Starting phenix.real_space_refine on Sun Sep 13 06:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.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 { model { file = "/net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uea_20752/09_2026/6uea_20752.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= -0.014 sd= 0.421 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 112 5.16 5 C 13427 2.51 5 N 3672 2.21 5 O 4088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 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: 21299 Number of models: 1 Model: "" Number of chains: 20 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: 4118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4118 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 507} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1038 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1656 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "G" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1666 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 8, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "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: "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: "I" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1536 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 11, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 98 Chain: "J" Number of atoms: 1476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1476 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 18, 'TRANS': 199} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 7, 'GLU:plan': 11, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 120 Chain: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "C" 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 Time building chain proxies: 5.13, per 1000 atoms: 0.24 Number of scatterers: 21299 At special positions: 0 Unit cell: (190.516, 156.895, 174.215, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4088 8.00 N 3672 7.00 C 13427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.05 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=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS D 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.01 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 239 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 253 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 367 " - pdb=" SG CYS C 377 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 485 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS D 72 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 134 " distance=2.04 Simple disulfide: pdb=" SG CYS F 242 " - pdb=" SG CYS G 299 " distance=2.04 Simple disulfide: pdb=" SG CYS F 266 " - pdb=" SG CYS F 323 " distance=2.04 Simple disulfide: pdb=" SG CYS F 299 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 369 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 266 " - pdb=" SG CYS G 323 " distance=2.04 Simple disulfide: pdb=" SG CYS G 369 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 471 " - pdb=" SG CYS E 471 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 Simple disulfide: pdb=" SG CYS L 369 " - pdb=" SG CYS L 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 369 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS H 266 " - pdb=" SG CYS H 323 " distance=2.04 Simple disulfide: pdb=" SG CYS H 369 " - pdb=" SG CYS H 432 " distance=2.04 Simple disulfide: pdb=" SG CYS I 242 " - pdb=" SG CYS J 299 " distance=2.03 Simple disulfide: pdb=" SG CYS I 266 " - pdb=" SG CYS I 323 " distance=2.04 Simple disulfide: pdb=" SG CYS I 299 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 369 " - pdb=" SG CYS I 432 " distance=2.03 Simple disulfide: pdb=" SG CYS J 266 " - pdb=" SG CYS J 323 " distance=2.03 Simple disulfide: pdb=" SG CYS J 369 " - pdb=" SG CYS J 432 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " NAG-ASN " NAG C 603 " - " ASN C 65 " " NAG C 606 " - " ASN C 403 " " NAG M 1 " - " ASN A 337 " " NAG N 1 " - " ASN B 337 " " NAG O 1 " - " ASN C 72 " " NAG P 1 " - " ASN C 451 " " NAG Q 1 " - " ASN D 49 " " NAG R 1 " - " ASN F 337 " " NAG S 1 " - " ASN G 337 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 873.0 milliseconds 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5410 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 66 sheets defined 9.7% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 391 through 395 removed outlier: 3.933A pdb=" N TYR A 395 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 426 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 357 through 362 removed outlier: 3.935A pdb=" N LEU B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.178A 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 421 through 427 removed outlier: 3.861A pdb=" N LYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 removed outlier: 3.805A pdb=" N HIS C 32 " --> pdb=" O SER C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 removed outlier: 3.762A pdb=" N SER C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.713A pdb=" N GLU C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 removed outlier: 3.688A pdb=" N ASP C 417 " --> pdb=" O THR C 414 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 418 " --> pdb=" O SER C 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 418' Processing helix chain 'C' and resid 467 through 471 removed outlier: 3.841A pdb=" N SER C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 removed outlier: 4.050A pdb=" N ASP C 520 " --> pdb=" O THR C 517 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 521 " --> pdb=" O ARG C 518 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 517 through 521' Processing helix chain 'D' and resid 64 through 69 Processing helix chain 'F' and resid 253 through 258 Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 357 through 362 removed outlier: 3.960A pdb=" N LEU F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 357 through 362' 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: 3.801A pdb=" N GLY F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 355 through 360 Processing helix chain 'G' and resid 421 through 427 removed outlier: 3.878A pdb=" N GLY G 427 " --> pdb=" O ASP G 423 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 311 through 318 removed outlier: 3.541A pdb=" N TRP K 315 " --> pdb=" O CYS K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 331 removed outlier: 3.549A pdb=" N LEU K 330 " --> pdb=" O HIS K 327 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS K 331 " --> pdb=" O PRO K 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 327 through 331' Processing helix chain 'K' and resid 356 through 362 removed outlier: 3.728A pdb=" N LEU K 361 " --> pdb=" O GLU K 357 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN K 362 " --> pdb=" O GLU K 358 " (cutoff:3.500A) Processing helix chain 'K' and resid 421 through 427 Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 311 through 316 removed outlier: 4.147A pdb=" N TRP L 315 " --> pdb=" O CYS L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 360 Processing helix chain 'L' and resid 391 through 393 No H-bonds generated for 'chain 'L' and resid 391 through 393' Processing helix chain 'L' and resid 421 through 427 removed outlier: 3.555A pdb=" N GLY L 427 " --> pdb=" O ASP L 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 Processing helix chain 'E' and resid 312 through 317 removed outlier: 3.535A pdb=" N TRP E 315 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASN E 316 " --> pdb=" O GLN E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 427 Processing helix chain 'H' and resid 252 through 256 Processing helix chain 'H' and resid 312 through 317 Processing helix chain 'H' and resid 421 through 427 removed outlier: 3.989A pdb=" N LYS H 425 " --> pdb=" O ALA H 421 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 258 Processing helix chain 'I' and resid 311 through 317 Processing helix chain 'I' and resid 356 through 360 removed outlier: 3.930A pdb=" N LEU I 359 " --> pdb=" O SER I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 427 Processing helix chain 'J' and resid 252 through 257 removed outlier: 3.985A pdb=" N LEU J 256 " --> pdb=" O ALA J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 317 removed outlier: 4.206A pdb=" N HIS J 317 " --> pdb=" O PRO J 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 355 through 360 removed outlier: 4.278A pdb=" N LEU J 359 " --> pdb=" O PRO J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 420 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 248 through 249 removed outlier: 4.030A pdb=" N THR A 265 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 280 through 281 Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.836A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 348 through 352 removed outlier: 3.836A pdb=" N THR A 368 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N TYR A 411 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR A 410 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 388 through 389 removed outlier: 3.555A pdb=" N SER A 431 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 446 " --> pdb=" O CYS A 432 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63 removed outlier: 8.471A pdb=" N PHE D 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N SER B 461 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N TYR D 63 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 463 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N HIS A 457 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL B 460 " --> pdb=" O HIS A 457 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN A 459 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL B 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 461 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N MET B 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 463 " --> pdb=" O MET B 464 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE K 458 " --> pdb=" O HIS L 457 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL I 463 " --> pdb=" O VAL L 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 245 through 249 removed outlier: 3.873A pdb=" N SER B 247 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B 249 " --> pdb=" O THR B 265 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS B 266 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY B 270 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR B 302 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 279 removed outlier: 3.632A pdb=" N ALA B 326 " --> pdb=" O THR B 278 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 320 through 323 removed outlier: 3.584A pdb=" N PHE B 321 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.599A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.599A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB5, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.241A pdb=" N VAL C 10 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N SER C 110 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER C 12 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 103 " --> pdb=" O CYS C 92 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS C 38 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY C 93 " --> pdb=" O TYR C 36 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR C 36 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N TRP C 37 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 18 through 23 removed outlier: 3.618A pdb=" N ILE C 79 " --> pdb=" O VAL C 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 122 through 124 removed outlier: 7.001A pdb=" N TYR C 122 " --> pdb=" O GLN C 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 removed outlier: 3.883A pdb=" N VAL C 130 " --> pdb=" O ILE C 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 147 through 151 removed outlier: 6.991A pdb=" N LEU C 147 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.598A pdb=" N ASP C 176 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 200 through 202 removed outlier: 3.534A pdb=" N CYS C 202 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 225 through 229 removed outlier: 3.521A pdb=" N GLY C 308 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 249 " --> pdb=" O HIS C 310 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS C 250 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN C 266 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU C 252 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.666A pdb=" N VAL C 292 " --> pdb=" O PHE C 237 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N CYS C 239 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE C 290 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 340 through 341 removed outlier: 6.534A pdb=" N LYS C 364 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASP C 382 " --> pdb=" O LYS C 364 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TRP C 366 " --> pdb=" O LEU C 380 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 349 through 354 removed outlier: 3.509A pdb=" N LEU C 410 " --> pdb=" O VAL C 349 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 408 " --> pdb=" O VAL C 351 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 405 " --> pdb=" O GLU C 400 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N GLU C 400 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 396 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 474 through 480 removed outlier: 3.772A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 478 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP C 523 " --> pdb=" O TRP C 480 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N PHE C 533 " --> pdb=" O GLN C 530 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 474 through 480 removed outlier: 3.772A pdb=" N TYR C 476 " --> pdb=" O GLY C 527 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS C 478 " --> pdb=" O TRP C 525 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N TRP C 523 " --> pdb=" O TRP C 480 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 6 through 11 removed outlier: 3.513A pdb=" N ILE D 6 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE D 18 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP D 10 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ALA D 16 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 23 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE D 33 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE F 458 " --> pdb=" O ASN G 459 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N SER G 461 " --> pdb=" O ILE F 458 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL F 460 " --> pdb=" O SER G 461 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL G 463 " --> pdb=" O VAL F 460 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL F 462 " --> pdb=" O VAL G 463 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 75 through 77 Processing sheet with id=AD2, first strand: chain 'D' and resid 111 through 114 Processing sheet with id=AD3, first strand: chain 'F' and resid 246 through 249 removed outlier: 4.207A pdb=" N SER F 247 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR F 267 " --> pdb=" O SER F 247 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS F 249 " --> pdb=" O THR F 265 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR F 265 " --> pdb=" O HIS F 249 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER F 306 " --> pdb=" O CYS F 266 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 278 through 280 removed outlier: 4.183A pdb=" N THR F 278 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA F 326 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR F 324 " --> pdb=" O THR F 280 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 320 through 321 Processing sheet with id=AD6, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.676A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 348 through 352 removed outlier: 3.676A pdb=" N THR F 368 " --> pdb=" O LEU F 352 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 388 through 389 removed outlier: 3.551A pdb=" N MET F 433 " --> pdb=" O ARG F 382 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 245 through 246 removed outlier: 3.586A pdb=" N LEU G 268 " --> pdb=" O VAL G 304 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 304 " --> pdb=" O LEU G 268 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 278 through 281 removed outlier: 3.814A pdb=" N THR G 278 " --> pdb=" O ALA G 326 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 326 " --> pdb=" O THR G 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 290 through 291 Processing sheet with id=AE3, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.062A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 348 through 352 removed outlier: 4.062A pdb=" N THR G 368 " --> pdb=" O LEU G 352 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N TYR G 411 " --> pdb=" O GLY G 373 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 388 through 389 removed outlier: 3.736A pdb=" N MET G 433 " --> pdb=" O ARG G 382 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 265 through 268 removed outlier: 3.540A pdb=" N VAL K 307 " --> pdb=" O VAL K 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 265 through 268 removed outlier: 3.683A pdb=" N LEU K 298 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER K 303 " --> pdb=" O ARG K 296 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ARG K 296 " --> pdb=" O SER K 303 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 320 through 323 removed outlier: 3.692A pdb=" N ALA K 336 " --> pdb=" O CYS K 323 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 348 through 352 removed outlier: 3.823A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL K 419 " --> pdb=" O VAL K 365 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR K 411 " --> pdb=" O GLY K 373 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 348 through 352 removed outlier: 3.823A pdb=" N THR K 368 " --> pdb=" O LEU K 352 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL K 419 " --> pdb=" O VAL K 365 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR K 411 " --> pdb=" O GLY K 373 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR K 410 " --> pdb=" O GLU K 403 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 388 through 389 removed outlier: 3.797A pdb=" N SER K 431 " --> pdb=" O LEU K 384 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE K 430 " --> pdb=" O ILE K 448 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 264 through 265 removed outlier: 3.711A pdb=" N LEU L 308 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.973A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 348 through 352 removed outlier: 3.973A pdb=" N ARG L 372 " --> pdb=" O GLU L 348 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR L 368 " --> pdb=" O LEU L 352 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA L 412 " --> pdb=" O ARG L 401 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 388 through 389 removed outlier: 3.893A pdb=" N VAL L 434 " --> pdb=" O THR L 444 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR L 444 " --> pdb=" O VAL L 434 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 245 through 247 removed outlier: 3.561A pdb=" N THR E 269 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER E 247 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR E 267 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 348 through 351 removed outlier: 3.772A pdb=" N ILE E 416 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU E 396 " --> pdb=" O ILE E 416 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 348 through 351 removed outlier: 4.344A pdb=" N THR E 410 " --> pdb=" O GLU E 403 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 412 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG E 401 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 388 through 389 removed outlier: 3.724A pdb=" N LEU E 380 " --> pdb=" O GLY E 435 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 384 " --> pdb=" O SER E 431 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER E 431 " --> pdb=" O LEU E 384 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS E 432 " --> pdb=" O GLN E 445 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 445 " --> pdb=" O CYS E 432 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 247 through 248 removed outlier: 3.690A pdb=" N THR H 267 " --> pdb=" O SER H 247 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.506A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 348 through 352 removed outlier: 3.506A pdb=" N GLU H 348 " --> pdb=" O ARG H 372 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR H 368 " --> pdb=" O LEU H 352 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 380 through 384 removed outlier: 3.533A pdb=" N MET H 433 " --> pdb=" O ARG H 382 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 431 " --> pdb=" O LEU H 384 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 248 through 249 removed outlier: 3.735A pdb=" N THR I 265 " --> pdb=" O HIS I 249 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 322 through 323 removed outlier: 3.918A pdb=" N CYS I 323 " --> pdb=" O ALA I 336 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA I 336 " --> pdb=" O CYS I 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'I' and resid 350 through 352 removed outlier: 4.159A pdb=" N THR I 368 " --> pdb=" O LEU I 352 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER I 415 " --> pdb=" O CYS I 369 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 416 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU I 396 " --> pdb=" O ILE I 416 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 388 through 389 removed outlier: 3.670A pdb=" N LEU I 380 " --> pdb=" O GLY I 435 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N MET I 433 " --> pdb=" O ARG I 382 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU I 384 " --> pdb=" O SER I 431 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR I 444 " --> pdb=" O VAL I 434 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 245 through 246 removed outlier: 4.109A pdb=" N ARG J 245 " --> pdb=" O THR J 269 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR J 269 " --> pdb=" O ARG J 245 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N CYS J 266 " --> pdb=" O SER J 306 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 348 through 352 removed outlier: 3.962A pdb=" N THR J 368 " --> pdb=" O LEU J 352 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL J 413 " --> pdb=" O ALA J 371 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA J 412 " --> pdb=" O ARG J 401 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG J 401 " --> pdb=" O ALA J 412 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 382 through 383 593 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 2.31 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: 6758 1.34 - 1.46: 5228 1.46 - 1.59: 9690 1.59 - 1.72: 0 1.72 - 1.84: 132 Bond restraints: 21808 Sorted by residual: bond pdb=" C THR J 282 " pdb=" N PRO J 283 " ideal model delta sigma weight residual 1.333 1.388 -0.054 1.01e-02 9.80e+03 2.89e+01 bond pdb=" C GLN F 313 " pdb=" N PRO F 314 " ideal model delta sigma weight residual 1.336 1.379 -0.044 1.23e-02 6.61e+03 1.25e+01 bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.19e+00 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" N GLU C 504 " pdb=" CA GLU C 504 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.44e+00 ... (remaining 21803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 28947 2.79 - 5.57: 827 5.57 - 8.36: 145 8.36 - 11.14: 17 11.14 - 13.93: 7 Bond angle restraints: 29943 Sorted by residual: angle pdb=" N PRO J 455 " pdb=" CA PRO J 455 " pdb=" CB PRO J 455 " ideal model delta sigma weight residual 103.25 111.96 -8.71 1.05e+00 9.07e-01 6.88e+01 angle pdb=" C ASN D 49 " pdb=" N ILE D 50 " pdb=" CA ILE D 50 " ideal model delta sigma weight residual 121.65 116.41 5.24 9.40e-01 1.13e+00 3.10e+01 angle pdb=" C LEU D 79 " pdb=" N ASP D 80 " pdb=" CA ASP D 80 " ideal model delta sigma weight residual 122.44 116.59 5.85 1.19e+00 7.06e-01 2.42e+01 angle pdb=" C LYS A 425 " pdb=" N LYS A 426 " pdb=" CA LYS A 426 " ideal model delta sigma weight residual 120.60 128.42 -7.82 1.60e+00 3.91e-01 2.39e+01 angle pdb=" C ASN G 337 " pdb=" N ILE G 338 " pdb=" CA ILE G 338 " ideal model delta sigma weight residual 121.97 126.79 -4.82 1.00e+00 1.00e+00 2.32e+01 ... (remaining 29938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 11562 17.99 - 35.98: 1126 35.98 - 53.96: 164 53.96 - 71.95: 22 71.95 - 89.94: 9 Dihedral angle restraints: 12883 sinusoidal: 4530 harmonic: 8353 Sorted by residual: dihedral pdb=" CB CYS E 369 " pdb=" SG CYS E 369 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual -86.00 -175.94 89.94 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS I 369 " pdb=" SG CYS I 369 " pdb=" SG CYS I 432 " pdb=" CB CYS I 432 " ideal model delta sinusoidal sigma weight residual 93.00 167.06 -74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA ASN G 337 " pdb=" C ASN G 337 " pdb=" N ILE G 338 " pdb=" CA ILE G 338 " ideal model delta harmonic sigma weight residual 180.00 138.47 41.53 0 5.00e+00 4.00e-02 6.90e+01 ... (remaining 12880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 3515 0.147 - 0.294: 117 0.294 - 0.441: 7 0.441 - 0.588: 0 0.588 - 0.735: 2 Chirality restraints: 3641 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 451 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" C1 NAG S 1 " pdb=" ND2 ASN G 337 " pdb=" C2 NAG S 1 " pdb=" O5 NAG S 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CB ILE E 448 " pdb=" CA ILE E 448 " pdb=" CG1 ILE E 448 " pdb=" CG2 ILE E 448 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.52e+00 ... (remaining 3638 not shown) Planarity restraints: 3838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN J 313 " 0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO J 314 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO J 314 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO J 314 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 292 " 0.052 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO K 293 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO K 293 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO K 293 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 166 " -0.051 5.00e-02 4.00e+02 7.79e-02 9.70e+00 pdb=" N PRO C 167 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO C 167 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 167 " -0.043 5.00e-02 4.00e+02 ... (remaining 3835 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 726 2.69 - 3.24: 17451 3.24 - 3.79: 30297 3.79 - 4.35: 35726 4.35 - 4.90: 63891 Nonbonded interactions: 148091 Sorted by model distance: nonbonded pdb=" CG GLU C 504 " pdb=" N ASN C 505 " model vdw 2.132 3.520 nonbonded pdb=" O CYS E 432 " pdb=" OG1 THR E 444 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR L 320 " pdb=" O ILE L 338 " model vdw 2.243 3.040 nonbonded pdb=" N ASP C 503 " pdb=" OD1 ASP C 503 " model vdw 2.274 3.120 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.278 3.120 ... (remaining 148086 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 417 or (resid 418 and (name N or name CA or name C or name O or name C \ B )) or resid 419 through 424 or (resid 425 through 426 and (name N or name CA o \ r 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 4 \ 57 through 459 and (name N or name CA or name C or name O or name CB )))) 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 417 or (resid 418 and (na \ me N or name CA or name C or name O or name CB )) or resid 419 through 424 or (r \ esid 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 nam \ e 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 457 through 459 and (name N or name \ CA or name C or name O or name CB )))) 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 417 o \ r (resid 418 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 19 through 450 or (resid 457 through 459 and (name N or name CA or name C or nam \ e O or name CB )))) 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 417 or (resid 418 and (name N or name CA or name C or nam \ e O or name CB )) or resid 419 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 through 445 or (resid \ 446 and (name N or name CA or name C or name O or name CB )) or resid 447 throu \ gh 449 or (resid 450 and (name N or name CA or name C or name O or name CB )) or \ (resid 457 through 459 and (name N or name CA or name C or name O or name CB )) \ )) 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 417 or (resid 418 and (name N or name CA or name C or \ name O or name CB )) or resid 419 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 thr \ ough 426 and (name N or name CA or name C or name O or name CB )) or resid 427 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 457 through 459 and (name N or name CA or name C or \ name O or name CB )))) 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 417 or (resid 418 and (name N or name CA or name C or name O or name \ CB )) or resid 419 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 through 450 or (resid 457 through \ 459 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'I' 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 417 or (resid 418 and (na \ me N or name CA or name C or name O or name CB )) or resid 419 through 450 or (r \ esid 457 through 459 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' 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 457 through 459)) 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 417 or (resid 418 and (name N or name \ CA or name C or name O or name CB )) or resid 419 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 o \ r (resid 457 through 459 and (name N or name CA or name C or name O or name CB ) \ ))) 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 417 or (resid 418 and (name N or name CA or name \ C or name O or name CB )) or resid 419 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 457 \ through 459 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'S' } 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.860 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 : 0.009 0.097 21870 Z= 0.374 Angle : 1.196 24.103 30086 Z= 0.611 Chirality : 0.067 0.735 3641 Planarity : 0.009 0.089 3829 Dihedral : 13.882 87.114 7344 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 13.42 % Favored : 86.55 % Rotamer: Outliers : 0.84 % Allowed : 10.49 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.19 % 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: -4.63 (0.13), residues: 2869 helix: -4.13 (0.23), residues: 178 sheet: -2.21 (0.16), residues: 898 loop : -3.62 (0.11), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 394 TYR 0.021 0.003 TYR F 395 PHE 0.032 0.003 PHE C 136 TRP 0.033 0.003 TRP C 369 HIS 0.014 0.002 HIS H 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00852 / 0.37 (21808) covalent geometry : angle 1.16141 / 0.60 (29943) SS BOND : bond 0.00757 / 0.56 ( 43) SS BOND : angle 1.67164 / 1.10 ( 86) hydrogen bonds : bond 0.27926 / 18.96 ( 498) hydrogen bonds : angle 9.29123 / 6.26 ( 1476) link_BETA1-4 : bond 0.01970 / 1.20 ( 10) link_BETA1-4 : angle 5.47370 / 3.72 ( 30) link_NAG-ASN : bond 0.01086 / 0.51 ( 9) link_NAG-ASN : angle 7.55335 / 6.65 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 574 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 317 HIS cc_start: 0.6463 (m90) cc_final: 0.5538 (m90) REVERT: L 248 LEU cc_start: 0.7575 (pt) cc_final: 0.7371 (pt) REVERT: L 433 MET cc_start: 0.6342 (tpp) cc_final: 0.6075 (tpt) REVERT: I 356 SER cc_start: 0.8219 (p) cc_final: 0.7803 (t) REVERT: J 265 THR cc_start: 0.6187 (t) cc_final: 0.5977 (m) REVERT: J 413 VAL cc_start: 0.6064 (t) cc_final: 0.5568 (p) outliers start: 18 outliers final: 9 residues processed: 588 average time/residue: 0.5563 time to fit residues: 372.9934 Evaluate side-chains 342 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 333 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 GLU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain G residue 396 LEU Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain J residue 434 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 ASN A 343 ASN A 445 GLN B 343 ASN B 406 GLN C 16 ASN C 133 ASN C 282 ASN C 314 GLN C 329 ASN C 530 GLN K 291 GLN K 445 GLN ** H 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 457 HIS I 337 ASN J 385 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.140234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.104997 restraints weight = 54519.735| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 4.55 r_work: 0.3523 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21870 Z= 0.173 Angle : 0.866 19.468 30086 Z= 0.415 Chirality : 0.048 0.581 3641 Planarity : 0.007 0.078 3829 Dihedral : 6.990 87.349 3060 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.27 % Favored : 90.69 % Rotamer: Outliers : 5.15 % Allowed : 20.60 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.76 (0.13), residues: 2869 helix: -3.20 (0.28), residues: 184 sheet: -1.60 (0.15), residues: 941 loop : -3.09 (0.13), residues: 1744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 336 TYR 0.012 0.001 TYR E 395 PHE 0.017 0.001 PHE C 75 TRP 0.019 0.002 TRP J 424 HIS 0.012 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (21808) covalent geometry : angle 0.84102 / 0.41 (29943) SS BOND : bond 0.00858 / 0.64 ( 43) SS BOND : angle 1.60026 / 1.06 ( 86) hydrogen bonds : bond 0.04172 / 2.87 ( 498) hydrogen bonds : angle 6.05807 / 4.07 ( 1476) link_BETA1-4 : bond 0.00790 / 0.42 ( 10) link_BETA1-4 : angle 2.89745 / 1.93 ( 30) link_NAG-ASN : bond 0.00933 / 0.52 ( 9) link_NAG-ASN : angle 5.73736 / 5.08 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 377 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.7890 (mp0) cc_final: 0.7494 (mp0) REVERT: A 428 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8614 (mt-10) REVERT: A 448 ILE cc_start: 0.8984 (tp) cc_final: 0.8736 (tt) REVERT: A 450 ARG cc_start: 0.8837 (ptm-80) cc_final: 0.8263 (tmm-80) REVERT: B 392 ARG cc_start: 0.8688 (tpp-160) cc_final: 0.8428 (tpp80) REVERT: B 403 GLU cc_start: 0.8518 (pt0) cc_final: 0.7916 (pm20) REVERT: B 428 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7767 (mp0) REVERT: C 8 GLU cc_start: 0.7656 (tp30) cc_final: 0.7285 (tp30) REVERT: C 16 ASN cc_start: 0.8790 (OUTLIER) cc_final: 0.8430 (m-40) REVERT: C 298 ARG cc_start: 0.8434 (mtt180) cc_final: 0.8077 (mpp80) REVERT: C 330 GLU cc_start: 0.7447 (pp20) cc_final: 0.7177 (pp20) REVERT: C 331 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7065 (mm-30) REVERT: C 477 TRP cc_start: 0.6214 (m100) cc_final: 0.5852 (m100) REVERT: D 22 ILE cc_start: 0.9105 (mt) cc_final: 0.8808 (tp) REVERT: D 65 LEU cc_start: 0.9058 (tt) cc_final: 0.8656 (tt) REVERT: F 463 VAL cc_start: 0.9165 (t) cc_final: 0.8942 (m) REVERT: F 464 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8991 (mtm) REVERT: G 410 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9049 (t) REVERT: G 423 ASP cc_start: 0.9331 (t0) cc_final: 0.9105 (m-30) REVERT: K 358 GLU cc_start: 0.8263 (tm-30) cc_final: 0.7392 (tm-30) REVERT: L 433 MET cc_start: 0.7897 (tpp) cc_final: 0.7576 (tpt) REVERT: H 385 GLN cc_start: 0.9310 (tm-30) cc_final: 0.9005 (tp-100) REVERT: I 320 THR cc_start: 0.6273 (OUTLIER) cc_final: 0.6047 (p) REVERT: I 380 LEU cc_start: 0.4529 (tt) cc_final: 0.4101 (tt) REVERT: I 395 TYR cc_start: 0.6493 (p90) cc_final: 0.5374 (p90) REVERT: I 449 ASP cc_start: 0.7812 (t0) cc_final: 0.7291 (t0) REVERT: J 369 CYS cc_start: 0.6978 (OUTLIER) cc_final: 0.5958 (p) REVERT: J 370 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8921 (tm) REVERT: J 413 VAL cc_start: 0.7448 (t) cc_final: 0.7229 (p) REVERT: J 430 PHE cc_start: 0.7580 (m-80) cc_final: 0.7343 (m-80) outliers start: 111 outliers final: 43 residues processed: 442 average time/residue: 0.4748 time to fit residues: 244.6934 Evaluate side-chains 384 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 335 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 380 LEU Chi-restraints excluded: chain F residue 464 MET Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 315 TRP Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 352 LEU Chi-restraints excluded: chain J residue 369 CYS Chi-restraints excluded: chain J residue 370 LEU Chi-restraints excluded: chain J residue 415 SER Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 144 optimal weight: 6.9990 chunk 105 optimal weight: 0.0370 chunk 82 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 135 optimal weight: 0.0980 chunk 81 optimal weight: 0.8980 chunk 213 optimal weight: 10.0000 chunk 237 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN F 327 HIS H 436 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.140653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105663 restraints weight = 54654.506| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 4.58 r_work: 0.3552 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 21870 Z= 0.129 Angle : 0.807 19.838 30086 Z= 0.380 Chirality : 0.046 0.539 3641 Planarity : 0.005 0.068 3829 Dihedral : 5.886 26.757 3046 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 5.29 % Allowed : 22.69 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.14), residues: 2869 helix: -2.55 (0.32), residues: 188 sheet: -1.09 (0.16), residues: 943 loop : -2.76 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 24 TYR 0.015 0.001 TYR J 411 PHE 0.015 0.001 PHE C 75 TRP 0.018 0.001 TRP A 281 HIS 0.015 0.001 HIS K 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (21808) covalent geometry : angle 0.78466 / 0.37 (29943) SS BOND : bond 0.00462 / 0.34 ( 43) SS BOND : angle 1.25216 / 0.77 ( 86) hydrogen bonds : bond 0.03307 / 2.28 ( 498) hydrogen bonds : angle 5.39867 / 3.61 ( 1476) link_BETA1-4 : bond 0.00677 / 0.37 ( 10) link_BETA1-4 : angle 2.76738 / 1.78 ( 30) link_NAG-ASN : bond 0.00738 / 0.40 ( 9) link_NAG-ASN : angle 5.45302 / 4.92 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 357 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 GLU cc_start: 0.7969 (mp0) cc_final: 0.7607 (mp0) REVERT: A 324 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.7906 (m) REVERT: A 428 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8547 (mp0) REVERT: A 448 ILE cc_start: 0.8965 (tp) cc_final: 0.8701 (tt) REVERT: A 450 ARG cc_start: 0.8794 (ptm-80) cc_final: 0.8309 (tmm-80) REVERT: B 403 GLU cc_start: 0.8494 (pt0) cc_final: 0.7992 (pm20) REVERT: B 428 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7758 (mp0) REVERT: C 8 GLU cc_start: 0.7905 (tp30) cc_final: 0.7532 (tp30) REVERT: C 111 GLN cc_start: 0.6922 (pm20) cc_final: 0.5791 (pm20) REVERT: C 134 CYS cc_start: 0.4198 (OUTLIER) cc_final: 0.3897 (t) REVERT: C 220 LEU cc_start: 0.8376 (pp) cc_final: 0.8004 (pp) REVERT: C 221 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6999 (mppt) REVERT: C 298 ARG cc_start: 0.8488 (mtt180) cc_final: 0.8213 (mpp80) REVERT: C 331 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6842 (mm-30) REVERT: C 366 TRP cc_start: 0.7679 (t-100) cc_final: 0.7406 (t-100) REVERT: C 536 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7448 (tm-30) REVERT: D 48 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8695 (mp0) REVERT: D 91 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9037 (pp) REVERT: G 346 ARG cc_start: 0.8839 (mtm-85) cc_final: 0.8531 (mtm-85) REVERT: G 449 ASP cc_start: 0.9062 (p0) cc_final: 0.8827 (p0) REVERT: K 358 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7425 (tm-30) REVERT: K 385 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8356 (tm-30) REVERT: L 433 MET cc_start: 0.7983 (tpp) cc_final: 0.7729 (tpp) REVERT: E 345 PHE cc_start: 0.7891 (m-80) cc_final: 0.7660 (m-80) REVERT: H 279 PHE cc_start: 0.5019 (m-80) cc_final: 0.4687 (m-80) REVERT: I 320 THR cc_start: 0.6760 (OUTLIER) cc_final: 0.6376 (p) REVERT: I 382 ARG cc_start: 0.7138 (mmm160) cc_final: 0.6622 (mpt180) REVERT: I 383 TRP cc_start: 0.7465 (m100) cc_final: 0.6867 (m100) REVERT: I 449 ASP cc_start: 0.7794 (t0) cc_final: 0.7240 (t0) REVERT: J 430 PHE cc_start: 0.7658 (m-80) cc_final: 0.7395 (m-80) outliers start: 114 outliers final: 47 residues processed: 436 average time/residue: 0.4723 time to fit residues: 239.5726 Evaluate side-chains 366 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 314 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 265 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 432 CYS Chi-restraints excluded: chain I residue 320 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 0.2980 chunk 144 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 239 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 251 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 45 ASN F 385 GLN K 316 ASN L 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.139760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.103297 restraints weight = 55001.835| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.73 r_work: 0.3525 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21870 Z= 0.135 Angle : 0.781 19.236 30086 Z= 0.367 Chirality : 0.046 0.549 3641 Planarity : 0.005 0.060 3829 Dihedral : 5.496 30.858 3045 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.02 % Favored : 91.95 % Rotamer: Outliers : 5.85 % Allowed : 22.92 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.83 (0.15), residues: 2869 helix: -2.02 (0.34), residues: 190 sheet: -0.84 (0.16), residues: 962 loop : -2.62 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 392 TYR 0.013 0.001 TYR C 24 PHE 0.015 0.001 PHE C 75 TRP 0.022 0.001 TRP L 315 HIS 0.012 0.001 HIS K 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (21808) covalent geometry : angle 0.75947 / 0.36 (29943) SS BOND : bond 0.00423 / 0.30 ( 43) SS BOND : angle 1.26654 / 0.79 ( 86) hydrogen bonds : bond 0.03048 / 2.07 ( 498) hydrogen bonds : angle 5.23706 / 3.50 ( 1476) link_BETA1-4 : bond 0.00635 / 0.35 ( 10) link_BETA1-4 : angle 2.56701 / 1.64 ( 30) link_NAG-ASN : bond 0.00702 / 0.38 ( 9) link_NAG-ASN : angle 5.30840 / 4.77 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 348 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8597 (mp0) REVERT: A 448 ILE cc_start: 0.9043 (tp) cc_final: 0.8787 (tt) REVERT: A 450 ARG cc_start: 0.8846 (ptm-80) cc_final: 0.8318 (tmm-80) REVERT: B 403 GLU cc_start: 0.8543 (pt0) cc_final: 0.8247 (pm20) REVERT: C 8 GLU cc_start: 0.8136 (tp30) cc_final: 0.7668 (tp30) REVERT: C 134 CYS cc_start: 0.4640 (OUTLIER) cc_final: 0.3803 (t) REVERT: C 298 ARG cc_start: 0.8502 (mtt180) cc_final: 0.8195 (mpp80) REVERT: C 331 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7040 (mm-30) REVERT: C 366 TRP cc_start: 0.7654 (t-100) cc_final: 0.7414 (t-100) REVERT: D 24 ARG cc_start: 0.9016 (tpp80) cc_final: 0.8769 (tpt-90) REVERT: D 48 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8662 (mp0) REVERT: F 358 GLU cc_start: 0.8648 (tt0) cc_final: 0.8390 (tt0) REVERT: G 243 HIS cc_start: 0.7334 (t70) cc_final: 0.6632 (t70) REVERT: G 346 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8611 (mtm-85) REVERT: G 410 THR cc_start: 0.9388 (OUTLIER) cc_final: 0.8865 (t) REVERT: G 433 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9050 (mmm) REVERT: G 449 ASP cc_start: 0.9082 (p0) cc_final: 0.8865 (p0) REVERT: K 358 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7406 (tm-30) REVERT: K 378 ASP cc_start: 0.8229 (m-30) cc_final: 0.7887 (m-30) REVERT: K 385 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8421 (tm-30) REVERT: K 394 LYS cc_start: 0.8966 (mmpt) cc_final: 0.8752 (mmpt) REVERT: E 345 PHE cc_start: 0.7916 (m-80) cc_final: 0.7704 (m-80) REVERT: E 403 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8240 (tm-30) REVERT: E 445 GLN cc_start: 0.7305 (tp-100) cc_final: 0.5365 (mt0) REVERT: H 423 ASP cc_start: 0.8893 (p0) cc_final: 0.8623 (OUTLIER) REVERT: H 426 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8636 (pptt) REVERT: H 454 LYS cc_start: 0.7607 (tppp) cc_final: 0.7276 (tptp) REVERT: I 416 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.7071 (pp) REVERT: I 423 ASP cc_start: 0.8017 (m-30) cc_final: 0.7782 (p0) REVERT: I 433 MET cc_start: 0.7215 (ppp) cc_final: 0.6919 (ppp) REVERT: I 449 ASP cc_start: 0.7700 (t0) cc_final: 0.7478 (t0) REVERT: J 369 CYS cc_start: 0.7101 (t) cc_final: 0.5923 (m) REVERT: J 372 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7535 (tmt90) REVERT: J 430 PHE cc_start: 0.7692 (m-80) cc_final: 0.7369 (m-80) outliers start: 126 outliers final: 63 residues processed: 432 average time/residue: 0.4899 time to fit residues: 246.4547 Evaluate side-chains 382 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 314 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 315 TRP Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 419 VAL Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 432 CYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 349 VAL Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 69 optimal weight: 0.0870 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 283 optimal weight: 10.0000 chunk 245 optimal weight: 5.9990 chunk 117 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN D 30 ASN D 45 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS ** K 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.134965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.101448 restraints weight = 53743.503| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 4.47 r_work: 0.3488 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 21870 Z= 0.192 Angle : 0.829 17.995 30086 Z= 0.394 Chirality : 0.047 0.571 3641 Planarity : 0.005 0.080 3829 Dihedral : 5.572 31.899 3045 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.27 % Favored : 90.69 % Rotamer: Outliers : 5.94 % Allowed : 24.36 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.73 (0.15), residues: 2869 helix: -1.90 (0.34), residues: 202 sheet: -0.78 (0.16), residues: 970 loop : -2.55 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 336 TYR 0.015 0.001 TYR B 472 PHE 0.017 0.002 PHE C 75 TRP 0.021 0.002 TRP L 315 HIS 0.017 0.001 HIS K 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (21808) covalent geometry : angle 0.80923 / 0.39 (29943) SS BOND : bond 0.00542 / 0.39 ( 43) SS BOND : angle 1.42851 / 0.95 ( 86) hydrogen bonds : bond 0.03593 / 2.45 ( 498) hydrogen bonds : angle 5.38682 / 3.62 ( 1476) link_BETA1-4 : bond 0.00624 / 0.34 ( 10) link_BETA1-4 : angle 2.52956 / 1.58 ( 30) link_NAG-ASN : bond 0.00694 / 0.37 ( 9) link_NAG-ASN : angle 5.11526 / 4.54 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 328 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8336 (t) REVERT: A 428 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: A 448 ILE cc_start: 0.9180 (tp) cc_final: 0.8938 (tt) REVERT: A 450 ARG cc_start: 0.9027 (ptm-80) cc_final: 0.8441 (tmm-80) REVERT: B 343 ASN cc_start: 0.8125 (t0) cc_final: 0.7913 (t0) REVERT: B 403 GLU cc_start: 0.8551 (pt0) cc_final: 0.8234 (pm20) REVERT: B 426 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8426 (tttm) REVERT: B 428 GLU cc_start: 0.7976 (mp0) cc_final: 0.7156 (mp0) REVERT: C 134 CYS cc_start: 0.5435 (OUTLIER) cc_final: 0.4095 (t) REVERT: C 298 ARG cc_start: 0.8615 (mtt180) cc_final: 0.8374 (mpp80) REVERT: C 504 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4520 (pt0) REVERT: D 28 ASP cc_start: 0.8883 (t0) cc_final: 0.8682 (t0) REVERT: D 45 ASN cc_start: 0.9311 (m-40) cc_final: 0.8669 (m110) REVERT: D 48 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8617 (mp0) REVERT: D 126 GLU cc_start: 0.7728 (pm20) cc_final: 0.7168 (pm20) REVERT: F 466 GLU cc_start: 0.8935 (tt0) cc_final: 0.8312 (tp30) REVERT: G 243 HIS cc_start: 0.7191 (t70) cc_final: 0.6409 (t70) REVERT: G 278 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8094 (p) REVERT: G 346 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8563 (mtm-85) REVERT: G 410 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.8935 (t) REVERT: G 423 ASP cc_start: 0.9320 (t0) cc_final: 0.9104 (t0) REVERT: G 425 LYS cc_start: 0.9590 (mmmm) cc_final: 0.9371 (mmmm) REVERT: G 449 ASP cc_start: 0.9118 (p0) cc_final: 0.8912 (p0) REVERT: K 348 GLU cc_start: 0.8569 (mp0) cc_final: 0.8345 (mp0) REVERT: K 358 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7377 (tm-30) REVERT: K 378 ASP cc_start: 0.8743 (m-30) cc_final: 0.8434 (m-30) REVERT: K 385 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8574 (tm-30) REVERT: L 433 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8518 (tmm) REVERT: E 348 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7977 (mm-30) REVERT: E 374 PHE cc_start: 0.6713 (p90) cc_final: 0.6441 (p90) REVERT: E 403 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8170 (tm-30) REVERT: E 445 GLN cc_start: 0.7195 (tp-100) cc_final: 0.5356 (mt0) REVERT: H 426 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8540 (pptt) REVERT: I 382 ARG cc_start: 0.7428 (mmm160) cc_final: 0.6957 (mpt180) REVERT: I 383 TRP cc_start: 0.7321 (m100) cc_final: 0.6674 (m100) REVERT: I 433 MET cc_start: 0.7318 (ppp) cc_final: 0.7043 (ppp) REVERT: I 449 ASP cc_start: 0.8172 (t0) cc_final: 0.7822 (t0) REVERT: J 369 CYS cc_start: 0.7027 (t) cc_final: 0.5986 (m) REVERT: J 370 LEU cc_start: 0.8972 (tm) cc_final: 0.8756 (tm) REVERT: J 372 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7572 (tmt90) REVERT: J 430 PHE cc_start: 0.7817 (m-80) cc_final: 0.7403 (m-80) outliers start: 128 outliers final: 69 residues processed: 419 average time/residue: 0.5218 time to fit residues: 252.6312 Evaluate side-chains 376 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 297 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 457 HIS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 542 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 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 433 MET Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 423 ASP Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 372 ARG Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 52 optimal weight: 0.9980 chunk 202 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 250 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 107 optimal weight: 0.0980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 ASN B 343 ASN C 329 ASN K 316 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.102437 restraints weight = 54689.900| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 4.52 r_work: 0.3511 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21870 Z= 0.131 Angle : 0.794 17.767 30086 Z= 0.373 Chirality : 0.046 0.573 3641 Planarity : 0.005 0.066 3829 Dihedral : 5.259 29.353 3045 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.08 % Favored : 92.89 % Rotamer: Outliers : 5.10 % Allowed : 26.45 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.47 (0.15), residues: 2869 helix: -1.60 (0.35), residues: 203 sheet: -0.55 (0.17), residues: 951 loop : -2.41 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 392 TYR 0.014 0.001 TYR D 63 PHE 0.016 0.001 PHE C 75 TRP 0.023 0.001 TRP A 281 HIS 0.023 0.001 HIS K 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (21808) covalent geometry : angle 0.77473 / 0.37 (29943) SS BOND : bond 0.00397 / 0.28 ( 43) SS BOND : angle 1.22087 / 0.81 ( 86) hydrogen bonds : bond 0.03004 / 2.04 ( 498) hydrogen bonds : angle 5.10105 / 3.43 ( 1476) link_BETA1-4 : bond 0.00643 / 0.35 ( 10) link_BETA1-4 : angle 2.46594 / 1.52 ( 30) link_NAG-ASN : bond 0.00689 / 0.37 ( 9) link_NAG-ASN : angle 4.99339 / 4.46 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 323 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ASP cc_start: 0.8979 (m-30) cc_final: 0.8524 (m-30) REVERT: A 410 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9006 (p) REVERT: A 428 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8523 (mp0) REVERT: A 448 ILE cc_start: 0.9138 (tp) cc_final: 0.8910 (tt) REVERT: A 450 ARG cc_start: 0.9015 (ptm-80) cc_final: 0.8432 (tmm-80) REVERT: B 403 GLU cc_start: 0.8569 (pt0) cc_final: 0.8272 (pm20) REVERT: B 428 GLU cc_start: 0.7910 (mp0) cc_final: 0.7076 (mp0) REVERT: C 8 GLU cc_start: 0.8433 (tp30) cc_final: 0.8188 (tp30) REVERT: C 134 CYS cc_start: 0.5718 (OUTLIER) cc_final: 0.4239 (t) REVERT: C 298 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8324 (mpp80) REVERT: D 45 ASN cc_start: 0.9354 (m-40) cc_final: 0.8812 (m110) REVERT: D 48 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8663 (mp0) REVERT: D 126 GLU cc_start: 0.7669 (pm20) cc_final: 0.7041 (pm20) REVERT: F 338 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8650 (tp) REVERT: F 346 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8096 (ptt-90) REVERT: F 466 GLU cc_start: 0.8902 (tt0) cc_final: 0.8352 (tp30) REVERT: G 243 HIS cc_start: 0.7243 (t70) cc_final: 0.6557 (t70) REVERT: G 278 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8000 (p) REVERT: G 346 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8588 (mtm-85) REVERT: G 410 THR cc_start: 0.9422 (OUTLIER) cc_final: 0.8905 (t) REVERT: G 423 ASP cc_start: 0.9320 (t0) cc_final: 0.9098 (t0) REVERT: G 425 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9388 (mmmm) REVERT: G 433 MET cc_start: 0.9236 (mmm) cc_final: 0.9024 (mmm) REVERT: G 466 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8766 (pt0) REVERT: K 348 GLU cc_start: 0.8613 (mp0) cc_final: 0.8407 (mp0) REVERT: K 358 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7517 (tm-30) REVERT: K 378 ASP cc_start: 0.8726 (m-30) cc_final: 0.8460 (m-30) REVERT: K 385 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8560 (tm-30) REVERT: L 433 MET cc_start: 0.8914 (ttm) cc_final: 0.8531 (tmm) REVERT: E 348 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7852 (mm-30) REVERT: E 374 PHE cc_start: 0.6695 (p90) cc_final: 0.6412 (p90) REVERT: E 403 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8300 (tm-30) REVERT: E 445 GLN cc_start: 0.7258 (tp-100) cc_final: 0.5423 (mt0) REVERT: H 410 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8494 (p) REVERT: H 454 LYS cc_start: 0.7672 (tppp) cc_final: 0.7406 (tptp) REVERT: I 382 ARG cc_start: 0.7198 (mmm160) cc_final: 0.6839 (mpt180) REVERT: I 383 TRP cc_start: 0.7183 (m100) cc_final: 0.6489 (m-10) REVERT: I 433 MET cc_start: 0.7352 (ppp) cc_final: 0.7092 (ppp) REVERT: I 449 ASP cc_start: 0.8135 (t0) cc_final: 0.7783 (t0) REVERT: J 369 CYS cc_start: 0.6983 (t) cc_final: 0.5879 (m) REVERT: J 403 GLU cc_start: 0.8055 (pm20) cc_final: 0.7739 (pm20) REVERT: J 430 PHE cc_start: 0.7957 (m-80) cc_final: 0.7474 (m-80) outliers start: 110 outliers final: 61 residues processed: 404 average time/residue: 0.5412 time to fit residues: 252.6639 Evaluate side-chains 367 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 298 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 384 LEU Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 464 MET Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 120 optimal weight: 8.9990 chunk 227 optimal weight: 0.0870 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN B 388 GLN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 263 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.136738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.102941 restraints weight = 54773.686| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 4.49 r_work: 0.3519 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 0.046 21870 Z= 0.129 Angle : 0.801 17.775 30086 Z= 0.373 Chirality : 0.046 0.567 3641 Planarity : 0.005 0.069 3829 Dihedral : 5.043 28.636 3045 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.33 % Rotamer: Outliers : 5.29 % Allowed : 27.38 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.30 (0.15), residues: 2869 helix: -1.45 (0.36), residues: 203 sheet: -0.35 (0.17), residues: 923 loop : -2.32 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 336 TYR 0.012 0.001 TYR C 24 PHE 0.021 0.001 PHE H 321 TRP 0.025 0.001 TRP C 366 HIS 0.011 0.001 HIS H 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (21808) covalent geometry : angle 0.78332 / 0.37 (29943) SS BOND : bond 0.00421 / 0.28 ( 43) SS BOND : angle 1.11407 / 0.70 ( 86) hydrogen bonds : bond 0.02848 / 1.95 ( 498) hydrogen bonds : angle 4.96074 / 3.33 ( 1476) link_BETA1-4 : bond 0.00609 / 0.33 ( 10) link_BETA1-4 : angle 2.35882 / 1.46 ( 30) link_NAG-ASN : bond 0.00700 / 0.38 ( 9) link_NAG-ASN : angle 4.91869 / 4.40 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 325 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 THR cc_start: 0.9366 (OUTLIER) cc_final: 0.9068 (p) REVERT: A 428 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8520 (mp0) REVERT: A 448 ILE cc_start: 0.9117 (tp) cc_final: 0.8866 (tt) REVERT: A 450 ARG cc_start: 0.9035 (ptm-80) cc_final: 0.8436 (tmm-80) REVERT: B 403 GLU cc_start: 0.8533 (pt0) cc_final: 0.8164 (pm20) REVERT: B 426 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8468 (tttp) REVERT: B 428 GLU cc_start: 0.7994 (mp0) cc_final: 0.7437 (mp0) REVERT: C 8 GLU cc_start: 0.8476 (tp30) cc_final: 0.8238 (tp30) REVERT: C 89 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8733 (mtm-85) REVERT: C 134 CYS cc_start: 0.5750 (OUTLIER) cc_final: 0.4260 (t) REVERT: C 298 ARG cc_start: 0.8624 (mtt180) cc_final: 0.8320 (mpp80) REVERT: C 504 GLU cc_start: 0.5376 (OUTLIER) cc_final: 0.4947 (pt0) REVERT: D 28 ASP cc_start: 0.8599 (t0) cc_final: 0.8129 (t0) REVERT: D 31 GLU cc_start: 0.6979 (pp20) cc_final: 0.6535 (pm20) REVERT: D 45 ASN cc_start: 0.9366 (m-40) cc_final: 0.8853 (m110) REVERT: D 48 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8660 (mp0) REVERT: D 126 GLU cc_start: 0.7670 (pm20) cc_final: 0.6982 (pm20) REVERT: F 338 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8637 (tp) REVERT: F 346 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.8139 (ptt-90) REVERT: F 466 GLU cc_start: 0.8907 (tt0) cc_final: 0.8357 (tp30) REVERT: G 243 HIS cc_start: 0.7254 (t70) cc_final: 0.6521 (t70) REVERT: G 278 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7946 (p) REVERT: G 346 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8592 (mtm-85) REVERT: G 410 THR cc_start: 0.9406 (OUTLIER) cc_final: 0.8884 (t) REVERT: G 423 ASP cc_start: 0.9278 (t0) cc_final: 0.9061 (t0) REVERT: G 425 LYS cc_start: 0.9613 (mmmm) cc_final: 0.9394 (mmmm) REVERT: G 433 MET cc_start: 0.9261 (mmm) cc_final: 0.9038 (mmm) REVERT: G 466 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8617 (pt0) REVERT: K 255 ASP cc_start: 0.8598 (p0) cc_final: 0.7814 (t0) REVERT: K 358 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7402 (tm-30) REVERT: K 378 ASP cc_start: 0.8751 (m-30) cc_final: 0.8437 (m-30) REVERT: K 385 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8538 (tm-30) REVERT: L 433 MET cc_start: 0.8815 (ttm) cc_final: 0.8586 (tmm) REVERT: L 464 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7018 (pmm) REVERT: E 348 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7906 (mm-30) REVERT: E 352 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9257 (mm) REVERT: E 374 PHE cc_start: 0.6762 (p90) cc_final: 0.6457 (p90) REVERT: E 403 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8428 (tm-30) REVERT: E 445 GLN cc_start: 0.7357 (tp-100) cc_final: 0.5436 (mt0) REVERT: E 451 LEU cc_start: 0.5987 (OUTLIER) cc_final: 0.5680 (pt) REVERT: H 454 LYS cc_start: 0.7735 (tppp) cc_final: 0.7370 (tptp) REVERT: I 382 ARG cc_start: 0.7238 (mmm160) cc_final: 0.6800 (mmt90) REVERT: I 383 TRP cc_start: 0.7234 (m100) cc_final: 0.6759 (m-10) REVERT: I 433 MET cc_start: 0.7377 (ppp) cc_final: 0.7129 (ppp) REVERT: I 449 ASP cc_start: 0.8102 (t0) cc_final: 0.7820 (t0) REVERT: I 464 MET cc_start: 0.7526 (mmt) cc_final: 0.7323 (mmt) REVERT: J 369 CYS cc_start: 0.7149 (t) cc_final: 0.6085 (m) REVERT: J 401 ARG cc_start: 0.6561 (mmt90) cc_final: 0.6294 (mmt-90) REVERT: J 437 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7457 (pm20) outliers start: 114 outliers final: 61 residues processed: 410 average time/residue: 0.5367 time to fit residues: 254.3989 Evaluate side-chains 371 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 298 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 134 CYS Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 542 VAL Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 366 THR Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 448 ILE Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 464 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 5 optimal weight: 0.0030 chunk 171 optimal weight: 9.9990 chunk 276 optimal weight: 0.0870 chunk 84 optimal weight: 4.9990 chunk 186 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 257 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 overall best weight: 2.4174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 HIS B 343 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 HIS H 249 HIS ** H 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 317 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.131616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.098838 restraints weight = 53933.369| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 4.38 r_work: 0.3453 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 21870 Z= 0.228 Angle : 0.899 17.322 30086 Z= 0.428 Chirality : 0.049 0.566 3641 Planarity : 0.005 0.070 3829 Dihedral : 5.612 31.957 3045 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.21 % Favored : 89.75 % Rotamer: Outliers : 5.71 % Allowed : 27.52 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.47 (0.15), residues: 2869 helix: -1.46 (0.35), residues: 213 sheet: -0.57 (0.16), residues: 967 loop : -2.44 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 392 TYR 0.016 0.002 TYR D 63 PHE 0.018 0.002 PHE C 75 TRP 0.033 0.002 TRP C 366 HIS 0.013 0.002 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (21808) covalent geometry : angle 0.88196 / 0.42 (29943) SS BOND : bond 0.00595 / 0.41 ( 43) SS BOND : angle 1.63380 / 1.02 ( 86) hydrogen bonds : bond 0.03833 / 2.58 ( 498) hydrogen bonds : angle 5.41769 / 3.63 ( 1476) link_BETA1-4 : bond 0.00597 / 0.34 ( 10) link_BETA1-4 : angle 2.34361 / 1.45 ( 30) link_NAG-ASN : bond 0.00737 / 0.39 ( 9) link_NAG-ASN : angle 4.88424 / 4.32 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 306 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8602 (ptm160) REVERT: A 410 THR cc_start: 0.9418 (OUTLIER) cc_final: 0.9059 (p) REVERT: A 428 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: A 448 ILE cc_start: 0.9200 (tp) cc_final: 0.8976 (tt) REVERT: B 403 GLU cc_start: 0.8543 (pt0) cc_final: 0.8253 (pm20) REVERT: B 426 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8444 (tttm) REVERT: C 89 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8808 (mpp80) REVERT: C 298 ARG cc_start: 0.8724 (mtt180) cc_final: 0.8407 (mpp80) REVERT: D 45 ASN cc_start: 0.9340 (m-40) cc_final: 0.8874 (m-40) REVERT: D 48 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8662 (mp0) REVERT: D 126 GLU cc_start: 0.7911 (pm20) cc_final: 0.7342 (pm20) REVERT: F 338 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8601 (tp) REVERT: F 346 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8127 (ptt-90) REVERT: F 358 GLU cc_start: 0.9006 (tt0) cc_final: 0.8676 (tm-30) REVERT: F 466 GLU cc_start: 0.9024 (tt0) cc_final: 0.8545 (tp30) REVERT: G 243 HIS cc_start: 0.7226 (t70) cc_final: 0.6329 (t70) REVERT: G 278 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7717 (p) REVERT: G 346 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8656 (mtm-85) REVERT: G 392 ARG cc_start: 0.8608 (ptm-80) cc_final: 0.7983 (ttp80) REVERT: G 425 LYS cc_start: 0.9612 (mmmm) cc_final: 0.9402 (mmmm) REVERT: G 433 MET cc_start: 0.9266 (mmm) cc_final: 0.9028 (mmm) REVERT: G 466 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: K 266 CYS cc_start: 0.6371 (t) cc_final: 0.5373 (p) REVERT: K 279 PHE cc_start: 0.8461 (m-80) cc_final: 0.7741 (m-80) REVERT: K 321 PHE cc_start: 0.8676 (m-80) cc_final: 0.8464 (m-10) REVERT: K 378 ASP cc_start: 0.8926 (m-30) cc_final: 0.8704 (m-30) REVERT: K 384 LEU cc_start: 0.9225 (mt) cc_final: 0.8936 (tp) REVERT: K 389 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: L 346 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.6649 (ttm-80) REVERT: L 348 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7945 (mp0) REVERT: L 433 MET cc_start: 0.8988 (ttm) cc_final: 0.8447 (tmm) REVERT: L 464 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7212 (pmm) REVERT: E 348 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7997 (mm-30) REVERT: E 352 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9117 (mm) REVERT: E 374 PHE cc_start: 0.7081 (p90) cc_final: 0.6642 (p90) REVERT: E 403 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8349 (tm-30) REVERT: E 445 GLN cc_start: 0.7329 (tp-100) cc_final: 0.5486 (mt0) REVERT: H 370 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7926 (tm) REVERT: H 410 THR cc_start: 0.8624 (OUTLIER) cc_final: 0.8416 (p) REVERT: H 423 ASP cc_start: 0.8985 (p0) cc_final: 0.8755 (OUTLIER) REVERT: H 426 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8781 (pptt) REVERT: H 454 LYS cc_start: 0.7904 (tppp) cc_final: 0.7542 (tptp) REVERT: I 382 ARG cc_start: 0.7482 (mmm160) cc_final: 0.7115 (mmt90) REVERT: I 383 TRP cc_start: 0.7959 (m100) cc_final: 0.7513 (m-10) REVERT: I 464 MET cc_start: 0.7549 (mmt) cc_final: 0.7267 (mmt) REVERT: J 369 CYS cc_start: 0.7168 (t) cc_final: 0.6456 (p) REVERT: J 437 GLU cc_start: 0.8659 (tm-30) cc_final: 0.7559 (pm20) outliers start: 123 outliers final: 71 residues processed: 400 average time/residue: 0.5251 time to fit residues: 244.0355 Evaluate side-chains 365 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 281 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 392 ARG Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 517 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain D residue 9 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 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 389 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 419 VAL Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain L residue 464 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 249 HIS Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 269 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 274 optimal weight: 20.0000 chunk 14 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 HIS B 343 ASN C 11 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 249 HIS ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 HIS H 313 GLN ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 327 HIS J 343 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.133403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.100117 restraints weight = 54727.622| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.45 r_work: 0.3479 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21870 Z= 0.154 Angle : 0.862 17.209 30086 Z= 0.407 Chirality : 0.047 0.561 3641 Planarity : 0.005 0.087 3829 Dihedral : 5.324 29.260 3045 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.51 % Rotamer: Outliers : 4.50 % Allowed : 29.33 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.48 % 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: -2.29 (0.15), residues: 2869 helix: -1.22 (0.37), residues: 207 sheet: -0.42 (0.17), residues: 958 loop : -2.33 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 392 TYR 0.012 0.001 TYR D 63 PHE 0.023 0.001 PHE H 321 TRP 0.046 0.002 TRP L 315 HIS 0.032 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (21808) covalent geometry : angle 0.84520 / 0.40 (29943) SS BOND : bond 0.00504 / 0.37 ( 43) SS BOND : angle 1.35731 / 0.89 ( 86) hydrogen bonds : bond 0.03274 / 2.21 ( 498) hydrogen bonds : angle 5.14922 / 3.45 ( 1476) link_BETA1-4 : bond 0.00621 / 0.34 ( 10) link_BETA1-4 : angle 2.32594 / 1.41 ( 30) link_NAG-ASN : bond 0.00707 / 0.38 ( 9) link_NAG-ASN : angle 4.79943 / 4.28 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 304 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 THR cc_start: 0.9357 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 428 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8525 (mp0) REVERT: A 448 ILE cc_start: 0.9174 (tp) cc_final: 0.8946 (tt) REVERT: B 264 LEU cc_start: 0.8329 (tt) cc_final: 0.7921 (mp) REVERT: B 403 GLU cc_start: 0.8585 (pt0) cc_final: 0.8263 (pm20) REVERT: B 426 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8458 (tttp) REVERT: B 428 GLU cc_start: 0.8107 (mp0) cc_final: 0.7351 (mp0) REVERT: C 89 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8853 (mpp80) REVERT: C 164 TYR cc_start: 0.7411 (m-10) cc_final: 0.6835 (t80) REVERT: C 298 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8399 (mpp80) REVERT: C 331 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7263 (mp0) REVERT: C 526 CYS cc_start: 0.7510 (t) cc_final: 0.7055 (p) REVERT: D 45 ASN cc_start: 0.9350 (m-40) cc_final: 0.8957 (m-40) REVERT: D 48 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8691 (mp0) REVERT: D 126 GLU cc_start: 0.7850 (pm20) cc_final: 0.7268 (pm20) REVERT: F 338 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8564 (tp) REVERT: F 358 GLU cc_start: 0.9001 (tt0) cc_final: 0.8548 (tm-30) REVERT: F 466 GLU cc_start: 0.9001 (tt0) cc_final: 0.8543 (tp30) REVERT: G 243 HIS cc_start: 0.7248 (t70) cc_final: 0.6392 (t70) REVERT: G 278 THR cc_start: 0.7943 (OUTLIER) cc_final: 0.7649 (p) REVERT: G 346 ARG cc_start: 0.8872 (mtm-85) cc_final: 0.8629 (mtm-85) REVERT: G 392 ARG cc_start: 0.8499 (ptm-80) cc_final: 0.7885 (ttp80) REVERT: G 425 LYS cc_start: 0.9628 (mmmm) cc_final: 0.9318 (mmmm) REVERT: G 433 MET cc_start: 0.9284 (mmm) cc_final: 0.9043 (mmm) REVERT: G 466 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: K 266 CYS cc_start: 0.6108 (t) cc_final: 0.5143 (p) REVERT: K 279 PHE cc_start: 0.8471 (m-80) cc_final: 0.7546 (m-10) REVERT: K 321 PHE cc_start: 0.8634 (m-80) cc_final: 0.8428 (m-10) REVERT: K 378 ASP cc_start: 0.8901 (m-30) cc_final: 0.8617 (m-30) REVERT: K 384 LEU cc_start: 0.9175 (mt) cc_final: 0.8910 (tp) REVERT: K 389 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: K 414 THR cc_start: 0.8967 (p) cc_final: 0.8748 (p) REVERT: L 346 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.6620 (ttm-80) REVERT: L 348 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7839 (mp0) REVERT: L 433 MET cc_start: 0.8979 (ttm) cc_final: 0.8721 (tmm) REVERT: L 464 MET cc_start: 0.7747 (mtm) cc_final: 0.7338 (pmm) REVERT: E 315 TRP cc_start: 0.5914 (t-100) cc_final: 0.5636 (t-100) REVERT: E 348 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7890 (mp0) REVERT: E 352 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9139 (mm) REVERT: E 374 PHE cc_start: 0.7072 (p90) cc_final: 0.6761 (p90) REVERT: E 403 GLU cc_start: 0.8578 (tm-30) cc_final: 0.8267 (tm-30) REVERT: E 445 GLN cc_start: 0.7297 (tp-100) cc_final: 0.5452 (mt0) REVERT: H 268 LEU cc_start: 0.7621 (tm) cc_final: 0.7356 (pp) REVERT: H 370 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7744 (tm) REVERT: H 423 ASP cc_start: 0.8965 (p0) cc_final: 0.8712 (OUTLIER) REVERT: H 426 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8776 (pptt) REVERT: H 454 LYS cc_start: 0.7898 (tppp) cc_final: 0.7558 (tptp) REVERT: I 345 PHE cc_start: 0.7420 (OUTLIER) cc_final: 0.7084 (t80) REVERT: I 382 ARG cc_start: 0.7396 (mmm160) cc_final: 0.7138 (mmt90) REVERT: I 383 TRP cc_start: 0.7720 (m100) cc_final: 0.7305 (m-10) REVERT: I 449 ASP cc_start: 0.7598 (t0) cc_final: 0.7284 (t0) REVERT: I 464 MET cc_start: 0.7487 (mmt) cc_final: 0.7238 (mmt) REVERT: J 369 CYS cc_start: 0.7267 (t) cc_final: 0.6247 (m) REVERT: J 437 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7561 (pm20) outliers start: 97 outliers final: 66 residues processed: 376 average time/residue: 0.5041 time to fit residues: 220.6753 Evaluate side-chains 367 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 292 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 343 ASN Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 389 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 423 ASP Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 448 ILE Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 343 ASN Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 206 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 273 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 230 optimal weight: 0.0870 chunk 177 optimal weight: 0.9980 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 327 HIS B 343 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 HIS ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.133336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.099936 restraints weight = 54847.188| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 4.48 r_work: 0.3476 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.380 21870 Z= 0.233 Angle : 1.021 59.200 30086 Z= 0.516 Chirality : 0.047 0.561 3641 Planarity : 0.006 0.180 3829 Dihedral : 5.308 29.186 3045 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.81 % Favored : 92.12 % Rotamer: Outliers : 3.85 % Allowed : 30.07 % Favored : 66.08 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.48 % 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: -2.27 (0.15), residues: 2869 helix: -1.23 (0.37), residues: 207 sheet: -0.41 (0.17), residues: 958 loop : -2.32 (0.14), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 392 TYR 0.010 0.001 TYR D 63 PHE 0.016 0.001 PHE C 75 TRP 0.039 0.002 TRP L 315 HIS 0.021 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (21808) covalent geometry : angle 0.99053 / 0.50 (29943) SS BOND : bond 0.00835 / 0.52 ( 43) SS BOND : angle 3.75358 / 2.32 ( 86) hydrogen bonds : bond 0.03235 / 2.18 ( 498) hydrogen bonds : angle 5.15230 / 3.46 ( 1476) link_BETA1-4 : bond 0.00580 / 0.33 ( 10) link_BETA1-4 : angle 2.31540 / 1.40 ( 30) link_NAG-ASN : bond 0.00700 / 0.37 ( 9) link_NAG-ASN : angle 4.79607 / 4.28 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5738 Ramachandran restraints generated. 2869 Oldfield, 0 Emsley, 2869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 293 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9063 (p) REVERT: A 428 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8526 (mp0) REVERT: A 448 ILE cc_start: 0.9177 (tp) cc_final: 0.8950 (tt) REVERT: B 264 LEU cc_start: 0.8333 (tt) cc_final: 0.7925 (mp) REVERT: B 403 GLU cc_start: 0.8574 (pt0) cc_final: 0.8251 (pm20) REVERT: B 426 LYS cc_start: 0.8795 (ttpp) cc_final: 0.8458 (tttp) REVERT: B 428 GLU cc_start: 0.8101 (mp0) cc_final: 0.7335 (mp0) REVERT: C 8 GLU cc_start: 0.8727 (tp30) cc_final: 0.8381 (tp30) REVERT: C 89 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8843 (mpp80) REVERT: C 125 ASP cc_start: 0.6773 (m-30) cc_final: 0.6060 (p0) REVERT: C 164 TYR cc_start: 0.7411 (m-10) cc_final: 0.6835 (t80) REVERT: C 298 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8399 (mpp80) REVERT: C 504 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5345 (pt0) REVERT: C 526 CYS cc_start: 0.7427 (t) cc_final: 0.7027 (p) REVERT: D 23 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8404 (pp) REVERT: D 45 ASN cc_start: 0.9354 (m-40) cc_final: 0.8964 (m-40) REVERT: D 48 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8687 (mp0) REVERT: D 126 GLU cc_start: 0.7850 (pm20) cc_final: 0.7268 (pm20) REVERT: F 338 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8563 (tp) REVERT: F 346 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.8228 (ptt-90) REVERT: F 358 GLU cc_start: 0.8998 (tt0) cc_final: 0.8538 (tm-30) REVERT: F 466 GLU cc_start: 0.8998 (tt0) cc_final: 0.8540 (tp30) REVERT: G 243 HIS cc_start: 0.7251 (t70) cc_final: 0.6396 (t70) REVERT: G 278 THR cc_start: 0.7945 (OUTLIER) cc_final: 0.7647 (p) REVERT: G 346 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8641 (mtm-85) REVERT: G 392 ARG cc_start: 0.8497 (ptm-80) cc_final: 0.7879 (ttp80) REVERT: G 425 LYS cc_start: 0.9620 (mmmm) cc_final: 0.9310 (mmmm) REVERT: G 433 MET cc_start: 0.9280 (mmm) cc_final: 0.9045 (mmm) REVERT: G 466 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: K 266 CYS cc_start: 0.6112 (t) cc_final: 0.5140 (p) REVERT: K 279 PHE cc_start: 0.8470 (m-80) cc_final: 0.7551 (m-10) REVERT: K 378 ASP cc_start: 0.8895 (m-30) cc_final: 0.8633 (m-30) REVERT: K 384 LEU cc_start: 0.9176 (mt) cc_final: 0.8908 (tp) REVERT: K 389 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: K 414 THR cc_start: 0.8970 (p) cc_final: 0.8751 (p) REVERT: L 348 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7845 (mp0) REVERT: L 433 MET cc_start: 0.8960 (ttm) cc_final: 0.8636 (ppp) REVERT: L 464 MET cc_start: 0.7754 (mtm) cc_final: 0.7344 (pmm) REVERT: E 315 TRP cc_start: 0.5917 (t-100) cc_final: 0.5644 (t-100) REVERT: E 348 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7890 (mp0) REVERT: E 352 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9135 (mm) REVERT: E 374 PHE cc_start: 0.7063 (p90) cc_final: 0.6751 (p90) REVERT: E 403 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8270 (tm-30) REVERT: E 445 GLN cc_start: 0.7304 (tp-100) cc_final: 0.5444 (mt0) REVERT: H 268 LEU cc_start: 0.7629 (tm) cc_final: 0.7364 (pp) REVERT: H 370 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7753 (tm) REVERT: H 423 ASP cc_start: 0.8957 (p0) cc_final: 0.8703 (OUTLIER) REVERT: H 426 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8776 (pptt) REVERT: H 454 LYS cc_start: 0.7898 (tppp) cc_final: 0.7555 (tptp) REVERT: I 345 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7083 (t80) REVERT: I 382 ARG cc_start: 0.7401 (mmm160) cc_final: 0.7137 (mmt90) REVERT: I 383 TRP cc_start: 0.7711 (m100) cc_final: 0.7289 (m-10) REVERT: I 449 ASP cc_start: 0.7526 (t0) cc_final: 0.7257 (t0) REVERT: I 464 MET cc_start: 0.7486 (mmt) cc_final: 0.7233 (mmt) REVERT: J 369 CYS cc_start: 0.7263 (t) cc_final: 0.6245 (m) REVERT: J 437 GLU cc_start: 0.8636 (tm-30) cc_final: 0.7539 (pm20) outliers start: 83 outliers final: 67 residues processed: 353 average time/residue: 0.5346 time to fit residues: 219.0764 Evaluate side-chains 371 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 292 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 287 LYS Chi-restraints excluded: chain A residue 368 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 327 HIS Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 23 ILE Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain F residue 346 ARG Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 359 LEU Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 389 GLU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 338 ILE Chi-restraints excluded: chain L residue 368 THR Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 417 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 448 ILE Chi-restraints excluded: chain L residue 457 HIS Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 249 HIS Chi-restraints excluded: chain H residue 322 THR Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 375 SER Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 426 LYS Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 449 ASP Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 385 GLN Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 381 VAL Chi-restraints excluded: chain J residue 434 VAL Chi-restraints excluded: chain J residue 444 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 249 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 264 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 208 optimal weight: 0.0030 chunk 171 optimal weight: 0.7980 chunk 156 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.133437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.100070 restraints weight = 54730.486| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 4.49 r_work: 0.3478 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.273 21870 Z= 0.207 Angle : 1.085 59.200 30086 Z= 0.596 Chirality : 0.047 0.563 3641 Planarity : 0.006 0.138 3829 Dihedral : 5.299 29.323 3045 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.02 % Favored : 91.95 % Rotamer: Outliers : 3.94 % Allowed : 30.16 % Favored : 65.89 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.48 % 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: -2.25 (0.15), residues: 2869 helix: -1.22 (0.37), residues: 207 sheet: -0.38 (0.17), residues: 957 loop : -2.31 (0.14), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 392 TYR 0.015 0.001 TYR D 63 PHE 0.015 0.001 PHE C 75 TRP 0.034 0.001 TRP L 315 HIS 0.118 0.003 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (21808) covalent geometry : angle 1.06611 / 0.59 (29943) SS BOND : bond 0.01008 / 0.56 ( 43) SS BOND : angle 2.60268 / 1.61 ( 86) hydrogen bonds : bond 0.03251 / 2.23 ( 498) hydrogen bonds : angle 5.14683 / 3.46 ( 1476) link_BETA1-4 : bond 0.00613 / 0.33 ( 10) link_BETA1-4 : angle 2.32431 / 1.41 ( 30) link_NAG-ASN : bond 0.00703 / 0.37 ( 9) link_NAG-ASN : angle 4.77916 / 4.27 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9158.08 seconds wall clock time: 156 minutes 22.37 seconds (9382.37 seconds total)