6147 time to fit residues: 180.2952 Evaluate side-chains 264 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 210 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 457 HIS Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 261 CYS Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 257 LEU Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain K residue 247 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 24 optimal weight: 7.9990 chunk 156 optimal weight: 0.1980 chunk 236 optimal weight: 0.9980 chunk 182 optimal weight: 0.0970 chunk 187 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 7 optimal weight: 0.4980 chunk 230 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN ** B 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS F 388 GLN H 291 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.133199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.098745 restraints weight = 46201.776| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 4.32 r_work: 0.3459 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18661 Z= 0.127 Angle : 0.756 11.265 25631 Z= 0.365 Chirality : 0.043 0.272 3068 Planarity : 0.005 0.079 3273 Dihedral : 4.601 29.556 2596 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 3.36 % Allowed : 27.44 % Favored : 69.21 % 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: -1.49 (0.17), residues: 2437 helix: -0.92 (0.47), residues: 130 sheet: 0.29 (0.18), residues: 799 loop : -1.82 (0.16), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 336 TYR 0.009 0.001 TYR B 472 PHE 0.017 0.001 PHE K 345 TRP 0.022 0.001 TRP H 315 HIS 0.012 0.001 HIS H 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (18614) covalent geometry : angle 0.75173 / 0.36 (25527) SS BOND : bond 0.00299 / 0.22 ( 37) SS BOND : angle 1.07343 / 0.63 ( 74) hydrogen bonds : bond 0.02923 / 1.92 ( 450) hydrogen bonds : angle 4.50256 / 3.10 ( 1398) link_BETA1-4 : bond 0.00419 / 0.21 ( 3) link_BETA1-4 : angle 1.73815 / 0.84 ( 9) link_NAG-ASN : bond 0.00436 / 0.18 ( 7) link_NAG-ASN : angle 2.23833 / 1.81 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4874 Ramachandran restraints generated. 2437 Oldfield, 0 Emsley, 2437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 225 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 403 GLU cc_start: 0.9228 (pt0) cc_final: 0.8778 (pt0) REVERT: B 255 ASP cc_start: 0.9006 (m-30) cc_final: 0.8726 (m-30) REVERT: B 265 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7560 (t) REVERT: B 392 ARG cc_start: 0.9035 (mmm-85) cc_final: 0.8825 (ttp-110) REVERT: B 403 GLU cc_start: 0.8663 (pt0) cc_final: 0.8223 (pm20) REVERT: B 428 GLU cc_start: 0.8418 (mp0) cc_final: 0.8000 (mp0) REVERT: C 330 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8813 (pp20) REVERT: C 424 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6765 (pp) REVERT: C 429 THR cc_start: 0.8329 (m) cc_final: 0.8043 (p) REVERT: C 447 LYS cc_start: 0.8666 (mttm) cc_final: 0.8257 (mptp) REVERT: D 76 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9139 (mm-30) REVERT: D 89 SER cc_start: 0.9444 (OUTLIER) cc_final: 0.9121 (t) REVERT: F 340 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7997 (ttmt) REVERT: F 358 GLU cc_start: 0.9099 (tt0) cc_final: 0.8676 (tt0) REVERT: F 402 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: G 348 GLU cc_start: 0.8309 (mp0) cc_final: 0.7891 (mp0) REVERT: E 352 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8305 (mm) REVERT: E 403 GLU cc_start: 0.8382 (pp20) cc_final: 0.8143 (pt0) REVERT: E 418 ARG cc_start: 0.8627 (mmm-85) cc_final: 0.8410 (tpp80) REVERT: E 448 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6367 (mp) REVERT: H 266 CYS cc_start: 0.6411 (OUTLIER) cc_final: 0.5154 (p) REVERT: H 368 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8188 (t) REVERT: H 385 GLN cc_start: 0.9372 (tt0) cc_final: 0.9008 (tp-100) REVERT: H 403 GLU cc_start: 0.8425 (pt0) cc_final: 0.8038 (pm20) REVERT: H 433 MET cc_start: 0.8442 (tpp) cc_final: 0.8050 (mmm) REVERT: K 317 HIS cc_start: 0.8307 (p-80) cc_final: 0.8058 (p-80) REVERT: K 338 ILE cc_start: 0.5784 (OUTLIER) cc_final: 0.5469 (mt) REVERT: K 358 GLU cc_start: 0.8368 (pt0) cc_final: 0.8096 (pt0) REVERT: K 378 ASP cc_start: 0.7998 (m-30) cc_final: 0.7714 (m-30) REVERT: K 385 GLN cc_start: 0.8585 (tp40) cc_final: 0.8262 (mm110) REVERT: K 403 GLU cc_start: 0.7620 (pt0) cc_final: 0.7080 (pm20) REVERT: K 418 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6862 (mmt180) REVERT: K 433 MET cc_start: 0.8601 (mmm) cc_final: 0.8086 (mmm) REVERT: L 401 ARG cc_start: 0.7493 (mmt-90) cc_final: 0.6595 (mmt180) REVERT: L 403 GLU cc_start: 0.8755 (pt0) cc_final: 0.8326 (pm20) REVERT: L 411 TYR cc_start: 0.6555 (m-10) cc_final: 0.6204 (m-10) REVERT: L 433 MET cc_start: 0.6441 (mpm) cc_final: 0.5779 (mmt) outliers start: 63 outliers final: 41 residues processed: 267 average time/residue: 0.5939 time to fit residues: 178.1265 Evaluate side-chains 265 residues out of total 2113 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain C residue 122 TYR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 330 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 114 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 388 GLN Chi-restraints excluded: chain F residue 402 GLN Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 370 LEU Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 323 CYS Chi-restraints excluded: chain H residue 334 LEU Chi-restraints excluded: chain H residue 345 PHE Chi-restraints excluded: chain H residue 365 VAL Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain K residue 247 SER Chi-restraints excluded: chain K residue 338 ILE Chi-restraints excluded: chain K residue 365 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 381 VAL Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 462 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 25 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 127 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 457 HIS B 343 ASN B 385 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 249 HIS H 291 GLN H 385 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.128980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094757 restraints weight = 46592.330| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 4.29 r_work: 0.3369 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 18661 Z= 0.244 Angle : 0.851 12.531 25631 Z= 0.417 Chirality : 0.047 0.252 3068 Planarity : 0.005 0.082 3273 Dihedral : 5.213 31.122 2596 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.14 % Allowed : 27.76 % Favored : 69.10 % 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: -1.71 (0.17), residues: 2437 helix: -1.12 (0.45), residues: 130 sheet: 0.11 (0.18), residues: 800 loop : -1.95 (0.15), residues: 1507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 336 TYR 0.015 0.002 TYR C 148 PHE 0.023 0.002 PHE K 345 TRP 0.022 0.002 TRP H 315 HIS 0.007 0.001 HIS H 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.24 (18614) covalent geometry : angle 0.84416 / 0.41 (25527) SS BOND : bond 0.00490 / 0.38 ( 37) SS BOND : angle 1.59585 / 0.92 ( 74) hydrogen bonds : bond 0.04050 / 2.73 ( 450) hydrogen bonds : angle 5.01661 / 3.47 ( 1398) link_BETA1-4 : bond 0.00539 / 0.27 ( 3) link_BETA1-4 : angle 1.85843 / 0.98 ( 9) link_NAG-ASN : bond 0.00651 / 0.32 ( 7) link_NAG-ASN : angle 2.51767 / 1.91 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7689.99 seconds wall clock time: 131 minutes 26.46 seconds (7886.46 seconds total)