Starting phenix.real_space_refine on Thu Feb 5 04:57:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9os5_70793/02_2026/9os5_70793.cif Found real_map, /net/cci-nas-00/data/ceres_data/9os5_70793/02_2026/9os5_70793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9os5_70793/02_2026/9os5_70793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9os5_70793/02_2026/9os5_70793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9os5_70793/02_2026/9os5_70793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9os5_70793/02_2026/9os5_70793.map" } resolution = 2.61 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= -0.001 sd= 0.076 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 78 5.16 5 C 9324 2.51 5 N 2505 2.21 5 O 2990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14897 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 540 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2666 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 337} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 544 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "D" Number of atoms: 2668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2668 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 338} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 544 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "F" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2676 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 945 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "J" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 762 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "H" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 945 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "K" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 762 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "I" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 945 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 762 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 93} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 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: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 3.28, per 1000 atoms: 0.22 Number of scatterers: 14897 At special positions: 0 Unit cell: (142.2, 135.09, 179.33, 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 78 16.00 O 2990 8.00 N 2505 7.00 C 9324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS B 407 " distance=2.04 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 311 " distance=2.04 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 335 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 384 " - pdb=" SG CYS B 390 " distance=2.02 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS D 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS D 182 " distance=2.03 Simple disulfide: pdb=" SG CYS D 283 " - pdb=" SG CYS D 311 " distance=2.04 Simple disulfide: pdb=" SG CYS D 292 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 326 " - pdb=" SG CYS D 335 " distance=2.03 Simple disulfide: pdb=" SG CYS D 350 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 384 " - pdb=" SG CYS D 390 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS F 407 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 311 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 326 " - pdb=" SG CYS F 335 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 384 " - pdb=" SG CYS F 390 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 16 " - pdb=" SG CYS J 81 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS K 16 " - pdb=" SG CYS K 81 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 16 " - pdb=" SG CYS L 81 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 57 " " NAG B 601 " - " ASN B 172 " " NAG B 602 " - " ASN B 353 " " NAG C 501 " - " ASN C 57 " " NAG D 601 " - " ASN D 172 " " NAG D 602 " - " ASN D 353 " " NAG E 501 " - " ASN E 57 " " NAG F 601 " - " ASN F 172 " " NAG F 602 " - " ASN F 353 " Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 574.5 milliseconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3596 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 25 sheets defined 28.8% alpha, 26.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 65 through 82 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'B' and resid 132 through 136 removed outlier: 4.141A pdb=" N ASN B 135 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 136 " --> pdb=" O GLU B 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 136' Processing helix chain 'B' and resid 137 through 211 removed outlier: 4.360A pdb=" N LEU B 173 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ARG B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE B 200 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 344 through 352 removed outlier: 3.568A pdb=" N ARG B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 481 removed outlier: 4.472A pdb=" N PHE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 481 " --> pdb=" O SER B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 83 removed outlier: 3.905A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 211 removed outlier: 4.290A pdb=" N ILE D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 141 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 173 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ARG D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE D 200 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 Processing helix chain 'D' and resid 237 through 247 Processing helix chain 'D' and resid 247 through 255 Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 344 through 352 removed outlier: 3.535A pdb=" N GLU D 349 " --> pdb=" O GLN D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 482 removed outlier: 3.924A pdb=" N PHE D 456 " --> pdb=" O PRO D 452 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA D 459 " --> pdb=" O GLN D 455 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 27 No H-bonds generated for 'chain 'E' and resid 25 through 27' Processing helix chain 'E' and resid 65 through 83 removed outlier: 3.830A pdb=" N THR E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 197 removed outlier: 3.853A pdb=" N LEU F 173 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N THR F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 211 Processing helix chain 'F' and resid 223 through 233 Processing helix chain 'F' and resid 237 through 247 Processing helix chain 'F' and resid 247 through 255 Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 344 through 352 removed outlier: 3.626A pdb=" N ARG F 348 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 349 " --> pdb=" O GLN F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 481 removed outlier: 3.775A pdb=" N PHE F 456 " --> pdb=" O PRO F 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'J' and resid 72 through 76 removed outlier: 3.987A pdb=" N PHE J 76 " --> pdb=" O PRO J 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'K' and resid 72 through 76 removed outlier: 3.867A pdb=" N PHE K 76 " --> pdb=" O PRO K 73 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 90 Processing helix chain 'L' and resid 72 through 76 removed outlier: 3.986A pdb=" N PHE L 76 " --> pdb=" O PRO L 73 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 29 through 51 current: chain 'B' and resid 256 through 263 removed outlier: 6.852A pdb=" N ILE B 268 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL B 262 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER B 266 " --> pdb=" O VAL B 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 317 through 320 current: chain 'B' and resid 332 through 335 Processing sheet with id=AA2, first strand: chain 'B' and resid 291 through 295 removed outlier: 3.519A pdb=" N CYS B 301 " --> pdb=" O GLY B 366 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 373 through 376 Processing sheet with id=AA4, first strand: chain 'B' and resid 399 through 402 Processing sheet with id=AA5, first strand: chain 'B' and resid 430 through 438 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 430 through 438 current: chain 'E' and resid 29 through 51 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 29 through 51 current: chain 'F' and resid 256 through 263 removed outlier: 6.857A pdb=" N ILE F 268 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL F 262 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 317 through 320 current: chain 'F' and resid 332 through 335 Processing sheet with id=AA6, first strand: chain 'C' and resid 20 through 24 removed outlier: 6.729A pdb=" N SER C 29 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA D 288 " --> pdb=" O SER C 29 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ILE C 31 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE D 286 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLU C 33 " --> pdb=" O TRP D 284 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TRP D 284 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TYR C 35 " --> pdb=" O PRO D 282 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER C 37 " --> pdb=" O ASP D 280 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 278 " --> pdb=" O LEU C 39 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 317 through 320 current: chain 'D' and resid 332 through 335 Processing sheet with id=AA7, first strand: chain 'D' and resid 213 through 214 removed outlier: 3.912A pdb=" N GLY D 257 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE D 268 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL D 262 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER D 266 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR C 45 " --> pdb=" O GLU F 433 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N HIS F 435 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL C 47 " --> pdb=" O HIS F 435 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE F 437 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N THR C 49 " --> pdb=" O ILE F 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 291 through 295 removed outlier: 3.575A pdb=" N CYS D 301 " --> pdb=" O GLY D 366 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 372 through 376 removed outlier: 3.522A pdb=" N MET D 372 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 399 through 402 removed outlier: 6.901A pdb=" N ILE D 392 " --> pdb=" O ILE D 400 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N GLN D 402 " --> pdb=" O CYS D 390 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N CYS D 390 " --> pdb=" O GLN D 402 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 291 through 295 removed outlier: 3.651A pdb=" N CYS F 301 " --> pdb=" O GLY F 366 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 372 through 376 removed outlier: 3.632A pdb=" N MET F 372 " --> pdb=" O ALA F 383 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY F 379 " --> pdb=" O SER F 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 399 through 402 removed outlier: 7.215A pdb=" N ILE F 392 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN F 402 " --> pdb=" O CYS F 390 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS F 390 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'G' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 11 through 12 current: chain 'G' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 106 through 114 Processing sheet with id=AB7, first strand: chain 'J' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 3 through 6 current: chain 'J' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 46 through 47 current: chain 'J' and resid 90 through 91 Processing sheet with id=AB8, first strand: chain 'J' and resid 12 through 17 removed outlier: 4.301A pdb=" N ASP J 63 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER J 60 " --> pdb=" O ASP J 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 106 through 114 Processing sheet with id=AC2, first strand: chain 'K' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 3 through 6 current: chain 'K' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 46 through 47 current: chain 'K' and resid 90 through 91 Processing sheet with id=AC3, first strand: chain 'K' and resid 12 through 17 removed outlier: 3.571A pdb=" N PHE K 64 " --> pdb=" O CYS K 16 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP K 63 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER K 60 " --> pdb=" O ASP K 63 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC5, first strand: chain 'I' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 11 through 12 current: chain 'I' and resid 46 through 51 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 57 through 59 current: chain 'I' and resid 106 through 114 Processing sheet with id=AC6, first strand: chain 'L' and resid 3 through 6 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 3 through 6 current: chain 'L' and resid 38 through 42 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 46 through 47 current: chain 'L' and resid 90 through 91 Processing sheet with id=AC7, first strand: chain 'L' and resid 12 through 17 removed outlier: 3.534A pdb=" N PHE L 64 " --> pdb=" O CYS L 16 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP L 63 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER L 60 " --> pdb=" O ASP L 63 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1740 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: 2.02 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4842 1.34 - 1.46: 3314 1.46 - 1.58: 6887 1.58 - 1.70: 0 1.70 - 1.82: 102 Bond restraints: 15145 Sorted by residual: bond pdb=" N PRO B 452 " pdb=" CA PRO B 452 " ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.40e+00 bond pdb=" N PRO C 64 " pdb=" CA PRO C 64 " ideal model delta sigma weight residual 1.469 1.482 -0.013 1.28e-02 6.10e+03 1.08e+00 bond pdb=" C SER L 23 " pdb=" O SER L 23 " ideal model delta sigma weight residual 1.243 1.234 0.009 9.50e-03 1.11e+04 9.34e-01 bond pdb=" C SER J 23 " pdb=" O SER J 23 " ideal model delta sigma weight residual 1.243 1.234 0.009 9.50e-03 1.11e+04 8.98e-01 bond pdb=" CG PRO J 88 " pdb=" CD PRO J 88 " ideal model delta sigma weight residual 1.512 1.490 0.022 2.70e-02 1.37e+03 6.76e-01 ... (remaining 15140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 20189 1.72 - 3.44: 344 3.44 - 5.16: 33 5.16 - 6.88: 5 6.88 - 8.60: 3 Bond angle restraints: 20574 Sorted by residual: angle pdb=" C SER L 23 " pdb=" CA SER L 23 " pdb=" CB SER L 23 " ideal model delta sigma weight residual 117.23 110.38 6.85 1.36e+00 5.41e-01 2.54e+01 angle pdb=" C SER J 23 " pdb=" CA SER J 23 " pdb=" CB SER J 23 " ideal model delta sigma weight residual 117.23 110.57 6.66 1.36e+00 5.41e-01 2.40e+01 angle pdb=" CA SER L 23 " pdb=" C SER L 23 " pdb=" N SER L 24 " ideal model delta sigma weight residual 119.98 116.95 3.03 8.50e-01 1.38e+00 1.27e+01 angle pdb=" CA SER J 23 " pdb=" C SER J 23 " pdb=" N SER J 24 " ideal model delta sigma weight residual 119.98 117.06 2.92 8.50e-01 1.38e+00 1.18e+01 angle pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " pdb=" C5 NAG A 501 " ideal model delta sigma weight residual 113.21 121.81 -8.60 3.00e+00 1.11e-01 8.22e+00 ... (remaining 20569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 8116 17.88 - 35.75: 845 35.75 - 53.63: 278 53.63 - 71.50: 70 71.50 - 89.37: 17 Dihedral angle restraints: 9326 sinusoidal: 3728 harmonic: 5598 Sorted by residual: dihedral pdb=" CB CYS B 384 " pdb=" SG CYS B 384 " pdb=" SG CYS B 390 " pdb=" CB CYS B 390 " ideal model delta sinusoidal sigma weight residual 93.00 172.26 -79.26 1 1.00e+01 1.00e-02 7.81e+01 dihedral pdb=" CB CYS L 16 " pdb=" SG CYS L 16 " pdb=" SG CYS L 81 " pdb=" CB CYS L 81 " ideal model delta sinusoidal sigma weight residual 93.00 166.66 -73.66 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS J 16 " pdb=" SG CYS J 16 " pdb=" SG CYS J 81 " pdb=" CB CYS J 81 " ideal model delta sinusoidal sigma weight residual 93.00 165.71 -72.71 1 1.00e+01 1.00e-02 6.75e+01 ... (remaining 9323 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1856 0.044 - 0.087: 396 0.087 - 0.131: 162 0.131 - 0.174: 8 0.174 - 0.218: 3 Chirality restraints: 2425 Sorted by residual: chirality pdb=" C1 NAG A 501 " pdb=" ND2 ASN A 57 " pdb=" C2 NAG A 501 " pdb=" O5 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE F 213 " pdb=" CA ILE F 213 " pdb=" CG1 ILE F 213 " pdb=" CG2 ILE F 213 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.89e-01 chirality pdb=" C1 NAG C 501 " pdb=" ND2 ASN C 57 " pdb=" C2 NAG C 501 " pdb=" O5 NAG C 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 2422 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 57 " -0.026 2.00e-02 2.50e+03 2.30e-02 6.59e+00 pdb=" CG ASN E 57 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN E 57 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN E 57 " 0.023 2.00e-02 2.50e+03 pdb=" C1 NAG E 501 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 376 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO B 377 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 377 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 377 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 376 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 377 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 377 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 377 " -0.022 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 381 2.70 - 3.25: 13695 3.25 - 3.80: 23489 3.80 - 4.35: 30822 4.35 - 4.90: 52543 Nonbonded interactions: 120930 Sorted by model distance: nonbonded pdb=" OG1 THR D 317 " pdb=" OE1 GLU D 345 " model vdw 2.153 3.040 nonbonded pdb=" OE2 GLU C 21 " pdb=" OG SER D 376 " model vdw 2.157 3.040 nonbonded pdb=" OG SER A 85 " pdb=" OD1 ASP A 87 " model vdw 2.192 3.040 nonbonded pdb=" OG SER B 477 " pdb=" OG1 THR D 143 " model vdw 2.205 3.040 nonbonded pdb=" O SER D 170 " pdb=" OG1 THR D 174 " model vdw 2.241 3.040 ... (remaining 120925 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' selection = (chain 'C' and (resid 19 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 501)) selection = (chain 'E' and (resid 19 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 501)) } ncs_group { reference = (chain 'B' and (resid 132 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 141 or (resid 142 and (name N \ or name CA or name C or name O or name CB )) or resid 143 through 385 or (resid \ 386 and (name N or name CA or name C or name O or name CB )) or resid 387 throug \ h 450 or (resid 451 and (name N or name CA or name C or name O or name CB )) or \ resid 452 through 602)) selection = (chain 'D' and (resid 132 through 165 or (resid 166 and (name N or name CA or na \ me C or name O or name CB )) or resid 167 through 395 or (resid 396 and (name N \ or name CA or name C or name O or name CB )) or resid 397 through 478 or (resid \ 479 and (name N or name CA or name C or name O or name CB )) or resid 480 throug \ h 482 or resid 601 through 602)) selection = (chain 'F' and (resid 132 through 137 or (resid 138 and (name N or name CA or na \ me C or name O or name CB )) or resid 139 through 141 or (resid 142 and (name N \ or name CA or name C or name O or name CB )) or resid 143 through 165 or (resid \ 166 and (name N or name CA or name C or name O or name CB )) or resid 167 throug \ h 395 or (resid 396 and (name N or name CA or name C or name O or name CB )) or \ resid 397 through 450 or (resid 451 and (name N or name CA or name C or name O o \ r name CB )) or resid 452 through 478 or (resid 479 and (name N or name CA or na \ me C or name O or name CB )) or resid 480 through 602)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.890 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.003 0.030 15181 Z= 0.124 Angle : 0.580 15.397 20655 Z= 0.305 Chirality : 0.043 0.218 2425 Planarity : 0.004 0.041 2621 Dihedral : 16.740 89.375 5649 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.95 % Allowed : 22.37 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1912 helix: 2.41 (0.24), residues: 486 sheet: 0.29 (0.22), residues: 531 loop : -0.69 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 396 TYR 0.017 0.001 TYR J 25 PHE 0.011 0.001 PHE D 200 TRP 0.011 0.002 TRP H 34 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd covalent geometry : bond 0.00260 (15145) covalent geometry : angle 0.54896 (20574) SS BOND : bond 0.00481 ( 27) SS BOND : angle 1.13005 ( 54) hydrogen bonds : bond 0.16327 ( 644) hydrogen bonds : angle 5.95925 ( 1740) link_NAG-ASN : bond 0.00589 ( 9) link_NAG-ASN : angle 5.02859 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.652 Fit side-chains REVERT: A 75 LYS cc_start: 0.8434 (ttpt) cc_final: 0.8195 (mtpp) REVERT: B 413 GLN cc_start: 0.6418 (mt0) cc_final: 0.6152 (mm110) REVERT: C 21 GLU cc_start: 0.8106 (tt0) cc_final: 0.7888 (tt0) REVERT: C 26 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: C 75 LYS cc_start: 0.8063 (ttpp) cc_final: 0.7511 (mttt) REVERT: D 166 LYS cc_start: 0.1664 (OUTLIER) cc_final: 0.0763 (mmtt) REVERT: D 221 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 329 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7837 (ttm170) REVERT: D 336 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.8029 (t70) REVERT: F 333 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8046 (t) REVERT: G 68 THR cc_start: 0.8493 (m) cc_final: 0.8088 (t) REVERT: G 109 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7713 (p0) REVERT: J 90 PHE cc_start: 0.7556 (t80) cc_final: 0.6869 (m-80) REVERT: J 96 LYS cc_start: 0.7692 (tptp) cc_final: 0.6602 (mttp) REVERT: J 97 LEU cc_start: 0.5668 (OUTLIER) cc_final: 0.5439 (mm) REVERT: H 5 GLN cc_start: 0.7951 (tt0) cc_final: 0.7367 (tp-100) REVERT: H 68 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8122 (t) REVERT: H 109 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7845 (p0) REVERT: K 72 GLN cc_start: 0.5714 (OUTLIER) cc_final: 0.5402 (mp10) REVERT: K 90 PHE cc_start: 0.7334 (t80) cc_final: 0.6625 (m-80) REVERT: K 96 LYS cc_start: 0.7368 (tttt) cc_final: 0.6917 (tptp) REVERT: I 68 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8157 (t) REVERT: L 90 PHE cc_start: 0.7450 (t80) cc_final: 0.6677 (m-80) outliers start: 49 outliers final: 29 residues processed: 217 average time/residue: 0.4978 time to fit residues: 119.7258 Evaluate side-chains 204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 351 ASN Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 411 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 109 ASP Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 109 ASP Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 74 SER Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain L residue 8 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 342 ASN ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN D 471 GLN G 56 ASN G 116 GLN H 56 ASN I 56 ASN I 116 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.188213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139882 restraints weight = 17497.776| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.04 r_work: 0.3555 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15181 Z= 0.128 Angle : 0.576 14.335 20655 Z= 0.289 Chirality : 0.044 0.218 2425 Planarity : 0.004 0.037 2621 Dihedral : 6.942 70.027 2342 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.17 % Allowed : 19.84 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.02 (0.20), residues: 1912 helix: 2.92 (0.23), residues: 460 sheet: 0.45 (0.21), residues: 581 loop : -0.37 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 396 TYR 0.014 0.001 TYR D 233 PHE 0.012 0.001 PHE C 48 TRP 0.012 0.002 TRP H 34 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd covalent geometry : bond 0.00293 (15145) covalent geometry : angle 0.55736 (20574) SS BOND : bond 0.00503 ( 27) SS BOND : angle 1.24505 ( 54) hydrogen bonds : bond 0.03921 ( 644) hydrogen bonds : angle 4.62674 ( 1740) link_NAG-ASN : bond 0.00709 ( 9) link_NAG-ASN : angle 3.76235 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 179 time to evaluate : 0.390 Fit side-chains REVERT: A 75 LYS cc_start: 0.8340 (ttpt) cc_final: 0.8034 (mtpp) REVERT: B 164 GLU cc_start: 0.2567 (OUTLIER) cc_final: 0.2046 (mm-30) REVERT: B 221 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7482 (mp) REVERT: B 294 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: B 413 GLN cc_start: 0.6445 (mt0) cc_final: 0.6099 (mm110) REVERT: C 26 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6736 (tt0) REVERT: D 166 LYS cc_start: 0.1701 (OUTLIER) cc_final: 0.0731 (mptt) REVERT: D 221 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 440 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7661 (mtp180) REVERT: F 166 LYS cc_start: 0.2749 (OUTLIER) cc_final: 0.1432 (mptt) REVERT: F 213 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7566 (mp) REVERT: F 336 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7867 (t70) REVERT: G 11 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7446 (tp) REVERT: G 68 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.7946 (t) REVERT: J 90 PHE cc_start: 0.7511 (t80) cc_final: 0.6784 (m-80) REVERT: J 96 LYS cc_start: 0.7577 (tptp) cc_final: 0.6472 (mttp) REVERT: H 5 GLN cc_start: 0.7538 (tt0) cc_final: 0.7011 (tp-100) REVERT: H 11 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7328 (tp) REVERT: H 68 THR cc_start: 0.8345 (m) cc_final: 0.8029 (t) REVERT: K 72 GLN cc_start: 0.5551 (OUTLIER) cc_final: 0.5103 (mp10) REVERT: K 90 PHE cc_start: 0.7314 (t80) cc_final: 0.6572 (m-80) REVERT: K 96 LYS cc_start: 0.7272 (tttt) cc_final: 0.6807 (tptt) REVERT: K 97 LEU cc_start: 0.5584 (OUTLIER) cc_final: 0.5104 (mm) REVERT: I 11 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7162 (tp) REVERT: I 68 THR cc_start: 0.8346 (m) cc_final: 0.7992 (t) REVERT: L 90 PHE cc_start: 0.7318 (t80) cc_final: 0.6534 (m-80) REVERT: L 97 LEU cc_start: 0.5681 (OUTLIER) cc_final: 0.5442 (mm) outliers start: 86 outliers final: 32 residues processed: 249 average time/residue: 0.5115 time to fit residues: 141.1339 Evaluate side-chains 217 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 13 THR Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN H 56 ASN I 5 GLN I 56 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.187002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138197 restraints weight = 17684.774| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.11 r_work: 0.3520 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15181 Z= 0.148 Angle : 0.587 14.153 20655 Z= 0.296 Chirality : 0.044 0.215 2425 Planarity : 0.004 0.042 2621 Dihedral : 6.071 57.020 2298 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.07 % Allowed : 20.08 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1912 helix: 2.91 (0.23), residues: 460 sheet: 0.34 (0.21), residues: 587 loop : -0.41 (0.22), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 248 TYR 0.015 0.002 TYR B 310 PHE 0.012 0.001 PHE C 48 TRP 0.012 0.002 TRP H 34 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd covalent geometry : bond 0.00346 (15145) covalent geometry : angle 0.56854 (20574) SS BOND : bond 0.00613 ( 27) SS BOND : angle 1.31134 ( 54) hydrogen bonds : bond 0.04045 ( 644) hydrogen bonds : angle 4.51491 ( 1740) link_NAG-ASN : bond 0.00661 ( 9) link_NAG-ASN : angle 3.67603 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 178 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8340 (ttpt) cc_final: 0.8015 (mtpp) REVERT: B 164 GLU cc_start: 0.2302 (OUTLIER) cc_final: 0.1897 (mm-30) REVERT: B 221 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7492 (mp) REVERT: B 294 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6792 (tt0) REVERT: B 413 GLN cc_start: 0.6517 (mt0) cc_final: 0.6144 (mm110) REVERT: C 26 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6661 (tt0) REVERT: D 166 LYS cc_start: 0.1440 (OUTLIER) cc_final: 0.0581 (mptt) REVERT: D 221 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7810 (mp) REVERT: D 440 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7697 (mtp180) REVERT: F 156 ARG cc_start: 0.2847 (OUTLIER) cc_final: 0.2382 (ttm110) REVERT: F 166 LYS cc_start: 0.2394 (OUTLIER) cc_final: 0.1218 (mptt) REVERT: F 213 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7496 (mp) REVERT: F 333 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8083 (t) REVERT: F 336 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7865 (t70) REVERT: G 11 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7346 (tp) REVERT: G 68 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.7953 (t) REVERT: J 90 PHE cc_start: 0.7518 (t80) cc_final: 0.6775 (m-80) REVERT: J 96 LYS cc_start: 0.7616 (tptp) cc_final: 0.6475 (mttp) REVERT: H 5 GLN cc_start: 0.7576 (tt0) cc_final: 0.7017 (tp-100) REVERT: H 11 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7335 (tp) REVERT: H 116 GLN cc_start: 0.8030 (mp10) cc_final: 0.7643 (mp10) REVERT: K 72 GLN cc_start: 0.5451 (OUTLIER) cc_final: 0.5062 (mp10) REVERT: K 90 PHE cc_start: 0.7344 (t80) cc_final: 0.6557 (m-80) REVERT: K 96 LYS cc_start: 0.7318 (tttt) cc_final: 0.6806 (tptt) REVERT: K 97 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5023 (mm) REVERT: I 11 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7164 (tp) REVERT: L 90 PHE cc_start: 0.7358 (t80) cc_final: 0.6542 (m-80) REVERT: L 97 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5312 (mm) outliers start: 101 outliers final: 46 residues processed: 264 average time/residue: 0.5319 time to fit residues: 156.1921 Evaluate side-chains 230 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 165 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 390 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 33 optimal weight: 0.0050 chunk 108 optimal weight: 4.9990 chunk 184 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN G 56 ASN H 56 ASN I 56 ASN 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 = 0.185978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145253 restraints weight = 17601.059| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.15 r_work: 0.3474 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15181 Z= 0.167 Angle : 0.612 14.634 20655 Z= 0.309 Chirality : 0.045 0.228 2425 Planarity : 0.004 0.038 2621 Dihedral : 6.105 57.158 2298 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 6.49 % Allowed : 19.78 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.20), residues: 1912 helix: 2.84 (0.23), residues: 459 sheet: 0.29 (0.21), residues: 582 loop : -0.52 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 252 TYR 0.015 0.002 TYR B 310 PHE 0.014 0.002 PHE C 48 TRP 0.012 0.002 TRP H 34 HIS 0.004 0.001 HIS D 332 Details of bonding type rmsd covalent geometry : bond 0.00396 (15145) covalent geometry : angle 0.59374 (20574) SS BOND : bond 0.00660 ( 27) SS BOND : angle 1.36234 ( 54) hydrogen bonds : bond 0.04194 ( 644) hydrogen bonds : angle 4.50323 ( 1740) link_NAG-ASN : bond 0.00379 ( 9) link_NAG-ASN : angle 3.79502 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 171 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8310 (ttpt) cc_final: 0.7920 (mtpp) REVERT: B 164 GLU cc_start: 0.2189 (OUTLIER) cc_final: 0.1822 (mm-30) REVERT: B 221 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7432 (mp) REVERT: B 294 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6725 (tt0) REVERT: B 386 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6372 (pttm) REVERT: B 413 GLN cc_start: 0.6417 (mt0) cc_final: 0.5965 (mm110) REVERT: C 26 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6194 (pm20) REVERT: C 75 LYS cc_start: 0.7929 (mtpm) cc_final: 0.7028 (mttt) REVERT: D 166 LYS cc_start: 0.1331 (OUTLIER) cc_final: 0.0522 (mptt) REVERT: D 221 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7765 (mp) REVERT: F 156 ARG cc_start: 0.2550 (OUTLIER) cc_final: 0.2151 (ttm110) REVERT: F 166 LYS cc_start: 0.2346 (OUTLIER) cc_final: 0.1226 (mptt) REVERT: F 213 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7517 (mp) REVERT: F 333 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8094 (t) REVERT: F 336 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7827 (t70) REVERT: G 11 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7206 (tp) REVERT: G 68 THR cc_start: 0.8327 (OUTLIER) cc_final: 0.7837 (t) REVERT: J 90 PHE cc_start: 0.7526 (t80) cc_final: 0.6668 (m-80) REVERT: J 96 LYS cc_start: 0.7411 (tptp) cc_final: 0.6279 (mttp) REVERT: J 97 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5306 (mm) REVERT: H 11 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7198 (tp) REVERT: K 72 GLN cc_start: 0.5145 (OUTLIER) cc_final: 0.4688 (mp10) REVERT: K 90 PHE cc_start: 0.7323 (t80) cc_final: 0.6412 (m-80) REVERT: K 96 LYS cc_start: 0.7215 (tttt) cc_final: 0.6623 (tptt) REVERT: I 11 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6972 (tp) REVERT: I 68 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.7863 (t) REVERT: L 90 PHE cc_start: 0.7365 (t80) cc_final: 0.6411 (m-80) REVERT: L 97 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4916 (mm) outliers start: 108 outliers final: 56 residues processed: 264 average time/residue: 0.4878 time to fit residues: 143.6526 Evaluate side-chains 241 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 165 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain B residue 163 ARG Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 376 SER Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 20 LYS Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 390 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 91 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN D 412 ASN G 56 ASN G 116 GLN H 56 ASN H 116 GLN I 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.186412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137817 restraints weight = 17618.918| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.10 r_work: 0.3517 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15181 Z= 0.152 Angle : 0.582 14.460 20655 Z= 0.296 Chirality : 0.044 0.224 2425 Planarity : 0.004 0.039 2621 Dihedral : 5.858 59.154 2296 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 6.55 % Allowed : 20.38 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1912 helix: 2.87 (0.23), residues: 459 sheet: 0.31 (0.21), residues: 582 loop : -0.52 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 348 TYR 0.015 0.002 TYR B 310 PHE 0.013 0.002 PHE C 48 TRP 0.012 0.002 TRP H 34 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd covalent geometry : bond 0.00357 (15145) covalent geometry : angle 0.57188 (20574) SS BOND : bond 0.00605 ( 27) SS BOND : angle 1.26613 ( 54) hydrogen bonds : bond 0.04021 ( 644) hydrogen bonds : angle 4.44115 ( 1740) link_NAG-ASN : bond 0.00353 ( 9) link_NAG-ASN : angle 2.58003 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 166 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7998 (mtpp) REVERT: B 164 GLU cc_start: 0.2391 (OUTLIER) cc_final: 0.1938 (mm-30) REVERT: B 221 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7519 (mp) REVERT: B 294 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6941 (tt0) REVERT: B 413 GLN cc_start: 0.6389 (mt0) cc_final: 0.6015 (mm110) REVERT: C 75 LYS cc_start: 0.8005 (mtpm) cc_final: 0.7107 (mttt) REVERT: D 166 LYS cc_start: 0.1500 (OUTLIER) cc_final: 0.0618 (mptt) REVERT: D 221 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 329 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7797 (ttm170) REVERT: D 440 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7698 (mtp180) REVERT: F 156 ARG cc_start: 0.2866 (OUTLIER) cc_final: 0.2407 (ttm110) REVERT: F 166 LYS cc_start: 0.2379 (OUTLIER) cc_final: 0.1202 (mptt) REVERT: F 213 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7505 (mp) REVERT: F 333 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.8104 (t) REVERT: F 336 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7886 (t70) REVERT: G 11 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7338 (tp) REVERT: G 68 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.7946 (t) REVERT: J 90 PHE cc_start: 0.7546 (t80) cc_final: 0.6778 (m-80) REVERT: J 96 LYS cc_start: 0.7624 (tptp) cc_final: 0.6501 (mttp) REVERT: H 11 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7334 (tp) REVERT: K 72 GLN cc_start: 0.5375 (OUTLIER) cc_final: 0.4825 (mp10) REVERT: K 90 PHE cc_start: 0.7361 (t80) cc_final: 0.6536 (m-80) REVERT: K 96 LYS cc_start: 0.7467 (tttt) cc_final: 0.6850 (tptt) REVERT: K 97 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.4879 (mp) REVERT: I 11 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7139 (tp) REVERT: L 90 PHE cc_start: 0.7434 (t80) cc_final: 0.6560 (m-80) REVERT: L 97 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.5066 (mm) outliers start: 109 outliers final: 60 residues processed: 257 average time/residue: 0.5206 time to fit residues: 148.1355 Evaluate side-chains 241 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 162 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 376 SER Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 390 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 184 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.0870 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN D 412 ASN G 56 ASN H 56 ASN H 116 GLN I 56 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.185792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137319 restraints weight = 17514.376| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.09 r_work: 0.3507 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15181 Z= 0.164 Angle : 0.608 14.572 20655 Z= 0.307 Chirality : 0.045 0.227 2425 Planarity : 0.004 0.039 2621 Dihedral : 5.910 58.910 2296 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 7.34 % Allowed : 19.24 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1912 helix: 2.81 (0.23), residues: 460 sheet: 0.27 (0.21), residues: 589 loop : -0.52 (0.22), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 252 TYR 0.016 0.002 TYR L 25 PHE 0.013 0.002 PHE C 48 TRP 0.013 0.002 TRP H 34 HIS 0.002 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00386 (15145) covalent geometry : angle 0.58781 (20574) SS BOND : bond 0.00638 ( 27) SS BOND : angle 1.29087 ( 54) hydrogen bonds : bond 0.04150 ( 644) hydrogen bonds : angle 4.46969 ( 1740) link_NAG-ASN : bond 0.00505 ( 9) link_NAG-ASN : angle 4.03354 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 168 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8027 (mtpp) REVERT: B 164 GLU cc_start: 0.2434 (OUTLIER) cc_final: 0.1972 (mm-30) REVERT: B 221 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7537 (mp) REVERT: B 294 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: B 413 GLN cc_start: 0.6373 (mt0) cc_final: 0.6004 (mm110) REVERT: D 166 LYS cc_start: 0.1509 (OUTLIER) cc_final: 0.0634 (mptt) REVERT: D 221 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7846 (mp) REVERT: D 329 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7824 (ttm170) REVERT: F 156 ARG cc_start: 0.2863 (OUTLIER) cc_final: 0.2397 (ttm110) REVERT: F 166 LYS cc_start: 0.2346 (OUTLIER) cc_final: 0.1186 (mptt) REVERT: F 213 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7472 (mp) REVERT: F 333 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8125 (t) REVERT: F 336 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7934 (t70) REVERT: F 421 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7882 (m-30) REVERT: G 11 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7396 (tp) REVERT: G 25 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8163 (p) REVERT: G 68 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.7976 (t) REVERT: J 82 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6476 (pt0) REVERT: J 90 PHE cc_start: 0.7556 (t80) cc_final: 0.6797 (m-80) REVERT: J 96 LYS cc_start: 0.7705 (tptp) cc_final: 0.6559 (mttp) REVERT: J 97 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5428 (mm) REVERT: H 11 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7380 (tp) REVERT: K 72 GLN cc_start: 0.5613 (OUTLIER) cc_final: 0.5078 (mp10) REVERT: K 90 PHE cc_start: 0.7390 (t80) cc_final: 0.6580 (m-80) REVERT: K 96 LYS cc_start: 0.7529 (tttt) cc_final: 0.6842 (mttm) REVERT: K 97 LEU cc_start: 0.5439 (OUTLIER) cc_final: 0.5041 (mp) REVERT: I 11 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7178 (tp) REVERT: I 68 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8006 (t) REVERT: L 82 GLN cc_start: 0.6846 (OUTLIER) cc_final: 0.5272 (tt0) REVERT: L 90 PHE cc_start: 0.7450 (t80) cc_final: 0.6548 (m-80) REVERT: L 97 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.5028 (mm) outliers start: 122 outliers final: 67 residues processed: 268 average time/residue: 0.5054 time to fit residues: 150.8718 Evaluate side-chains 255 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 164 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 376 SER Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 440 ARG Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 390 CYS Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 421 ASP Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 82 GLN Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 170 optimal weight: 0.0030 chunk 160 optimal weight: 10.0000 chunk 175 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN C 46 ASN D 412 ASN F 332 HIS G 56 ASN H 56 ASN I 56 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.187437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.146963 restraints weight = 17363.960| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.72 r_work: 0.3526 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15181 Z= 0.103 Angle : 0.532 14.074 20655 Z= 0.266 Chirality : 0.043 0.267 2425 Planarity : 0.004 0.037 2621 Dihedral : 5.501 59.249 2296 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.65 % Allowed : 21.05 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.02 (0.20), residues: 1912 helix: 3.02 (0.23), residues: 460 sheet: 0.55 (0.22), residues: 536 loop : -0.47 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 348 TYR 0.013 0.001 TYR L 25 PHE 0.010 0.001 PHE D 200 TRP 0.012 0.001 TRP H 34 HIS 0.002 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00226 (15145) covalent geometry : angle 0.51376 (20574) SS BOND : bond 0.00408 ( 27) SS BOND : angle 0.91084 ( 54) hydrogen bonds : bond 0.03479 ( 644) hydrogen bonds : angle 4.25188 ( 1740) link_NAG-ASN : bond 0.00483 ( 9) link_NAG-ASN : angle 3.73687 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 169 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7892 (mtpp) REVERT: B 164 GLU cc_start: 0.2180 (OUTLIER) cc_final: 0.1847 (mm-30) REVERT: B 221 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7351 (mp) REVERT: B 413 GLN cc_start: 0.6335 (mt0) cc_final: 0.5888 (mm110) REVERT: C 26 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6018 (pm20) REVERT: C 75 LYS cc_start: 0.7904 (mtpm) cc_final: 0.6997 (mttt) REVERT: D 166 LYS cc_start: 0.1386 (OUTLIER) cc_final: 0.0579 (mptt) REVERT: D 221 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7640 (mp) REVERT: D 329 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7760 (ttm170) REVERT: F 156 ARG cc_start: 0.2622 (OUTLIER) cc_final: 0.2203 (ttm110) REVERT: F 166 LYS cc_start: 0.2231 (OUTLIER) cc_final: 0.1157 (mptt) REVERT: F 213 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7405 (mp) REVERT: F 333 VAL cc_start: 0.8245 (OUTLIER) cc_final: 0.8028 (t) REVERT: F 336 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7819 (t70) REVERT: G 11 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7270 (tp) REVERT: G 68 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.7808 (t) REVERT: G 81 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7281 (mttp) REVERT: J 89 LEU cc_start: 0.7552 (mt) cc_final: 0.7328 (mp) REVERT: J 90 PHE cc_start: 0.7427 (t80) cc_final: 0.6600 (m-80) REVERT: J 96 LYS cc_start: 0.7342 (tptp) cc_final: 0.6215 (mttp) REVERT: H 11 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7172 (tp) REVERT: H 68 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.7874 (t) REVERT: H 81 LYS cc_start: 0.7630 (mttp) cc_final: 0.7332 (mptt) REVERT: K 72 GLN cc_start: 0.4949 (OUTLIER) cc_final: 0.4182 (mp10) REVERT: K 90 PHE cc_start: 0.7235 (t80) cc_final: 0.6388 (m-80) REVERT: K 96 LYS cc_start: 0.7278 (tttt) cc_final: 0.6516 (mttm) REVERT: K 97 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4757 (mm) REVERT: I 11 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6987 (tp) REVERT: L 90 PHE cc_start: 0.7369 (t80) cc_final: 0.6430 (m-80) REVERT: L 97 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4861 (mm) outliers start: 94 outliers final: 52 residues processed: 249 average time/residue: 0.4851 time to fit residues: 134.7457 Evaluate side-chains 235 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 163 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 442 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 388 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain J residue 45 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 5 GLN Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 24 SER Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 9 optimal weight: 9.9990 chunk 127 optimal weight: 0.2980 chunk 105 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 20 optimal weight: 0.0070 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 185 optimal weight: 0.1980 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 HIS ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN D 412 ASN H 56 ASN I 56 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.191063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.143371 restraints weight = 17650.487| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.08 r_work: 0.3590 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15181 Z= 0.082 Angle : 0.479 13.400 20655 Z= 0.241 Chirality : 0.041 0.179 2425 Planarity : 0.004 0.035 2621 Dihedral : 5.098 58.964 2296 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.49 % Allowed : 23.03 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.22 (0.20), residues: 1912 helix: 3.14 (0.23), residues: 460 sheet: 0.80 (0.23), residues: 515 loop : -0.38 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 348 TYR 0.014 0.001 TYR H 33 PHE 0.008 0.001 PHE D 200 TRP 0.012 0.001 TRP H 34 HIS 0.002 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00173 (15145) covalent geometry : angle 0.46742 (20574) SS BOND : bond 0.00283 ( 27) SS BOND : angle 0.70159 ( 54) hydrogen bonds : bond 0.03063 ( 644) hydrogen bonds : angle 4.05303 ( 1740) link_NAG-ASN : bond 0.00325 ( 9) link_NAG-ASN : angle 2.80958 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 175 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8260 (ttpt) cc_final: 0.7943 (mtpm) REVERT: B 164 GLU cc_start: 0.2365 (OUTLIER) cc_final: 0.1941 (mm-30) REVERT: B 413 GLN cc_start: 0.6329 (mt0) cc_final: 0.5994 (mm110) REVERT: C 26 GLU cc_start: 0.6802 (pm20) cc_final: 0.6382 (tt0) REVERT: C 75 LYS cc_start: 0.7965 (mtpm) cc_final: 0.7082 (mttt) REVERT: D 166 LYS cc_start: 0.1475 (OUTLIER) cc_final: 0.0612 (mptt) REVERT: D 221 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7582 (mp) REVERT: D 329 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7775 (ttm170) REVERT: F 156 ARG cc_start: 0.2762 (OUTLIER) cc_final: 0.2295 (ttm110) REVERT: F 166 LYS cc_start: 0.2226 (OUTLIER) cc_final: 0.1140 (mptt) REVERT: F 412 ASN cc_start: 0.7109 (p0) cc_final: 0.6824 (p0) REVERT: G 11 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7432 (tp) REVERT: G 25 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.7982 (p) REVERT: G 68 THR cc_start: 0.8306 (m) cc_final: 0.7930 (t) REVERT: J 17 ARG cc_start: 0.7613 (ttp80) cc_final: 0.7399 (ttp80) REVERT: J 90 PHE cc_start: 0.7380 (t80) cc_final: 0.6614 (m-80) REVERT: J 96 LYS cc_start: 0.7581 (tptp) cc_final: 0.6474 (mttp) REVERT: H 11 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7243 (tp) REVERT: H 68 THR cc_start: 0.8313 (m) cc_final: 0.7944 (t) REVERT: K 72 GLN cc_start: 0.5344 (OUTLIER) cc_final: 0.4547 (mp10) REVERT: K 90 PHE cc_start: 0.7238 (t80) cc_final: 0.6486 (m-80) REVERT: K 96 LYS cc_start: 0.7449 (tttt) cc_final: 0.6708 (mttm) REVERT: K 97 LEU cc_start: 0.5336 (OUTLIER) cc_final: 0.4946 (mm) REVERT: I 11 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7128 (tp) REVERT: L 90 PHE cc_start: 0.7380 (t80) cc_final: 0.6580 (m-80) REVERT: L 97 LEU cc_start: 0.5706 (OUTLIER) cc_final: 0.5347 (mm) outliers start: 58 outliers final: 32 residues processed: 228 average time/residue: 0.5167 time to fit residues: 130.4516 Evaluate side-chains 209 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 GLU Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 362 LYS Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 329 ARG Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 21 optimal weight: 3.9990 chunk 101 optimal weight: 0.0170 chunk 170 optimal weight: 0.2980 chunk 76 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 141 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 overall best weight: 0.3176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN I 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.191299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144196 restraints weight = 17648.137| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.02 r_work: 0.3609 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15181 Z= 0.081 Angle : 0.483 14.203 20655 Z= 0.240 Chirality : 0.041 0.164 2425 Planarity : 0.004 0.035 2621 Dihedral : 4.860 58.232 2290 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.25 % Allowed : 23.45 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.34 (0.20), residues: 1912 helix: 3.21 (0.23), residues: 460 sheet: 0.91 (0.22), residues: 536 loop : -0.34 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 348 TYR 0.017 0.001 TYR G 33 PHE 0.008 0.001 PHE D 200 TRP 0.011 0.001 TRP H 34 HIS 0.002 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00171 (15145) covalent geometry : angle 0.46121 (20574) SS BOND : bond 0.00285 ( 27) SS BOND : angle 0.67809 ( 54) hydrogen bonds : bond 0.02984 ( 644) hydrogen bonds : angle 3.96428 ( 1740) link_NAG-ASN : bond 0.00394 ( 9) link_NAG-ASN : angle 3.91066 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7905 (mtpp) REVERT: B 164 GLU cc_start: 0.2480 (OUTLIER) cc_final: 0.2031 (mm-30) REVERT: B 413 GLN cc_start: 0.6303 (mt0) cc_final: 0.5899 (mm110) REVERT: D 166 LYS cc_start: 0.1556 (OUTLIER) cc_final: 0.0656 (mptt) REVERT: D 221 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7596 (mp) REVERT: E 47 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8247 (t) REVERT: F 156 ARG cc_start: 0.2892 (OUTLIER) cc_final: 0.2425 (ttm110) REVERT: F 166 LYS cc_start: 0.2463 (OUTLIER) cc_final: 0.1296 (mptt) REVERT: F 412 ASN cc_start: 0.7109 (p0) cc_final: 0.6822 (p0) REVERT: G 11 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7414 (tp) REVERT: G 25 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7936 (p) REVERT: G 68 THR cc_start: 0.8275 (m) cc_final: 0.7912 (t) REVERT: J 17 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7393 (ttp80) REVERT: J 90 PHE cc_start: 0.7360 (t80) cc_final: 0.6610 (m-80) REVERT: J 96 LYS cc_start: 0.7611 (tptp) cc_final: 0.6494 (mttp) REVERT: H 11 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7275 (tp) REVERT: H 68 THR cc_start: 0.8312 (m) cc_final: 0.7953 (t) REVERT: H 81 LYS cc_start: 0.7544 (mptt) cc_final: 0.7302 (mptt) REVERT: K 72 GLN cc_start: 0.5350 (OUTLIER) cc_final: 0.4892 (mp10) REVERT: K 90 PHE cc_start: 0.7202 (t80) cc_final: 0.6458 (m-80) REVERT: K 96 LYS cc_start: 0.7379 (tttt) cc_final: 0.6691 (mttm) REVERT: K 97 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4940 (mm) REVERT: I 11 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7125 (tp) REVERT: L 90 PHE cc_start: 0.7379 (t80) cc_final: 0.6586 (m-80) REVERT: L 97 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5403 (mm) outliers start: 54 outliers final: 31 residues processed: 218 average time/residue: 0.5425 time to fit residues: 131.2237 Evaluate side-chains 204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 392 ILE Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain L residue 8 VAL Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 144 optimal weight: 5.9990 chunk 166 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 chunk 156 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN D 412 ASN I 56 ASN I 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.189823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141833 restraints weight = 17526.405| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.11 r_work: 0.3567 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15181 Z= 0.098 Angle : 0.507 13.481 20655 Z= 0.253 Chirality : 0.042 0.177 2425 Planarity : 0.004 0.036 2621 Dihedral : 4.863 57.046 2290 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.25 % Allowed : 23.93 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.35 (0.20), residues: 1912 helix: 3.19 (0.23), residues: 460 sheet: 0.93 (0.22), residues: 536 loop : -0.33 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 348 TYR 0.018 0.001 TYR J 25 PHE 0.009 0.001 PHE D 200 TRP 0.009 0.001 TRP H 34 HIS 0.002 0.001 HIS F 435 Details of bonding type rmsd covalent geometry : bond 0.00219 (15145) covalent geometry : angle 0.48831 (20574) SS BOND : bond 0.00375 ( 27) SS BOND : angle 0.81309 ( 54) hydrogen bonds : bond 0.03265 ( 644) hydrogen bonds : angle 4.01996 ( 1740) link_NAG-ASN : bond 0.00527 ( 9) link_NAG-ASN : angle 3.68547 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 157 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7922 (mtpm) REVERT: B 164 GLU cc_start: 0.2330 (OUTLIER) cc_final: 0.1961 (mm-30) REVERT: B 413 GLN cc_start: 0.6313 (mt0) cc_final: 0.5905 (mm110) REVERT: D 166 LYS cc_start: 0.1374 (OUTLIER) cc_final: 0.0556 (mptt) REVERT: D 221 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7655 (mp) REVERT: F 156 ARG cc_start: 0.2690 (OUTLIER) cc_final: 0.2241 (ttm110) REVERT: F 166 LYS cc_start: 0.2322 (OUTLIER) cc_final: 0.1234 (mptt) REVERT: F 213 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7333 (mp) REVERT: G 11 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7443 (tp) REVERT: G 25 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7988 (p) REVERT: G 68 THR cc_start: 0.8315 (m) cc_final: 0.7939 (t) REVERT: J 90 PHE cc_start: 0.7358 (t80) cc_final: 0.6603 (m-80) REVERT: J 96 LYS cc_start: 0.7613 (tptp) cc_final: 0.6504 (mttp) REVERT: H 11 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7264 (tp) REVERT: H 68 THR cc_start: 0.8356 (m) cc_final: 0.7981 (t) REVERT: H 81 LYS cc_start: 0.7500 (mptt) cc_final: 0.7284 (mptt) REVERT: K 72 GLN cc_start: 0.5523 (OUTLIER) cc_final: 0.4982 (mp10) REVERT: K 90 PHE cc_start: 0.7221 (t80) cc_final: 0.6480 (m-80) REVERT: K 96 LYS cc_start: 0.7412 (tttt) cc_final: 0.6719 (mttm) REVERT: K 97 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.4964 (mm) REVERT: I 11 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7143 (tp) REVERT: L 90 PHE cc_start: 0.7376 (t80) cc_final: 0.6591 (m-80) REVERT: L 97 LEU cc_start: 0.5458 (OUTLIER) cc_final: 0.5194 (mm) outliers start: 54 outliers final: 30 residues processed: 209 average time/residue: 0.5507 time to fit residues: 127.3128 Evaluate side-chains 198 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 283 CYS Chi-restraints excluded: chain B residue 333 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 478 ASN Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain D residue 166 LYS Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 481 LEU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 ARG Chi-restraints excluded: chain F residue 166 LYS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 480 ILE Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 25 SER Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 17 THR Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 85 VAL Chi-restraints excluded: chain K residue 8 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 72 GLN Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 116 GLN Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 ASN C 46 ASN D 412 ASN H 116 GLN I 56 ASN I 116 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.186174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.137867 restraints weight = 17536.925| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.08 r_work: 0.3516 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15181 Z= 0.164 Angle : 0.595 13.815 20655 Z= 0.301 Chirality : 0.045 0.219 2425 Planarity : 0.004 0.040 2621 Dihedral : 5.268 54.715 2290 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.25 % Allowed : 23.93 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.12 (0.20), residues: 1912 helix: 3.02 (0.23), residues: 460 sheet: 0.62 (0.21), residues: 580 loop : -0.40 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 348 TYR 0.026 0.002 TYR J 25 PHE 0.012 0.002 PHE C 48 TRP 0.010 0.002 TRP G 110 HIS 0.003 0.001 HIS D 332 Details of bonding type rmsd covalent geometry : bond 0.00390 (15145) covalent geometry : angle 0.57775 (20574) SS BOND : bond 0.00639 ( 27) SS BOND : angle 1.23171 ( 54) hydrogen bonds : bond 0.04058 ( 644) hydrogen bonds : angle 4.28908 ( 1740) link_NAG-ASN : bond 0.00566 ( 9) link_NAG-ASN : angle 3.67211 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7895.19 seconds wall clock time: 134 minutes 31.51 seconds (8071.51 seconds total)