Starting phenix.real_space_refine on Thu Mar 5 10:25:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uea_20752/03_2026/6uea_20752.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uea_20752/03_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_20752/03_2026/6uea_20752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uea_20752/03_2026/6uea_20752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uea_20752/03_2026/6uea_20752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uea_20752/03_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-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.25, per 1000 atoms: 0.25 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: 1.81 Conformation dependent library (CDL) restraints added in 982.9 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: 0.91 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: 4.13 Time building geometry restraints manager: 2.46 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 - 21.10: 12170 21.10 - 42.19: 954 42.19 - 63.29: 107 63.29 - 84.39: 30 84.39 - 105.49: 15 Dihedral angle restraints: 13276 sinusoidal: 4923 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 13273 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: 4.760 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.480 Find NCS groups from input model: 0.500 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:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 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 : 15.177 105.485 7737 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 covalent geometry : bond 0.00852 (21808) covalent geometry : angle 1.16141 (29943) SS BOND : bond 0.00757 ( 43) SS BOND : angle 1.67164 ( 86) hydrogen bonds : bond 0.27926 ( 498) hydrogen bonds : angle 9.29123 ( 1476) link_BETA1-4 : bond 0.01970 ( 10) link_BETA1-4 : angle 5.47370 ( 30) link_NAG-ASN : bond 0.01086 ( 9) link_NAG-ASN : angle 7.55335 ( 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 : 0.887 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: 0.5832 time to fit residues: 389.1576 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 : 0.755 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 343 ASN A 445 GLN B 327 HIS 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.140265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.104870 restraints weight = 54621.786| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 4.66 r_work: 0.3536 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21870 Z= 0.171 Angle : 0.869 19.158 30086 Z= 0.416 Chirality : 0.049 0.619 3641 Planarity : 0.007 0.080 3829 Dihedral : 9.723 86.264 3453 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.34 % Favored : 90.62 % Rotamer: Outliers : 5.24 % Allowed : 20.51 % 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: -3.77 (0.13), residues: 2869 helix: -3.19 (0.28), residues: 183 sheet: -1.65 (0.15), residues: 951 loop : -3.08 (0.13), residues: 1735 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 0.020 0.001 PHE E 430 TRP 0.019 0.002 TRP J 424 HIS 0.012 0.001 HIS B 243 Details of bonding type rmsd covalent geometry : bond 0.00398 (21808) covalent geometry : angle 0.84321 (29943) SS BOND : bond 0.00593 ( 43) SS BOND : angle 1.51510 ( 86) hydrogen bonds : bond 0.04151 ( 498) hydrogen bonds : angle 6.05681 ( 1476) link_BETA1-4 : bond 0.00849 ( 10) link_BETA1-4 : angle 3.41553 ( 30) link_NAG-ASN : bond 0.00918 ( 9) link_NAG-ASN : angle 5.77262 ( 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: 113 poor density : 375 time to evaluate : 0.843 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: A 319 GLU cc_start: 0.7906 (mp0) cc_final: 0.7555 (mp0) REVERT: A 428 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8565 (mt-10) REVERT: A 448 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8744 (tt) REVERT: A 450 ARG cc_start: 0.8835 (ptm-80) cc_final: 0.8281 (tmm-80) REVERT: B 403 GLU cc_start: 0.8515 (pt0) cc_final: 0.7910 (pm20) REVERT: B 428 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7749 (mp0) REVERT: C 8 GLU cc_start: 0.7623 (tp30) cc_final: 0.7210 (tp30) REVERT: C 16 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8437 (m-40) REVERT: C 298 ARG cc_start: 0.8458 (mtt180) cc_final: 0.8124 (mpp80) REVERT: C 330 GLU cc_start: 0.7432 (pp20) cc_final: 0.7114 (pp20) REVERT: C 331 GLU cc_start: 0.7576 (mm-30) cc_final: 0.6947 (mm-30) REVERT: C 477 TRP cc_start: 0.6243 (m100) cc_final: 0.5883 (m100) REVERT: D 22 ILE cc_start: 0.9106 (mt) cc_final: 0.8811 (tp) REVERT: D 69 CYS cc_start: 0.7581 (m) cc_final: 0.7317 (m) REVERT: F 463 VAL cc_start: 0.9167 (t) cc_final: 0.8949 (m) REVERT: G 410 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.9050 (t) REVERT: G 423 ASP cc_start: 0.9340 (t0) cc_final: 0.9100 (m-30) REVERT: K 346 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7530 (mtp85) REVERT: K 358 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7381 (tm-30) REVERT: K 384 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8987 (mt) REVERT: L 315 TRP cc_start: 0.4116 (t-100) cc_final: 0.3903 (OUTLIER) REVERT: L 433 MET cc_start: 0.7905 (tpp) cc_final: 0.7582 (tpt) REVERT: I 320 THR cc_start: 0.6298 (OUTLIER) cc_final: 0.6069 (p) REVERT: I 380 LEU cc_start: 0.4574 (tt) cc_final: 0.4130 (tt) REVERT: I 395 TYR cc_start: 0.6536 (p90) cc_final: 0.5443 (p90) REVERT: I 449 ASP cc_start: 0.7809 (t0) cc_final: 0.7282 (t0) REVERT: J 369 CYS cc_start: 0.6978 (OUTLIER) cc_final: 0.5992 (p) REVERT: J 370 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8884 (tm) REVERT: J 410 THR cc_start: 0.7007 (t) cc_final: 0.6715 (m) REVERT: J 430 PHE cc_start: 0.7584 (m-80) cc_final: 0.7336 (m-80) outliers start: 113 outliers final: 43 residues processed: 442 average time/residue: 0.4912 time to fit residues: 251.8900 Evaluate side-chains 381 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 332 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 448 ILE 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 327 HIS 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 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 384 LEU Chi-restraints excluded: chain K residue 460 VAL Chi-restraints excluded: chain L residue 257 LEU 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 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: 5.9990 chunk 105 optimal weight: 0.0870 chunk 82 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 135 optimal weight: 0.0040 chunk 81 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.2174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN ** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN F 327 HIS K 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.138253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.103438 restraints weight = 54658.605| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 4.58 r_work: 0.3516 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21870 Z= 0.156 Angle : 0.823 19.743 30086 Z= 0.390 Chirality : 0.048 0.613 3641 Planarity : 0.006 0.069 3829 Dihedral : 7.988 58.797 3439 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.06 % Favored : 90.90 % Rotamer: Outliers : 5.99 % Allowed : 22.69 % Favored : 71.32 % 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: -3.21 (0.14), residues: 2869 helix: -2.47 (0.32), residues: 188 sheet: -1.17 (0.16), residues: 945 loop : -2.78 (0.13), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 392 TYR 0.014 0.001 TYR J 411 PHE 0.017 0.001 PHE C 75 TRP 0.016 0.001 TRP A 281 HIS 0.015 0.001 HIS K 317 Details of bonding type rmsd covalent geometry : bond 0.00366 (21808) covalent geometry : angle 0.79841 (29943) SS BOND : bond 0.00473 ( 43) SS BOND : angle 1.26652 ( 86) hydrogen bonds : bond 0.03669 ( 498) hydrogen bonds : angle 5.45545 ( 1476) link_BETA1-4 : bond 0.00807 ( 10) link_BETA1-4 : angle 3.40936 ( 30) link_NAG-ASN : bond 0.00731 ( 9) link_NAG-ASN : angle 5.49577 ( 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 482 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 353 time to evaluate : 0.840 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 319 GLU cc_start: 0.8002 (mp0) cc_final: 0.7643 (mp0) REVERT: A 324 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.7903 (m) REVERT: A 428 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8556 (mp0) REVERT: A 448 ILE cc_start: 0.9063 (tp) cc_final: 0.8807 (tt) REVERT: A 450 ARG cc_start: 0.8832 (ptm-80) cc_final: 0.8377 (tmm-80) REVERT: B 392 ARG cc_start: 0.8625 (tpp-160) cc_final: 0.8302 (tpt90) REVERT: B 403 GLU cc_start: 0.8478 (pt0) cc_final: 0.8197 (pm20) REVERT: B 428 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7743 (mp0) REVERT: C 8 GLU cc_start: 0.8128 (tp30) cc_final: 0.7692 (tp30) REVERT: C 134 CYS cc_start: 0.4519 (OUTLIER) cc_final: 0.3866 (t) REVERT: C 298 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8217 (mpp80) REVERT: C 331 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6981 (mm-30) REVERT: C 366 TRP cc_start: 0.7721 (t-100) cc_final: 0.7512 (t-100) REVERT: C 542 VAL cc_start: 0.8155 (OUTLIER) cc_final: 0.7932 (p) REVERT: D 48 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8611 (mp0) REVERT: D 91 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9047 (pp) REVERT: D 126 GLU cc_start: 0.7626 (pm20) cc_final: 0.7077 (pm20) REVERT: F 463 VAL cc_start: 0.9170 (t) cc_final: 0.8969 (m) REVERT: F 464 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8879 (mtm) REVERT: G 243 HIS cc_start: 0.7241 (t70) cc_final: 0.6779 (t70) REVERT: G 346 ARG cc_start: 0.8874 (mtm-85) cc_final: 0.8581 (mtm-85) REVERT: G 410 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.8884 (t) REVERT: G 433 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.9026 (mmm) REVERT: G 449 ASP cc_start: 0.9112 (p0) cc_final: 0.8882 (p0) REVERT: K 348 GLU cc_start: 0.8506 (mp0) cc_final: 0.8065 (mp0) REVERT: K 358 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7426 (tm-30) REVERT: K 385 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8401 (tm-30) REVERT: K 394 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8782 (mmpt) REVERT: L 315 TRP cc_start: 0.4169 (t-100) cc_final: 0.3949 (OUTLIER) REVERT: I 320 THR cc_start: 0.6902 (OUTLIER) cc_final: 0.6538 (p) REVERT: I 382 ARG cc_start: 0.7302 (mmm160) cc_final: 0.6707 (mmt90) REVERT: I 383 TRP cc_start: 0.7717 (m100) cc_final: 0.7138 (m-10) REVERT: I 449 ASP cc_start: 0.7816 (t0) cc_final: 0.7268 (t0) REVERT: J 369 CYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6906 (p) REVERT: J 372 ARG cc_start: 0.8496 (ttt90) cc_final: 0.8151 (tmt90) REVERT: J 430 PHE cc_start: 0.7643 (m-80) cc_final: 0.7381 (m-80) outliers start: 129 outliers final: 62 residues processed: 438 average time/residue: 0.5009 time to fit residues: 255.4311 Evaluate side-chains 381 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 311 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 268 LEU 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 124 VAL 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 332 SER 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 451 ASN 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 C residue 542 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 F residue 380 LEU Chi-restraints excluded: chain F residue 448 ILE 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 417 LEU 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 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 390 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 339 THR Chi-restraints excluded: chain E residue 368 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 423 ASP Chi-restraints excluded: chain H residue 432 CYS 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 344 THR Chi-restraints excluded: chain I residue 417 LEU Chi-restraints excluded: chain I residue 429 THR Chi-restraints excluded: chain J residue 349 VAL Chi-restraints excluded: chain J residue 369 CYS Chi-restraints excluded: chain J residue 434 VAL 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: 0.9980 chunk 3 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 239 optimal weight: 0.0270 chunk 31 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 251 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 268 optimal weight: 9.9990 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 HIS D 45 ASN F 385 GLN K 316 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.138213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.102067 restraints weight = 55204.008| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.73 r_work: 0.3505 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21870 Z= 0.142 Angle : 0.791 19.168 30086 Z= 0.372 Chirality : 0.047 0.633 3641 Planarity : 0.005 0.062 3829 Dihedral : 7.274 57.551 3438 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 6.13 % Allowed : 23.16 % Favored : 70.72 % 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: -2.89 (0.15), residues: 2869 helix: -1.95 (0.35), residues: 185 sheet: -0.96 (0.16), residues: 975 loop : -2.63 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 392 TYR 0.011 0.001 TYR C 24 PHE 0.016 0.001 PHE C 75 TRP 0.017 0.001 TRP A 281 HIS 0.010 0.001 HIS K 317 Details of bonding type rmsd covalent geometry : bond 0.00338 (21808) covalent geometry : angle 0.76697 (29943) SS BOND : bond 0.00406 ( 43) SS BOND : angle 1.21697 ( 86) hydrogen bonds : bond 0.03194 ( 498) hydrogen bonds : angle 5.31440 ( 1476) link_BETA1-4 : bond 0.00835 ( 10) link_BETA1-4 : angle 3.27985 ( 30) link_NAG-ASN : bond 0.00712 ( 9) link_NAG-ASN : angle 5.33224 ( 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 480 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 348 time to evaluate : 0.681 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: 0.9075 (mt-10) cc_final: 0.8617 (mp0) REVERT: A 448 ILE cc_start: 0.9107 (tp) cc_final: 0.8875 (tt) REVERT: A 450 ARG cc_start: 0.8966 (ptm-80) cc_final: 0.8441 (tmm-80) REVERT: B 343 ASN cc_start: 0.7970 (t0) cc_final: 0.7726 (t0) REVERT: B 403 GLU cc_start: 0.8566 (pt0) cc_final: 0.8264 (pm20) REVERT: C 8 GLU cc_start: 0.8286 (tp30) cc_final: 0.7918 (tp30) REVERT: C 134 CYS cc_start: 0.4680 (OUTLIER) cc_final: 0.3822 (t) REVERT: C 298 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8244 (mpp80) REVERT: C 331 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7215 (mm-30) REVERT: C 366 TRP cc_start: 0.7745 (t-100) cc_final: 0.7462 (t-100) REVERT: D 48 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8572 (mp0) REVERT: D 71 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8482 (ptpp) REVERT: D 88 GLN cc_start: 0.9516 (OUTLIER) cc_final: 0.9253 (mt0) REVERT: D 126 GLU cc_start: 0.7725 (pm20) cc_final: 0.7137 (pm20) REVERT: F 358 GLU cc_start: 0.8667 (tt0) cc_final: 0.8456 (tt0) REVERT: F 463 VAL cc_start: 0.9141 (t) cc_final: 0.8937 (m) REVERT: F 464 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8890 (mtm) REVERT: G 243 HIS cc_start: 0.7253 (t70) cc_final: 0.6550 (t70) REVERT: G 278 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8182 (p) REVERT: G 346 ARG cc_start: 0.8892 (mtm-85) cc_final: 0.8621 (mtm-85) REVERT: G 410 THR cc_start: 0.9414 (OUTLIER) cc_final: 0.8900 (t) REVERT: G 433 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9059 (mmm) REVERT: G 449 ASP cc_start: 0.9102 (p0) cc_final: 0.8891 (p0) REVERT: K 346 ARG cc_start: 0.8097 (mtm-85) cc_final: 0.7808 (mtm-85) REVERT: K 348 GLU cc_start: 0.8508 (mp0) cc_final: 0.8188 (mp0) REVERT: K 358 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7411 (tm-30) REVERT: K 378 ASP cc_start: 0.8329 (m-30) cc_final: 0.8038 (m-30) REVERT: K 385 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8505 (tm-30) REVERT: K 394 LYS cc_start: 0.9017 (mmpt) cc_final: 0.8769 (mmpt) REVERT: L 315 TRP cc_start: 0.4287 (t-100) cc_final: 0.3943 (OUTLIER) REVERT: E 345 PHE cc_start: 0.7871 (m-80) cc_final: 0.7643 (m-80) REVERT: E 444 THR cc_start: 0.7108 (OUTLIER) cc_final: 0.6711 (t) REVERT: E 445 GLN cc_start: 0.7313 (tp-100) cc_final: 0.5461 (mt0) REVERT: H 454 LYS cc_start: 0.7707 (tppp) cc_final: 0.7394 (tptp) REVERT: I 382 ARG cc_start: 0.7231 (mmm160) cc_final: 0.6753 (mmt-90) REVERT: I 383 TRP cc_start: 0.7591 (m100) cc_final: 0.6954 (m-10) REVERT: I 423 ASP cc_start: 0.8047 (m-30) cc_final: 0.7800 (p0) REVERT: I 449 ASP cc_start: 0.7694 (t0) cc_final: 0.7487 (t0) REVERT: J 430 PHE cc_start: 0.7680 (m-80) cc_final: 0.7333 (m-80) outliers start: 132 outliers final: 70 residues processed: 440 average time/residue: 0.5135 time to fit residues: 261.9530 Evaluate side-chains 392 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 279 PHE 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 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 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 451 ASN Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 528 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 71 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 88 GLN 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 380 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 464 MET 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 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 351 LEU Chi-restraints excluded: chain K residue 379 VAL 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 370 LEU Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 417 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 444 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 423 ASP 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 417 LEU Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 434 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: 4.9990 chunk 255 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 69 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 132 optimal weight: 0.3980 chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN C 329 ASN D 45 ASN K 316 ASN H 327 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.137716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.103557 restraints weight = 54949.635| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 4.56 r_work: 0.3521 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21870 Z= 0.131 Angle : 0.781 18.292 30086 Z= 0.367 Chirality : 0.047 0.665 3641 Planarity : 0.005 0.060 3829 Dihedral : 6.885 56.870 3438 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.05 % Favored : 91.91 % Rotamer: Outliers : 5.61 % Allowed : 24.87 % Favored : 69.51 % 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: -2.69 (0.15), residues: 2869 helix: -1.89 (0.34), residues: 204 sheet: -0.75 (0.16), residues: 967 loop : -2.52 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 392 TYR 0.010 0.001 TYR E 395 PHE 0.020 0.001 PHE K 345 TRP 0.022 0.001 TRP A 281 HIS 0.007 0.001 HIS H 327 Details of bonding type rmsd covalent geometry : bond 0.00315 (21808) covalent geometry : angle 0.75756 (29943) SS BOND : bond 0.00579 ( 43) SS BOND : angle 1.36977 ( 86) hydrogen bonds : bond 0.03062 ( 498) hydrogen bonds : angle 5.17165 ( 1476) link_BETA1-4 : bond 0.00708 ( 10) link_BETA1-4 : angle 3.14537 ( 30) link_NAG-ASN : bond 0.00728 ( 9) link_NAG-ASN : angle 5.14748 ( 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 458 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 337 time to evaluate : 0.542 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: 0.9013 (mt-10) cc_final: 0.8551 (mp0) REVERT: A 448 ILE cc_start: 0.9131 (tp) cc_final: 0.8861 (tt) REVERT: A 450 ARG cc_start: 0.9013 (ptm-80) cc_final: 0.8421 (tmm-80) REVERT: B 343 ASN cc_start: 0.8106 (t0) cc_final: 0.7802 (t0) REVERT: B 403 GLU cc_start: 0.8534 (pt0) cc_final: 0.8221 (pm20) REVERT: B 426 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8557 (ttpp) REVERT: C 8 GLU cc_start: 0.8350 (tp30) cc_final: 0.7992 (tp30) REVERT: C 82 LEU cc_start: 0.9489 (mp) cc_final: 0.9279 (mm) REVERT: C 134 CYS cc_start: 0.4969 (OUTLIER) cc_final: 0.3944 (t) REVERT: C 298 ARG cc_start: 0.8558 (mtt180) cc_final: 0.8296 (mpp80) REVERT: C 331 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7219 (mm-30) REVERT: C 366 TRP cc_start: 0.7603 (t-100) cc_final: 0.7358 (t-100) REVERT: C 504 GLU cc_start: 0.5365 (OUTLIER) cc_final: 0.4987 (pt0) REVERT: D 48 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8612 (mp0) REVERT: D 71 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8424 (ptpp) REVERT: D 88 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9252 (mt0) REVERT: D 126 GLU cc_start: 0.7667 (pm20) cc_final: 0.7046 (pm20) REVERT: F 463 VAL cc_start: 0.9112 (t) cc_final: 0.8911 (m) REVERT: G 243 HIS cc_start: 0.7181 (t70) cc_final: 0.6442 (t70) REVERT: G 278 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8167 (p) REVERT: G 346 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8526 (mtm-85) REVERT: G 410 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.8882 (t) REVERT: G 425 LYS cc_start: 0.9591 (mmmm) cc_final: 0.9361 (mmmm) REVERT: G 433 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9050 (mmm) REVERT: G 449 ASP cc_start: 0.9088 (p0) cc_final: 0.8886 (p0) REVERT: K 346 ARG cc_start: 0.8140 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: K 348 GLU cc_start: 0.8573 (mp0) cc_final: 0.8313 (mp0) REVERT: K 358 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7449 (tm-30) REVERT: K 378 ASP cc_start: 0.8459 (m-30) cc_final: 0.8006 (m-30) REVERT: K 385 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8506 (tm-30) REVERT: K 394 LYS cc_start: 0.8975 (mmpt) cc_final: 0.8713 (mmpt) REVERT: L 315 TRP cc_start: 0.4264 (t-100) cc_final: 0.4002 (OUTLIER) REVERT: E 345 PHE cc_start: 0.7990 (m-80) cc_final: 0.7767 (m-80) REVERT: E 403 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7952 (tm-30) REVERT: E 445 GLN cc_start: 0.7160 (tp-100) cc_final: 0.5323 (mt0) REVERT: H 410 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8552 (p) REVERT: H 423 ASP cc_start: 0.8808 (p0) cc_final: 0.8538 (p0) REVERT: H 426 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8686 (pptt) REVERT: H 454 LYS cc_start: 0.7676 (tppp) cc_final: 0.7390 (tptp) REVERT: I 449 ASP cc_start: 0.8127 (t0) cc_final: 0.7727 (t0) REVERT: J 369 CYS cc_start: 0.6960 (t) cc_final: 0.6434 (m) REVERT: J 430 PHE cc_start: 0.7776 (m-80) cc_final: 0.7325 (m-80) outliers start: 121 outliers final: 74 residues processed: 422 average time/residue: 0.5090 time to fit residues: 247.8041 Evaluate side-chains 395 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 313 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 279 PHE 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 17 SER 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 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 451 ASN 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 15 CYS 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 71 LYS Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain F residue 282 THR Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 380 LEU 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 375 SER Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 417 LEU 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 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 VAL 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 338 ILE Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 390 LEU Chi-restraints excluded: chain L residue 434 VAL Chi-restraints excluded: chain L residue 444 THR Chi-restraints excluded: chain L residue 460 VAL Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 368 THR Chi-restraints excluded: chain E residue 369 CYS 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 410 THR 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 429 THR Chi-restraints excluded: chain J residue 290 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 52 optimal weight: 0.6980 chunk 202 optimal weight: 0.0370 chunk 124 optimal weight: 5.9990 chunk 217 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 250 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 246 optimal weight: 9.9990 chunk 107 optimal weight: 0.0010 overall best weight: 0.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN D 45 ASN H 327 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.138643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.104638 restraints weight = 55040.088| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.51 r_work: 0.3540 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4501 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= 0.124 Angle : 0.779 18.094 30086 Z= 0.365 Chirality : 0.046 0.661 3641 Planarity : 0.005 0.064 3829 Dihedral : 6.581 56.398 3438 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.48 % Rotamer: Outliers : 5.48 % Allowed : 26.45 % Favored : 68.07 % 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: -2.44 (0.15), residues: 2869 helix: -1.63 (0.35), residues: 204 sheet: -0.51 (0.17), residues: 948 loop : -2.38 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 392 TYR 0.013 0.001 TYR C 24 PHE 0.016 0.001 PHE H 321 TRP 0.019 0.001 TRP I 383 HIS 0.012 0.001 HIS H 327 Details of bonding type rmsd covalent geometry : bond 0.00298 (21808) covalent geometry : angle 0.75412 (29943) SS BOND : bond 0.00415 ( 43) SS BOND : angle 1.65606 ( 86) hydrogen bonds : bond 0.02715 ( 498) hydrogen bonds : angle 5.00827 ( 1476) link_BETA1-4 : bond 0.00764 ( 10) link_BETA1-4 : angle 3.08246 ( 30) link_NAG-ASN : bond 0.00694 ( 9) link_NAG-ASN : angle 5.04717 ( 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 459 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 341 time to evaluate : 0.802 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: A 410 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 428 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8536 (mp0) REVERT: A 448 ILE cc_start: 0.9118 (tp) cc_final: 0.8868 (tt) REVERT: A 450 ARG cc_start: 0.8975 (ptm-80) cc_final: 0.8369 (ttp80) REVERT: B 343 ASN cc_start: 0.8070 (t0) cc_final: 0.7764 (t0) REVERT: B 403 GLU cc_start: 0.8507 (pt0) cc_final: 0.8051 (pm20) REVERT: B 426 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8559 (ttpp) REVERT: B 428 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8086 (mm-30) REVERT: C 8 GLU cc_start: 0.8388 (tp30) cc_final: 0.8040 (tp30) REVERT: C 134 CYS cc_start: 0.4936 (OUTLIER) cc_final: 0.3875 (t) REVERT: C 298 ARG cc_start: 0.8521 (mtt180) cc_final: 0.8278 (mpp80) REVERT: C 331 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7017 (mm-30) REVERT: C 366 TRP cc_start: 0.7430 (t-100) cc_final: 0.7217 (t-100) REVERT: C 504 GLU cc_start: 0.5324 (OUTLIER) cc_final: 0.4872 (pt0) REVERT: D 28 ASP cc_start: 0.8555 (t0) cc_final: 0.8092 (t0) REVERT: D 31 GLU cc_start: 0.6838 (pp20) cc_final: 0.6423 (pm20) REVERT: D 45 ASN cc_start: 0.9226 (m-40) cc_final: 0.8995 (m-40) REVERT: D 48 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8711 (mp0) REVERT: D 88 GLN cc_start: 0.9477 (OUTLIER) cc_final: 0.9194 (mt0) REVERT: D 126 GLU cc_start: 0.7640 (pm20) cc_final: 0.7056 (pm20) REVERT: F 346 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8065 (ptt-90) REVERT: F 416 ILE cc_start: 0.9181 (pt) cc_final: 0.8976 (pp) REVERT: F 466 GLU cc_start: 0.8839 (tt0) cc_final: 0.8295 (tp30) REVERT: G 243 HIS cc_start: 0.7248 (t70) cc_final: 0.6515 (t70) REVERT: G 346 ARG cc_start: 0.8815 (mtm-85) cc_final: 0.8546 (mtm-85) REVERT: G 423 ASP cc_start: 0.9254 (t0) cc_final: 0.9035 (t0) REVERT: G 425 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9375 (mmmm) REVERT: G 431 SER cc_start: 0.9334 (m) cc_final: 0.9096 (p) REVERT: G 433 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8987 (mmm) REVERT: G 466 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8575 (pt0) REVERT: K 346 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7899 (mtm-85) REVERT: K 348 GLU cc_start: 0.8579 (mp0) cc_final: 0.8361 (mp0) REVERT: K 358 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7585 (tm-30) REVERT: K 378 ASP cc_start: 0.8541 (m-30) cc_final: 0.8258 (m-30) REVERT: K 385 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8479 (tm-30) REVERT: K 394 LYS cc_start: 0.8978 (mmpt) cc_final: 0.8706 (mmpt) REVERT: L 315 TRP cc_start: 0.4245 (t-100) cc_final: 0.3991 (OUTLIER) REVERT: E 345 PHE cc_start: 0.8030 (m-80) cc_final: 0.7792 (m-80) REVERT: E 403 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8070 (tm-30) REVERT: E 445 GLN cc_start: 0.7211 (tp-100) cc_final: 0.5508 (mt0) REVERT: H 410 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8557 (p) REVERT: I 351 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8129 (tt) REVERT: I 382 ARG cc_start: 0.7240 (mmm160) cc_final: 0.6825 (mmt-90) REVERT: I 383 TRP cc_start: 0.6760 (m-10) cc_final: 0.6361 (m-10) REVERT: I 449 ASP cc_start: 0.8072 (t0) cc_final: 0.7723 (t0) REVERT: J 257 LEU cc_start: 0.4788 (OUTLIER) cc_final: 0.4577 (tm) REVERT: J 369 CYS cc_start: 0.7094 (t) cc_final: 0.6631 (m) REVERT: J 430 PHE cc_start: 0.7950 (m-80) cc_final: 0.7464 (m-80) outliers start: 118 outliers final: 68 residues processed: 419 average time/residue: 0.5268 time to fit residues: 255.1714 Evaluate side-chains 392 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 315 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 17 SER Chi-restraints excluded: chain C residue 124 VAL 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 446 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 15 CYS 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 88 GLN Chi-restraints excluded: chain F residue 282 THR 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 280 THR Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 433 MET 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 327 HIS Chi-restraints excluded: chain K residue 379 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 390 LEU 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 368 THR Chi-restraints excluded: chain E residue 374 PHE Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE 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 426 LYS 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 351 LEU 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 257 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 120 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 327 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.137839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.103775 restraints weight = 54934.308| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.52 r_work: 0.3526 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21870 Z= 0.132 Angle : 0.785 17.802 30086 Z= 0.369 Chirality : 0.046 0.686 3641 Planarity : 0.005 0.066 3829 Dihedral : 6.417 57.599 3438 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.51 % Rotamer: Outliers : 5.10 % Allowed : 27.24 % Favored : 67.66 % 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: -2.31 (0.15), residues: 2869 helix: -1.51 (0.36), residues: 210 sheet: -0.38 (0.17), residues: 953 loop : -2.34 (0.14), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 392 TYR 0.009 0.001 TYR B 472 PHE 0.015 0.001 PHE C 75 TRP 0.027 0.001 TRP A 281 HIS 0.010 0.001 HIS H 327 Details of bonding type rmsd covalent geometry : bond 0.00320 (21808) covalent geometry : angle 0.76326 (29943) SS BOND : bond 0.00469 ( 43) SS BOND : angle 1.28259 ( 86) hydrogen bonds : bond 0.02821 ( 498) hydrogen bonds : angle 4.95622 ( 1476) link_BETA1-4 : bond 0.00673 ( 10) link_BETA1-4 : angle 3.02706 ( 30) link_NAG-ASN : bond 0.00795 ( 9) link_NAG-ASN : angle 4.99735 ( 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 438 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 328 time to evaluate : 0.790 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 255 ASP cc_start: 0.8939 (m-30) cc_final: 0.8652 (m-30) REVERT: A 280 THR cc_start: 0.8779 (p) cc_final: 0.8430 (p) REVERT: A 410 THR cc_start: 0.9340 (OUTLIER) cc_final: 0.9031 (p) REVERT: A 428 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8535 (mp0) REVERT: A 448 ILE cc_start: 0.9083 (tp) cc_final: 0.8847 (tt) REVERT: A 450 ARG cc_start: 0.9010 (ptm-80) cc_final: 0.8361 (ttp80) REVERT: B 343 ASN cc_start: 0.8231 (t0) cc_final: 0.7905 (t0) REVERT: B 403 GLU cc_start: 0.8597 (pt0) cc_final: 0.8275 (pm20) REVERT: B 426 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8575 (ttpp) REVERT: B 428 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8174 (mm-30) REVERT: C 8 GLU cc_start: 0.8461 (tp30) cc_final: 0.8188 (tp30) REVERT: C 89 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8769 (mtm-85) REVERT: C 134 CYS cc_start: 0.5620 (OUTLIER) cc_final: 0.4135 (t) REVERT: C 298 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8276 (mpp80) REVERT: C 331 GLU cc_start: 0.7315 (mm-30) cc_final: 0.7054 (mm-30) REVERT: C 366 TRP cc_start: 0.7515 (t-100) cc_final: 0.7309 (t-100) REVERT: C 504 GLU cc_start: 0.5290 (OUTLIER) cc_final: 0.4867 (pt0) REVERT: D 28 ASP cc_start: 0.8612 (t0) cc_final: 0.8160 (t0) REVERT: D 31 GLU cc_start: 0.7025 (pp20) cc_final: 0.6452 (pm20) REVERT: D 45 ASN cc_start: 0.9275 (m-40) cc_final: 0.8681 (m110) REVERT: D 48 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8691 (mp0) REVERT: D 88 GLN cc_start: 0.9432 (OUTLIER) cc_final: 0.9168 (mt0) REVERT: D 126 GLU cc_start: 0.7657 (pm20) cc_final: 0.7124 (pm20) REVERT: F 338 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8721 (tp) REVERT: F 346 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8138 (ptt-90) REVERT: F 466 GLU cc_start: 0.8921 (tt0) cc_final: 0.8314 (tp30) REVERT: G 243 HIS cc_start: 0.7218 (t70) cc_final: 0.6482 (t70) REVERT: G 278 THR cc_start: 0.8294 (OUTLIER) cc_final: 0.8045 (p) REVERT: G 410 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.8778 (t) REVERT: G 423 ASP cc_start: 0.9288 (t0) cc_final: 0.9062 (t0) REVERT: G 425 LYS cc_start: 0.9619 (mmmm) cc_final: 0.9407 (mmmm) REVERT: G 431 SER cc_start: 0.9329 (m) cc_final: 0.9100 (p) REVERT: G 433 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8977 (mmm) REVERT: G 449 ASP cc_start: 0.8894 (p0) cc_final: 0.8611 (p0) REVERT: G 466 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8432 (pt0) REVERT: K 255 ASP cc_start: 0.8583 (p0) cc_final: 0.7755 (t0) REVERT: K 346 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: K 348 GLU cc_start: 0.8607 (mp0) cc_final: 0.8394 (mp0) REVERT: K 358 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7444 (tm-30) REVERT: K 378 ASP cc_start: 0.8696 (m-30) cc_final: 0.8401 (m-30) REVERT: K 385 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8526 (tm-30) REVERT: L 315 TRP cc_start: 0.4446 (t-100) cc_final: 0.4026 (t-100) REVERT: L 464 MET cc_start: 0.7579 (mtm) cc_final: 0.7107 (pmm) REVERT: E 345 PHE cc_start: 0.8024 (m-80) cc_final: 0.7785 (m-80) REVERT: E 348 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7937 (mp0) REVERT: E 445 GLN cc_start: 0.7275 (tp-100) cc_final: 0.5558 (mt0) REVERT: H 410 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8565 (p) REVERT: H 426 LYS cc_start: 0.9246 (OUTLIER) cc_final: 0.8666 (pptt) REVERT: I 351 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8117 (tt) REVERT: I 382 ARG cc_start: 0.7313 (mmm160) cc_final: 0.6799 (mpt180) REVERT: I 383 TRP cc_start: 0.6703 (m-10) cc_final: 0.6345 (m-10) REVERT: I 449 ASP cc_start: 0.8110 (t0) cc_final: 0.7770 (t0) REVERT: I 464 MET cc_start: 0.7535 (mmt) cc_final: 0.7309 (mmt) REVERT: J 369 CYS cc_start: 0.7246 (t) cc_final: 0.6744 (m) REVERT: J 430 PHE cc_start: 0.8055 (m-80) cc_final: 0.7517 (m-80) REVERT: J 437 GLU cc_start: 0.8576 (tm-30) cc_final: 0.7470 (pm20) outliers start: 110 outliers final: 75 residues processed: 403 average time/residue: 0.5074 time to fit residues: 236.6217 Evaluate side-chains 392 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 303 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 17 SER Chi-restraints excluded: chain C residue 89 ARG 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 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 451 ASN Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 THR 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 D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 30 ASN 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 69 CYS Chi-restraints excluded: chain D residue 88 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 257 LEU Chi-restraints excluded: chain G residue 278 THR Chi-restraints excluded: chain G residue 280 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 433 MET Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 307 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 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 384 LEU Chi-restraints excluded: chain L residue 390 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 368 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 266 CYS 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 322 THR Chi-restraints excluded: chain I residue 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 351 LEU 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 365 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 5 optimal weight: 0.0010 chunk 171 optimal weight: 5.9990 chunk 276 optimal weight: 0.0020 chunk 84 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 229 optimal weight: 9.9990 chunk 217 optimal weight: 0.0980 chunk 273 optimal weight: 20.0000 chunk 257 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 246 optimal weight: 0.5980 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN C 11 ASN C 191 GLN L 445 GLN H 327 HIS J 263 ASN J 327 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.138834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.104998 restraints weight = 55067.556| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 4.51 r_work: 0.3547 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21870 Z= 0.127 Angle : 0.794 17.746 30086 Z= 0.371 Chirality : 0.046 0.671 3641 Planarity : 0.005 0.073 3829 Dihedral : 6.212 56.944 3438 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 4.36 % Allowed : 28.86 % Favored : 66.77 % 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: -2.15 (0.15), residues: 2869 helix: -1.38 (0.36), residues: 210 sheet: -0.19 (0.17), residues: 933 loop : -2.26 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 392 TYR 0.010 0.001 TYR E 395 PHE 0.022 0.001 PHE H 321 TRP 0.025 0.001 TRP A 281 HIS 0.007 0.001 HIS H 327 Details of bonding type rmsd covalent geometry : bond 0.00311 (21808) covalent geometry : angle 0.77381 (29943) SS BOND : bond 0.00346 ( 43) SS BOND : angle 1.23667 ( 86) hydrogen bonds : bond 0.02600 ( 498) hydrogen bonds : angle 4.88676 ( 1476) link_BETA1-4 : bond 0.00734 ( 10) link_BETA1-4 : angle 3.01192 ( 30) link_NAG-ASN : bond 0.00804 ( 9) link_NAG-ASN : angle 4.91877 ( 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 420 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 326 time to evaluate : 0.800 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: A 410 THR cc_start: 0.9267 (OUTLIER) cc_final: 0.8957 (p) REVERT: A 428 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8541 (mp0) REVERT: A 448 ILE cc_start: 0.9100 (tp) cc_final: 0.8851 (tt) REVERT: A 450 ARG cc_start: 0.8961 (ptm-80) cc_final: 0.8340 (ttp80) REVERT: B 264 LEU cc_start: 0.8286 (tt) cc_final: 0.7855 (mp) REVERT: B 291 GLN cc_start: 0.8565 (mp10) cc_final: 0.8324 (mm-40) REVERT: B 343 ASN cc_start: 0.8160 (t0) cc_final: 0.7843 (t0) REVERT: B 403 GLU cc_start: 0.8456 (pt0) cc_final: 0.8024 (pm20) REVERT: B 426 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8601 (ttpp) REVERT: B 428 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8165 (mm-30) REVERT: C 8 GLU cc_start: 0.8456 (tp30) cc_final: 0.8235 (tp30) REVERT: C 134 CYS cc_start: 0.5632 (OUTLIER) cc_final: 0.4136 (t) REVERT: C 298 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8202 (mpp80) REVERT: C 331 GLU cc_start: 0.7227 (mm-30) cc_final: 0.7003 (mm-30) REVERT: D 23 ILE cc_start: 0.7777 (pp) cc_final: 0.7164 (pp) REVERT: D 24 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7862 (mmm160) REVERT: D 28 ASP cc_start: 0.8576 (t0) cc_final: 0.8057 (t0) REVERT: D 31 GLU cc_start: 0.6827 (pp20) cc_final: 0.6208 (pm20) REVERT: D 45 ASN cc_start: 0.9261 (m-40) cc_final: 0.8715 (m110) REVERT: D 48 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8784 (mp0) REVERT: D 88 GLN cc_start: 0.9413 (OUTLIER) cc_final: 0.9177 (mt0) REVERT: D 126 GLU cc_start: 0.7654 (pm20) cc_final: 0.7051 (pm20) REVERT: D 127 THR cc_start: 0.9286 (m) cc_final: 0.8833 (p) REVERT: F 416 ILE cc_start: 0.9133 (pt) cc_final: 0.8930 (pp) REVERT: F 466 GLU cc_start: 0.8817 (tt0) cc_final: 0.8295 (tp30) REVERT: G 243 HIS cc_start: 0.7220 (t70) cc_final: 0.6498 (t70) REVERT: G 278 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.8017 (p) REVERT: G 392 ARG cc_start: 0.8340 (ptm-80) cc_final: 0.8080 (ptm160) REVERT: G 410 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.8729 (t) REVERT: G 423 ASP cc_start: 0.9240 (t0) cc_final: 0.9027 (t0) REVERT: G 425 LYS cc_start: 0.9603 (mmmm) cc_final: 0.9397 (mmmm) REVERT: G 431 SER cc_start: 0.9289 (m) cc_final: 0.9038 (p) REVERT: G 433 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8996 (mmm) REVERT: G 449 ASP cc_start: 0.8874 (p0) cc_final: 0.8603 (p0) REVERT: G 466 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8252 (pt0) REVERT: K 255 ASP cc_start: 0.8552 (p0) cc_final: 0.7749 (t0) REVERT: K 358 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7475 (tm-30) REVERT: K 378 ASP cc_start: 0.8680 (m-30) cc_final: 0.8370 (m-30) REVERT: K 385 GLN cc_start: 0.8814 (tm-30) cc_final: 0.8552 (tm-30) REVERT: L 315 TRP cc_start: 0.4429 (t-100) cc_final: 0.3984 (t-100) REVERT: L 464 MET cc_start: 0.7695 (mtm) cc_final: 0.7384 (pmm) REVERT: E 345 PHE cc_start: 0.8052 (m-80) cc_final: 0.7817 (m-80) REVERT: E 348 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8032 (mp0) REVERT: E 445 GLN cc_start: 0.7247 (tp-100) cc_final: 0.5566 (mt0) REVERT: I 382 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6787 (mmt180) REVERT: I 383 TRP cc_start: 0.6714 (m100) cc_final: 0.6362 (m-10) REVERT: I 449 ASP cc_start: 0.8039 (t0) cc_final: 0.7715 (t70) REVERT: I 464 MET cc_start: 0.7531 (mmt) cc_final: 0.7311 (mmt) REVERT: J 369 CYS cc_start: 0.7266 (t) cc_final: 0.6757 (m) REVERT: J 437 GLU cc_start: 0.8647 (tm-30) cc_final: 0.7595 (pm20) outliers start: 94 outliers final: 63 residues processed: 389 average time/residue: 0.5218 time to fit residues: 233.4889 Evaluate side-chains 382 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 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 457 HIS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 89 ARG 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 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 459 THR Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 30 ASN 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 69 CYS Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain F residue 282 THR 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 410 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 VAL 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 384 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 E residue 368 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 266 CYS 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 I residue 307 VAL 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 434 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 269 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 138 optimal weight: 0.0570 chunk 186 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 chunk 274 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN D 81 ASN K 327 HIS J 343 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.136687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.102746 restraints weight = 54525.813| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.50 r_work: 0.3514 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21870 Z= 0.149 Angle : 0.828 17.932 30086 Z= 0.388 Chirality : 0.046 0.641 3641 Planarity : 0.005 0.078 3829 Dihedral : 6.255 57.228 3438 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.81 % Favored : 92.16 % Rotamer: Outliers : 4.18 % Allowed : 29.00 % Favored : 66.82 % 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: -2.08 (0.15), residues: 2869 helix: -1.21 (0.38), residues: 210 sheet: -0.16 (0.17), residues: 928 loop : -2.23 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 392 TYR 0.017 0.001 TYR D 63 PHE 0.015 0.001 PHE C 75 TRP 0.029 0.001 TRP J 315 HIS 0.007 0.001 HIS H 436 Details of bonding type rmsd covalent geometry : bond 0.00365 (21808) covalent geometry : angle 0.80757 (29943) SS BOND : bond 0.00439 ( 43) SS BOND : angle 1.45462 ( 86) hydrogen bonds : bond 0.02900 ( 498) hydrogen bonds : angle 4.89118 ( 1476) link_BETA1-4 : bond 0.00696 ( 10) link_BETA1-4 : angle 2.97366 ( 30) link_NAG-ASN : bond 0.00743 ( 9) link_NAG-ASN : angle 4.91454 ( 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 412 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 322 time to evaluate : 0.852 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: A 410 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.8981 (p) REVERT: A 428 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8536 (mp0) REVERT: A 448 ILE cc_start: 0.9099 (tp) cc_final: 0.8867 (tt) REVERT: A 450 ARG cc_start: 0.9019 (ptm-80) cc_final: 0.8327 (ttp80) REVERT: B 264 LEU cc_start: 0.8290 (tt) cc_final: 0.7909 (mp) REVERT: B 343 ASN cc_start: 0.8178 (t0) cc_final: 0.7824 (t0) REVERT: B 392 ARG cc_start: 0.8057 (tpp80) cc_final: 0.7830 (tpt90) REVERT: B 403 GLU cc_start: 0.8576 (pt0) cc_final: 0.8036 (pm20) REVERT: B 426 LYS cc_start: 0.8935 (ttmm) cc_final: 0.8607 (ttpp) REVERT: C 89 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8821 (mpp80) REVERT: C 134 CYS cc_start: 0.5877 (OUTLIER) cc_final: 0.4389 (t) REVERT: C 298 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8300 (mpp80) REVERT: D 28 ASP cc_start: 0.8672 (t0) cc_final: 0.8454 (t0) REVERT: D 45 ASN cc_start: 0.9316 (m-40) cc_final: 0.8904 (m110) REVERT: D 48 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8662 (mp0) REVERT: D 80 ASP cc_start: 0.8640 (p0) cc_final: 0.8434 (p0) REVERT: D 126 GLU cc_start: 0.7740 (pm20) cc_final: 0.7136 (pm20) REVERT: F 338 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8670 (tp) REVERT: F 466 GLU cc_start: 0.8956 (tt0) cc_final: 0.8369 (tp30) REVERT: G 243 HIS cc_start: 0.7296 (t70) cc_final: 0.6540 (t70) REVERT: G 278 THR cc_start: 0.8235 (OUTLIER) cc_final: 0.7976 (p) REVERT: G 410 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.8767 (t) REVERT: G 423 ASP cc_start: 0.9295 (t0) cc_final: 0.9081 (t0) REVERT: G 425 LYS cc_start: 0.9606 (mmmm) cc_final: 0.9320 (mmmm) REVERT: G 431 SER cc_start: 0.9275 (m) cc_final: 0.9070 (p) REVERT: G 433 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.9029 (mmm) REVERT: G 449 ASP cc_start: 0.8920 (p0) cc_final: 0.8635 (p0) REVERT: G 466 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8206 (pt0) REVERT: K 255 ASP cc_start: 0.8589 (p0) cc_final: 0.7776 (t0) REVERT: K 346 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.8044 (mtm-85) REVERT: K 358 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7498 (tm-30) REVERT: K 378 ASP cc_start: 0.8824 (m-30) cc_final: 0.8524 (m-30) REVERT: K 385 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8615 (tm-30) REVERT: K 394 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8740 (mmpt) REVERT: L 315 TRP cc_start: 0.4523 (t-100) cc_final: 0.4051 (t-100) REVERT: L 464 MET cc_start: 0.7834 (mtm) cc_final: 0.7479 (pmm) REVERT: E 345 PHE cc_start: 0.8033 (m-80) cc_final: 0.7794 (m-80) REVERT: E 348 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8027 (mp0) REVERT: E 445 GLN cc_start: 0.7298 (tp-100) cc_final: 0.5698 (mt0) REVERT: I 449 ASP cc_start: 0.7976 (t0) cc_final: 0.7702 (t70) REVERT: I 464 MET cc_start: 0.7555 (mmt) cc_final: 0.7245 (mmt) REVERT: J 369 CYS cc_start: 0.7355 (t) cc_final: 0.6921 (m) REVERT: J 437 GLU cc_start: 0.8636 (tm-30) cc_final: 0.7569 (pm20) outliers start: 90 outliers final: 59 residues processed: 386 average time/residue: 0.5277 time to fit residues: 235.3535 Evaluate side-chains 367 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 300 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 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 423 ASP Chi-restraints excluded: chain A residue 429 THR 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 18 VAL 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 351 VAL Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 451 ASN Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 528 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 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 410 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 379 VAL Chi-restraints excluded: chain K residue 460 VAL 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 368 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 266 CYS 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 I residue 307 VAL 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 343 ASN Chi-restraints excluded: chain J residue 351 LEU Chi-restraints excluded: chain J residue 365 VAL 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: 0.6980 chunk 109 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 273 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 230 optimal weight: 0.9980 chunk 177 optimal weight: 0.0370 overall best weight: 1.1260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.136314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.102448 restraints weight = 54886.102| |-----------------------------------------------------------------------------| 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: 0.7657 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21870 Z= 0.148 Angle : 0.837 17.826 30086 Z= 0.395 Chirality : 0.046 0.639 3641 Planarity : 0.005 0.082 3829 Dihedral : 6.223 56.945 3438 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.46 % Favored : 92.51 % Rotamer: Outliers : 3.62 % Allowed : 29.98 % Favored : 66.40 % 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: -2.06 (0.15), residues: 2869 helix: -1.15 (0.38), residues: 210 sheet: -0.17 (0.17), residues: 936 loop : -2.20 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 392 TYR 0.018 0.001 TYR D 63 PHE 0.034 0.001 PHE A 279 TRP 0.034 0.001 TRP J 315 HIS 0.007 0.001 HIS K 327 Details of bonding type rmsd covalent geometry : bond 0.00364 (21808) covalent geometry : angle 0.81733 (29943) SS BOND : bond 0.00391 ( 43) SS BOND : angle 1.33407 ( 86) hydrogen bonds : bond 0.02943 ( 498) hydrogen bonds : angle 4.93130 ( 1476) link_BETA1-4 : bond 0.00682 ( 10) link_BETA1-4 : angle 2.95821 ( 30) link_NAG-ASN : bond 0.00693 ( 9) link_NAG-ASN : angle 4.91535 ( 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 389 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 311 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: symmetry clash revert: symmetry clash REVERT: A 410 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.8980 (p) REVERT: A 428 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8539 (mp0) REVERT: A 448 ILE cc_start: 0.9130 (tp) cc_final: 0.8872 (tt) REVERT: A 450 ARG cc_start: 0.9022 (ptm-80) cc_final: 0.8329 (ttp80) REVERT: B 264 LEU cc_start: 0.8288 (tt) cc_final: 0.7935 (mp) REVERT: B 343 ASN cc_start: 0.8200 (t0) cc_final: 0.7853 (t0) REVERT: B 403 GLU cc_start: 0.8588 (pt0) cc_final: 0.8045 (pm20) REVERT: B 426 LYS cc_start: 0.8976 (ttmm) cc_final: 0.8662 (tmmm) REVERT: C 89 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8836 (mpp80) REVERT: C 134 CYS cc_start: 0.5944 (OUTLIER) cc_final: 0.4436 (t) REVERT: C 298 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8353 (mpp80) REVERT: C 330 GLU cc_start: 0.7568 (pp20) cc_final: 0.7207 (pp20) REVERT: C 331 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6869 (mp0) REVERT: C 526 CYS cc_start: 0.7411 (t) cc_final: 0.6926 (p) REVERT: D 24 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7912 (mmm160) REVERT: D 45 ASN cc_start: 0.9334 (m-40) cc_final: 0.8948 (m110) REVERT: D 48 GLU cc_start: 0.9261 (mt-10) cc_final: 0.8669 (mp0) REVERT: D 80 ASP cc_start: 0.8664 (p0) cc_final: 0.8447 (p0) REVERT: D 126 GLU cc_start: 0.7762 (pm20) cc_final: 0.7158 (pm20) REVERT: F 338 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8662 (tp) REVERT: F 358 GLU cc_start: 0.8913 (tt0) cc_final: 0.8477 (tm-30) REVERT: F 466 GLU cc_start: 0.8965 (tt0) cc_final: 0.8359 (tp30) REVERT: G 243 HIS cc_start: 0.7383 (t70) cc_final: 0.6644 (t70) REVERT: G 278 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7868 (p) REVERT: G 410 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9010 (p) REVERT: G 423 ASP cc_start: 0.9265 (t0) cc_final: 0.9053 (t0) REVERT: G 425 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9325 (mmmm) REVERT: G 433 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9040 (mmm) REVERT: G 449 ASP cc_start: 0.8953 (p0) cc_final: 0.8675 (p0) REVERT: G 466 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: K 358 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7402 (tm-30) REVERT: K 378 ASP cc_start: 0.8866 (m-30) cc_final: 0.8624 (m-30) REVERT: K 385 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8629 (tm-30) REVERT: L 315 TRP cc_start: 0.4498 (t-100) cc_final: 0.3933 (t-100) REVERT: L 346 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7733 (mmp80) REVERT: L 464 MET cc_start: 0.7848 (mtm) cc_final: 0.7499 (pmm) REVERT: E 345 PHE cc_start: 0.7989 (m-80) cc_final: 0.7778 (m-80) REVERT: E 348 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8023 (mp0) REVERT: E 403 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8201 (tm-30) REVERT: E 445 GLN cc_start: 0.7315 (tp-100) cc_final: 0.5884 (mt0) REVERT: I 449 ASP cc_start: 0.7937 (t0) cc_final: 0.7638 (t70) REVERT: I 464 MET cc_start: 0.7560 (mmt) cc_final: 0.7252 (mmt) REVERT: J 369 CYS cc_start: 0.7335 (t) cc_final: 0.6914 (m) REVERT: J 376 PRO cc_start: 0.4996 (Cg_exo) cc_final: 0.4546 (Cg_endo) REVERT: J 437 GLU cc_start: 0.8633 (tm-30) cc_final: 0.7611 (pm20) outliers start: 78 outliers final: 65 residues processed: 367 average time/residue: 0.5395 time to fit residues: 227.9413 Evaluate side-chains 377 residues out of total 2484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 303 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 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 423 ASP 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 17 SER Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 89 ARG Chi-restraints excluded: chain C residue 124 VAL 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 451 ASN Chi-restraints excluded: chain C residue 485 CYS Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 ARG 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 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 410 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 433 MET Chi-restraints excluded: chain G residue 434 VAL Chi-restraints excluded: chain G residue 466 GLU Chi-restraints excluded: chain K residue 379 VAL 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 338 ILE Chi-restraints excluded: chain L residue 366 THR 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 368 THR Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain H residue 266 CYS Chi-restraints excluded: chain H residue 368 THR 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 344 THR Chi-restraints excluded: chain I residue 345 PHE Chi-restraints excluded: chain I residue 385 GLN 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 365 VAL 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: 4.9990 chunk 192 optimal weight: 3.9990 chunk 142 optimal weight: 0.2980 chunk 204 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 208 optimal weight: 0.0270 chunk 171 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN ** I 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.136449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.102795 restraints weight = 54507.892| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.50 r_work: 0.3516 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21870 Z= 0.139 Angle : 0.839 17.808 30086 Z= 0.393 Chirality : 0.046 0.633 3641 Planarity : 0.005 0.082 3829 Dihedral : 6.157 56.837 3438 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.53 % Favored : 92.44 % Rotamer: Outliers : 3.81 % Allowed : 29.93 % Favored : 66.26 % 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: -1.99 (0.15), residues: 2869 helix: -1.11 (0.38), residues: 210 sheet: -0.10 (0.17), residues: 928 loop : -2.16 (0.14), residues: 1731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 392 TYR 0.017 0.001 TYR D 63 PHE 0.016 0.001 PHE A 279 TRP 0.039 0.001 TRP A 281 HIS 0.005 0.001 HIS H 327 Details of bonding type rmsd covalent geometry : bond 0.00343 (21808) covalent geometry : angle 0.81844 (29943) SS BOND : bond 0.00437 ( 43) SS BOND : angle 1.54465 ( 86) hydrogen bonds : bond 0.02848 ( 498) hydrogen bonds : angle 4.88467 ( 1476) link_BETA1-4 : bond 0.00700 ( 10) link_BETA1-4 : angle 2.95216 ( 30) link_NAG-ASN : bond 0.00710 ( 9) link_NAG-ASN : angle 4.89454 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9449.18 seconds wall clock time: 160 minutes 52.50 seconds (9652.50 seconds total)