Starting phenix.real_space_refine on Tue Apr 7 14:58:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yrc_73365/04_2026/9yrc_73365.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yrc_73365/04_2026/9yrc_73365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yrc_73365/04_2026/9yrc_73365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yrc_73365/04_2026/9yrc_73365.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yrc_73365/04_2026/9yrc_73365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yrc_73365/04_2026/9yrc_73365.map" } resolution = 2.97 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= 0.003 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 138 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 30 5.49 5 S 137 5.16 5 C 17624 2.51 5 N 4960 2.21 5 O 5367 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28118 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4295 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 4369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4369 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 533} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 4264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4264 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4367 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 532} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4296 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 522} Chain breaks: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2020 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 13, 'TRANS': 248} Chain: "G" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3632 Classifications: {'peptide': 453} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 426} Chain breaks: 1 Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 162 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain: "I" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 384 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.11, per 1000 atoms: 0.22 Number of scatterers: 28118 At special positions: 0 Unit cell: (156.303, 145.552, 151.341, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 137 16.00 P 30 15.00 O 5367 8.00 N 4960 7.00 C 17624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 691 " - pdb=" SG CYS B 695 " distance=2.08 Simple disulfide: pdb=" SG CYS C 691 " - pdb=" SG CYS C 695 " distance=2.07 Simple disulfide: pdb=" SG CYS D 691 " - pdb=" SG CYS D 695 " distance=2.09 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 194 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 205 " - pdb=" SG CYS G 208 " 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 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6644 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 16 sheets defined 54.3% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.774A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 258 through 263' Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 279 through 291 Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.506A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 385 Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.522A pdb=" N VAL A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 402 " --> pdb=" O GLN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.859A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 459 removed outlier: 3.509A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 499 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 499 through 507 removed outlier: 4.007A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 535 Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.778A pdb=" N LEU A 547 " --> pdb=" O GLY A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 569 Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.582A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 592 removed outlier: 4.054A pdb=" N GLY A 591 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 587 through 592' Processing helix chain 'A' and resid 596 through 611 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 630 through 635 removed outlier: 3.851A pdb=" N LEU A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 661 Processing helix chain 'A' and resid 671 through 679 removed outlier: 3.555A pdb=" N LEU A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 714 Processing helix chain 'A' and resid 732 through 742 removed outlier: 3.827A pdb=" N PHE A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 766 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.737A pdb=" N ILE B 206 " --> pdb=" O TYR B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 226 through 233 removed outlier: 4.611A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.693A pdb=" N SER B 284 " --> pdb=" O GLY B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 309 Processing helix chain 'B' and resid 318 through 333 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.745A pdb=" N ILE B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 Processing helix chain 'B' and resid 373 through 385 Processing helix chain 'B' and resid 395 through 403 Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 438 through 445 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 475 through 479 removed outlier: 3.557A pdb=" N ILE B 479 " --> pdb=" O TRP B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 499 removed outlier: 3.686A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 499 through 507 removed outlier: 3.878A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 535 Processing helix chain 'B' and resid 544 through 548 Processing helix chain 'B' and resid 553 through 569 Processing helix chain 'B' and resid 578 through 582 Processing helix chain 'B' and resid 591 through 609 removed outlier: 3.962A pdb=" N GLY B 595 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA B 597 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASP B 598 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 649 through 661 Processing helix chain 'B' and resid 671 through 679 Processing helix chain 'B' and resid 683 through 714 removed outlier: 3.695A pdb=" N CYS B 691 " --> pdb=" O LEU B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.653A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 767 Processing helix chain 'C' and resid 202 through 206 removed outlier: 3.848A pdb=" N ILE C 206 " --> pdb=" O TYR C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 226 removed outlier: 3.910A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 234 removed outlier: 4.107A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.535A pdb=" N GLU C 273 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.893A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.674A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 358 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 395 through 403 Processing helix chain 'C' and resid 408 through 428 Processing helix chain 'C' and resid 438 through 444 Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 499 removed outlier: 3.583A pdb=" N VAL C 493 " --> pdb=" O LEU C 489 " (cutoff:3.500A) Proline residue: C 496 - end of helix Processing helix chain 'C' and resid 499 through 507 removed outlier: 4.171A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 535 Processing helix chain 'C' and resid 553 through 569 Processing helix chain 'C' and resid 579 through 582 Processing helix chain 'C' and resid 595 through 609 Processing helix chain 'C' and resid 649 through 661 Processing helix chain 'C' and resid 671 through 679 Processing helix chain 'C' and resid 683 through 709 removed outlier: 3.598A pdb=" N CYS C 691 " --> pdb=" O LEU C 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 removed outlier: 3.661A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 767 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 210 through 226 removed outlier: 4.313A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 228 through 233 removed outlier: 3.669A pdb=" N ALA D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 233 " --> pdb=" O LEU D 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 228 through 233' Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 276 removed outlier: 3.624A pdb=" N SER D 276 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 296 Processing helix chain 'D' and resid 305 through 310 removed outlier: 4.269A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 395 through 403 Processing helix chain 'D' and resid 407 through 428 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.631A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 465 Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.581A pdb=" N ILE D 479 " --> pdb=" O TRP D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 499 Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 501 through 506 Processing helix chain 'D' and resid 523 through 531 Processing helix chain 'D' and resid 553 through 569 removed outlier: 3.685A pdb=" N ALA D 557 " --> pdb=" O GLY D 553 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 582 Processing helix chain 'D' and resid 595 through 609 removed outlier: 3.503A pdb=" N ILE D 601 " --> pdb=" O ALA D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 Processing helix chain 'D' and resid 671 through 679 Processing helix chain 'D' and resid 683 through 714 removed outlier: 4.239A pdb=" N CYS D 691 " --> pdb=" O LEU D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.702A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 767 removed outlier: 3.738A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 767 " --> pdb=" O GLN D 763 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.515A pdb=" N LEU E 213 " --> pdb=" O CYS E 209 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 226 Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 250 through 261 Processing helix chain 'E' and resid 270 through 277 removed outlier: 3.724A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 296 Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.797A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 335 removed outlier: 4.059A pdb=" N ARG E 323 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 374 through 384 removed outlier: 4.014A pdb=" N LEU E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 409 through 417 removed outlier: 3.573A pdb=" N ALA E 413 " --> pdb=" O ALA E 409 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER E 416 " --> pdb=" O ALA E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 425 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 451 through 459 Processing helix chain 'E' and resid 482 through 499 removed outlier: 3.503A pdb=" N LYS E 486 " --> pdb=" O LEU E 482 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU E 488 " --> pdb=" O ASP E 484 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 489 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN E 494 " --> pdb=" O GLN E 490 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix removed outlier: 3.943A pdb=" N HIS E 499 " --> pdb=" O TYR E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 503 Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 544 through 548 removed outlier: 3.549A pdb=" N LEU E 548 " --> pdb=" O GLY E 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 544 through 548' Processing helix chain 'E' and resid 553 through 570 removed outlier: 3.699A pdb=" N GLN E 568 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 578 through 582 Processing helix chain 'E' and resid 593 through 612 removed outlier: 3.670A pdb=" N VAL E 600 " --> pdb=" O ALA E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.959A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 removed outlier: 3.606A pdb=" N LEU E 634 " --> pdb=" O ASP E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 661 Processing helix chain 'E' and resid 671 through 679 removed outlier: 3.642A pdb=" N LEU E 675 " --> pdb=" O ASP E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 714 removed outlier: 3.548A pdb=" N GLN E 714 " --> pdb=" O GLU E 710 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 743 Processing helix chain 'E' and resid 748 through 766 removed outlier: 3.570A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.559A pdb=" N GLU F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 226 Processing helix chain 'F' and resid 226 through 233 removed outlier: 4.242A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 262 Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 280 through 295 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 312 through 316 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 336 through 340 Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 removed outlier: 3.617A pdb=" N ARG F 358 " --> pdb=" O ASP F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 395 through 403 removed outlier: 3.683A pdb=" N GLU F 402 " --> pdb=" O GLN F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 428 removed outlier: 3.653A pdb=" N ALA F 412 " --> pdb=" O GLY F 408 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 445 Processing helix chain 'F' and resid 448 through 458 removed outlier: 3.710A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 115 Processing helix chain 'G' and resid 164 through 173 Processing helix chain 'G' and resid 230 through 245 removed outlier: 4.162A pdb=" N ALA G 234 " --> pdb=" O ASN G 230 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE G 240 " --> pdb=" O ARG G 236 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N TRP G 241 " --> pdb=" O PHE G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 303 Processing helix chain 'G' and resid 337 through 351 Processing helix chain 'G' and resid 388 through 397 removed outlier: 3.785A pdb=" N ASP G 397 " --> pdb=" O ALA G 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 484 through 495 Processing helix chain 'G' and resid 499 through 505 removed outlier: 4.073A pdb=" N THR G 503 " --> pdb=" O VAL G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 515 Processing helix chain 'G' and resid 525 through 535 Processing helix chain 'G' and resid 536 through 545 Processing helix chain 'G' and resid 546 through 555 Processing helix chain 'I' and resid 22 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 538 through 542 removed outlier: 6.639A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 513 " --> pdb=" O GLN A 641 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE A 643 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU A 515 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 365 through 368 removed outlier: 6.605A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 538 through 542 removed outlier: 6.665A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.382A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 538 through 542 removed outlier: 6.685A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 365 through 368 removed outlier: 6.299A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE D 266 " --> pdb=" O LYS G 137 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 538 through 543 removed outlier: 6.708A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 300 through 302 removed outlier: 6.011A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 516 through 517 Processing sheet with id=AB1, first strand: chain 'E' and resid 538 through 543 removed outlier: 5.768A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASP E 577 " --> pdb=" O ILE E 540 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE E 542 " --> pdb=" O ASP E 577 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 242 through 243 removed outlier: 5.831A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 162 through 163 removed outlier: 6.400A pdb=" N MET G 162 " --> pdb=" O ARG G 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'I' and resid 40 through 41 removed outlier: 3.593A pdb=" N GLY G 384 " --> pdb=" O ILE G 452 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR G 454 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE G 382 " --> pdb=" O THR G 454 " (cutoff:3.500A) removed outlier: 11.542A pdb=" N PHE G 456 " --> pdb=" O VAL G 380 " (cutoff:3.500A) removed outlier: 16.076A pdb=" N VAL G 380 " --> pdb=" O PHE G 456 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N VAL G 368 " --> pdb=" O ARG G 306 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL G 308 " --> pdb=" O VAL G 368 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ALA G 370 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP G 310 " --> pdb=" O ALA G 370 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ALA G 372 " --> pdb=" O TRP G 310 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE G 312 " --> pdb=" O ALA G 372 " (cutoff:3.500A) removed outlier: 8.837A pdb=" N GLY G 374 " --> pdb=" O PHE G 312 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ASP G 314 " --> pdb=" O GLY G 374 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LYS G 307 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY G 254 " --> pdb=" O LYS G 307 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY G 309 " --> pdb=" O LEU G 252 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ARG G 255 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N VAL G 270 " --> pdb=" O ARG G 255 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR G 257 " --> pdb=" O ALA G 268 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA G 268 " --> pdb=" O THR G 257 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS G 259 " --> pdb=" O ILE G 266 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE G 266 " --> pdb=" O HIS G 259 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASN G 225 " --> pdb=" O ALA G 268 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N VAL G 270 " --> pdb=" O ASN G 225 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET G 227 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA G 272 " --> pdb=" O MET G 227 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 352 through 354 removed outlier: 4.715A pdb=" N GLY G 364 " --> pdb=" O ASN G 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 400 through 402 Processing sheet with id=AB7, first strand: chain 'G' and resid 425 through 429 1266 hydrogen bonds defined for protein. 3609 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.94 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 9664 1.36 - 1.50: 7016 1.50 - 1.64: 11721 1.64 - 1.78: 21 1.78 - 1.92: 204 Bond restraints: 28626 Sorted by residual: bond pdb=" C LEU C 634 " pdb=" N ARG C 635 " ideal model delta sigma weight residual 1.329 1.271 0.058 1.60e-02 3.91e+03 1.30e+01 bond pdb=" CB CYS B 691 " pdb=" SG CYS B 691 " ideal model delta sigma weight residual 1.808 1.924 -0.116 3.30e-02 9.18e+02 1.24e+01 bond pdb=" CA GLU A 470 " pdb=" CB GLU A 470 " ideal model delta sigma weight residual 1.525 1.569 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N VAL F 235 " pdb=" CA VAL F 235 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.59e+00 bond pdb=" CB CYS C 691 " pdb=" SG CYS C 691 " ideal model delta sigma weight residual 1.808 1.907 -0.099 3.30e-02 9.18e+02 9.00e+00 ... (remaining 28621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.00: 38680 6.00 - 12.00: 40 12.00 - 18.00: 0 18.00 - 24.00: 1 24.00 - 30.00: 1 Bond angle restraints: 38722 Sorted by residual: angle pdb=" CA CYS D 695 " pdb=" CB CYS D 695 " pdb=" SG CYS D 695 " ideal model delta sigma weight residual 114.40 144.40 -30.00 2.30e+00 1.89e-01 1.70e+02 angle pdb=" CA CYS B 695 " pdb=" CB CYS B 695 " pdb=" SG CYS B 695 " ideal model delta sigma weight residual 114.40 137.59 -23.19 2.30e+00 1.89e-01 1.02e+02 angle pdb=" N GLN C 337 " pdb=" CA GLN C 337 " pdb=" C GLN C 337 " ideal model delta sigma weight residual 108.74 119.53 -10.79 1.38e+00 5.25e-01 6.12e+01 angle pdb=" C CYS B 695 " pdb=" CA CYS B 695 " pdb=" CB CYS B 695 " ideal model delta sigma weight residual 109.34 121.03 -11.69 1.55e+00 4.16e-01 5.68e+01 angle pdb=" N CYS B 695 " pdb=" CA CYS B 695 " pdb=" CB CYS B 695 " ideal model delta sigma weight residual 110.40 99.82 10.58 1.45e+00 4.76e-01 5.33e+01 ... (remaining 38717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 16843 26.40 - 52.81: 799 52.81 - 79.21: 116 79.21 - 105.61: 10 105.61 - 132.02: 3 Dihedral angle restraints: 17771 sinusoidal: 7524 harmonic: 10247 Sorted by residual: dihedral pdb=" CA GLU G 156 " pdb=" C GLU G 156 " pdb=" N PRO G 157 " pdb=" CA PRO G 157 " ideal model delta harmonic sigma weight residual 180.00 128.23 51.77 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CB CYS D 691 " pdb=" SG CYS D 691 " pdb=" SG CYS D 695 " pdb=" CB CYS D 695 " ideal model delta sinusoidal sigma weight residual -86.00 -14.24 -71.76 1 1.00e+01 1.00e-02 6.59e+01 dihedral pdb=" CB CYS G 194 " pdb=" SG CYS G 194 " pdb=" SG CYS G 205 " pdb=" CB CYS G 205 " ideal model delta sinusoidal sigma weight residual 93.00 162.71 -69.71 1 1.00e+01 1.00e-02 6.27e+01 ... (remaining 17768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 3329 0.053 - 0.107: 832 0.107 - 0.160: 133 0.160 - 0.214: 15 0.214 - 0.267: 5 Chirality restraints: 4314 Sorted by residual: chirality pdb=" CB ILE F 300 " pdb=" CA ILE F 300 " pdb=" CG1 ILE F 300 " pdb=" CG2 ILE F 300 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ILE F 233 " pdb=" N ILE F 233 " pdb=" C ILE F 233 " pdb=" CB ILE F 233 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 4311 not shown) Planarity restraints: 5058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN D 692 " -0.019 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C GLN D 692 " 0.067 2.00e-02 2.50e+03 pdb=" O GLN D 692 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG D 693 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 695 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C CYS B 695 " 0.059 2.00e-02 2.50e+03 pdb=" O CYS B 695 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS B 696 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU G 156 " 0.054 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO G 157 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " 0.045 5.00e-02 4.00e+02 ... (remaining 5055 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 484 2.63 - 3.20: 27081 3.20 - 3.77: 45458 3.77 - 4.33: 62899 4.33 - 4.90: 100423 Nonbonded interactions: 236345 Sorted by model distance: nonbonded pdb=" OG1 THR D 448 " pdb=" OD1 ASP D 450 " model vdw 2.064 3.040 nonbonded pdb=" OG1 THR F 448 " pdb=" OD1 ASP F 450 " model vdw 2.090 3.040 nonbonded pdb=" OH TYR A 203 " pdb=" O ALA A 255 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR E 252 " pdb=" O1A ADP E 902 " model vdw 2.130 3.040 nonbonded pdb=" NH2 ARG B 256 " pdb=" O LEU C 335 " model vdw 2.148 3.120 ... (remaining 236340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 202 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 461 or resid 471 through 507 o \ r (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 09 through 533 or (resid 534 and (name N or name CA or name C or name O or name \ CB )) or resid 535 through 553 or (resid 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 through 709 or resid 727 through 766)) selection = (chain 'B' and (resid 202 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 461 or resid 471 through 507 o \ r (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 09 through 533 or (resid 534 and (name N or name CA or name C or name O or name \ CB )) or resid 535 through 553 or (resid 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 through 709 or resid 727 through 766)) selection = (chain 'C' and (resid 202 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 461 or resid 471 through 507 o \ r (resid 508 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 09 through 533 or (resid 534 and (name N or name CA or name C or name O or name \ CB )) or resid 535 through 553 or (resid 554 and (name N or name CA or name C or \ name O or name CB )) or resid 555 through 764 or (resid 765 through 766 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'D' and (resid 202 through 461 or resid 471 through 507 or (resid 508 and \ (name N or name CA or name C or name O or name CB )) or resid 509 through 553 o \ r (resid 554 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 55 through 709 or resid 727 through 762 or (resid 763 through 766 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 202 through 238 or (resid 239 and (name N or name CA or na \ me C or name O or name CB )) or resid 240 through 533 or (resid 534 and (name N \ or name CA or name C or name O or name CB )) or resid 535 through 588 or (resid \ 589 through 590 and (name N or name CA or name C or name O or name CB )) or resi \ d 591 or (resid 592 and (name N or name CA or name C or name O or name CB )) or \ resid 593 through 709 or resid 727 through 764 or (resid 765 through 766 and (na \ me N or name CA or name C or name O or name CB )))) } 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: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 22.080 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 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 : 0.005 0.116 28632 Z= 0.256 Angle : 0.861 29.997 38734 Z= 0.498 Chirality : 0.048 0.267 4314 Planarity : 0.005 0.083 5058 Dihedral : 14.668 132.018 11109 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.87 % Favored : 92.70 % Rotamer: Outliers : 0.44 % Allowed : 0.41 % Favored : 99.16 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.06 % 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: -0.50 (0.14), residues: 3536 helix: 0.54 (0.13), residues: 1638 sheet: -0.98 (0.25), residues: 370 loop : -1.05 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 287 TYR 0.028 0.002 TYR B 244 PHE 0.020 0.002 PHE A 302 TRP 0.046 0.003 TRP E 551 HIS 0.011 0.001 HIS G 231 Details of bonding type rmsd covalent geometry : bond 0.00532 (28626) covalent geometry : angle 0.85663 (38722) SS BOND : bond 0.03418 ( 6) SS BOND : angle 4.84372 ( 12) hydrogen bonds : bond 0.16779 ( 1266) hydrogen bonds : angle 6.32617 ( 3609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 363 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.8780 (mmt) cc_final: 0.8569 (mpp) REVERT: A 611 MET cc_start: 0.8349 (ptp) cc_final: 0.7972 (ppp) REVERT: B 466 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 773 PHE cc_start: 0.7961 (m-10) cc_final: 0.7675 (m-10) REVERT: D 561 GLU cc_start: 0.8453 (pp20) cc_final: 0.8116 (pp20) REVERT: E 301 ILE cc_start: 0.9353 (mm) cc_final: 0.8848 (pp) REVERT: E 344 MET cc_start: 0.8750 (tpp) cc_final: 0.8508 (mmm) REVERT: E 377 ARG cc_start: 0.8452 (ptm160) cc_final: 0.8240 (ptm-80) REVERT: F 344 MET cc_start: 0.8020 (ptm) cc_final: 0.7412 (pmt) REVERT: G 481 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7500 (mp0) REVERT: G 495 ASN cc_start: 0.8144 (m-40) cc_final: 0.7932 (m110) REVERT: G 548 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8457 (mp10) REVERT: I 13 ILE cc_start: 0.8681 (mm) cc_final: 0.8140 (mp) REVERT: I 21 ASP cc_start: 0.8466 (m-30) cc_final: 0.8007 (m-30) REVERT: I 39 ASP cc_start: 0.9114 (p0) cc_final: 0.8693 (p0) outliers start: 13 outliers final: 2 residues processed: 373 average time/residue: 0.7480 time to fit residues: 318.6473 Evaluate side-chains 246 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 757 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN D 340 HIS E 327 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 317 HIS F 404 HIS G 381 HIS G 486 HIS ** I 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.103165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.070352 restraints weight = 74653.372| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.30 r_work: 0.3015 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 28632 Z= 0.195 Angle : 0.738 13.930 38734 Z= 0.375 Chirality : 0.046 0.230 4314 Planarity : 0.005 0.076 5058 Dihedral : 11.209 133.056 4157 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.79 % Favored : 92.93 % Rotamer: Outliers : 1.45 % Allowed : 8.92 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.29 (0.14), residues: 3536 helix: 0.66 (0.13), residues: 1680 sheet: -1.17 (0.25), residues: 380 loop : -0.81 (0.17), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 210 TYR 0.021 0.002 TYR B 244 PHE 0.021 0.002 PHE G 512 TRP 0.015 0.002 TRP F 454 HIS 0.009 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00450 (28626) covalent geometry : angle 0.73338 (38722) SS BOND : bond 0.02980 ( 6) SS BOND : angle 4.80551 ( 12) hydrogen bonds : bond 0.05109 ( 1266) hydrogen bonds : angle 5.13479 ( 3609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.8940 (mmt) cc_final: 0.8607 (mpp) REVERT: B 561 GLU cc_start: 0.9054 (tp30) cc_final: 0.8806 (tp30) REVERT: B 773 PHE cc_start: 0.7527 (m-10) cc_final: 0.7203 (m-10) REVERT: C 277 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8991 (mmmm) REVERT: C 321 GLU cc_start: 0.8785 (mp0) cc_final: 0.8430 (mp0) REVERT: C 442 MET cc_start: 0.8778 (tpt) cc_final: 0.8532 (tpp) REVERT: C 757 MET cc_start: 0.8866 (ttp) cc_final: 0.8326 (ptt) REVERT: C 760 GLN cc_start: 0.9001 (tp40) cc_final: 0.8660 (mm-40) REVERT: D 561 GLU cc_start: 0.8888 (pp20) cc_final: 0.8530 (pp20) REVERT: D 740 MET cc_start: 0.8035 (tmm) cc_final: 0.7730 (tmm) REVERT: E 301 ILE cc_start: 0.9366 (mm) cc_final: 0.8908 (pp) REVERT: E 304 ASP cc_start: 0.7955 (p0) cc_final: 0.7720 (p0) REVERT: E 377 ARG cc_start: 0.8698 (ptm160) cc_final: 0.8333 (ttm170) REVERT: E 406 HIS cc_start: 0.5503 (p90) cc_final: 0.5280 (p90) REVERT: E 550 MET cc_start: 0.7816 (mpt) cc_final: 0.6511 (ttp) REVERT: E 678 MET cc_start: 0.6361 (ptt) cc_final: 0.5828 (pmm) REVERT: F 219 MET cc_start: 0.8427 (mpp) cc_final: 0.8166 (mpp) REVERT: F 256 ARG cc_start: 0.7190 (tmt170) cc_final: 0.6900 (tmt170) REVERT: F 260 ASN cc_start: 0.8369 (p0) cc_final: 0.8009 (p0) REVERT: F 302 PHE cc_start: 0.8032 (t80) cc_final: 0.7629 (t80) REVERT: F 337 GLN cc_start: 0.8249 (tt0) cc_final: 0.8021 (tm-30) REVERT: F 340 HIS cc_start: 0.6434 (m-70) cc_final: 0.6207 (m90) REVERT: F 344 MET cc_start: 0.8103 (ptm) cc_final: 0.7390 (pmt) REVERT: F 443 ASN cc_start: 0.8813 (p0) cc_final: 0.8607 (p0) REVERT: F 454 TRP cc_start: 0.8422 (t-100) cc_final: 0.8108 (t-100) REVERT: G 481 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7443 (mp0) REVERT: G 519 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7346 (ppp) REVERT: G 548 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8402 (mp10) REVERT: I 1 MET cc_start: 0.7413 (ttm) cc_final: 0.7040 (ttm) REVERT: I 13 ILE cc_start: 0.8803 (mm) cc_final: 0.8160 (mp) REVERT: I 21 ASP cc_start: 0.8916 (m-30) cc_final: 0.8435 (m-30) REVERT: I 39 ASP cc_start: 0.9459 (p0) cc_final: 0.9036 (p0) outliers start: 43 outliers final: 12 residues processed: 298 average time/residue: 0.6633 time to fit residues: 229.8674 Evaluate side-chains 264 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain E residue 423 ILE Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 360 PHE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 519 MET Chi-restraints excluded: chain H residue 273 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 14 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 173 optimal weight: 8.9990 chunk 196 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 204 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 308 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 538 ASN ** C 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 HIS ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 404 HIS G 486 HIS I 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.104147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.071320 restraints weight = 74776.340| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.32 r_work: 0.3034 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 28632 Z= 0.145 Angle : 0.682 17.409 38734 Z= 0.343 Chirality : 0.044 0.218 4314 Planarity : 0.004 0.074 5058 Dihedral : 10.794 133.241 4150 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.42 % Favored : 93.27 % Rotamer: Outliers : 2.13 % Allowed : 10.98 % Favored : 86.89 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.12 (0.15), residues: 3536 helix: 0.80 (0.13), residues: 1692 sheet: -1.07 (0.25), residues: 373 loop : -0.75 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 210 TYR 0.015 0.001 TYR A 517 PHE 0.027 0.001 PHE F 266 TRP 0.012 0.001 TRP E 476 HIS 0.008 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00320 (28626) covalent geometry : angle 0.67585 (38722) SS BOND : bond 0.03503 ( 6) SS BOND : angle 5.17244 ( 12) hydrogen bonds : bond 0.04285 ( 1266) hydrogen bonds : angle 4.84903 ( 3609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 286 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.8879 (mmt) cc_final: 0.8572 (mpp) REVERT: A 611 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8089 (ttt) REVERT: B 561 GLU cc_start: 0.9129 (tp30) cc_final: 0.8859 (tp30) REVERT: B 760 GLN cc_start: 0.8271 (mm-40) cc_final: 0.8032 (mm110) REVERT: B 773 PHE cc_start: 0.7455 (m-10) cc_final: 0.7248 (m-10) REVERT: C 321 GLU cc_start: 0.8829 (mp0) cc_final: 0.8462 (mp0) REVERT: C 695 CYS cc_start: 0.5624 (OUTLIER) cc_final: 0.5314 (p) REVERT: C 757 MET cc_start: 0.8916 (ttp) cc_final: 0.8334 (ptt) REVERT: C 760 GLN cc_start: 0.9025 (tp40) cc_final: 0.8654 (mm-40) REVERT: D 427 MET cc_start: 0.8527 (tmm) cc_final: 0.7910 (ppp) REVERT: D 561 GLU cc_start: 0.8908 (pp20) cc_final: 0.8672 (pp20) REVERT: D 740 MET cc_start: 0.7858 (OUTLIER) cc_final: 0.7466 (tmm) REVERT: E 304 ASP cc_start: 0.7884 (p0) cc_final: 0.7601 (p0) REVERT: E 406 HIS cc_start: 0.5527 (p90) cc_final: 0.5207 (p90) REVERT: E 449 MET cc_start: 0.7141 (tpp) cc_final: 0.6699 (tpp) REVERT: E 550 MET cc_start: 0.7814 (mpt) cc_final: 0.6477 (ttp) REVERT: E 689 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6134 (pp20) REVERT: F 256 ARG cc_start: 0.7233 (tmt170) cc_final: 0.6948 (tmt170) REVERT: F 267 PHE cc_start: 0.8770 (t80) cc_final: 0.8476 (t80) REVERT: F 337 GLN cc_start: 0.8309 (tt0) cc_final: 0.8042 (tm-30) REVERT: F 340 HIS cc_start: 0.6488 (m-70) cc_final: 0.6228 (m90) REVERT: F 344 MET cc_start: 0.8150 (ptm) cc_final: 0.7476 (pmt) REVERT: F 454 TRP cc_start: 0.8487 (t-100) cc_final: 0.8120 (t-100) REVERT: G 150 ASP cc_start: 0.8774 (t0) cc_final: 0.7814 (t0) REVERT: G 154 HIS cc_start: 0.8235 (m170) cc_final: 0.7608 (m170) REVERT: G 481 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7598 (mp0) REVERT: G 495 ASN cc_start: 0.8247 (m-40) cc_final: 0.7792 (m110) REVERT: G 519 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7531 (ppp) REVERT: G 548 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8458 (mp10) REVERT: H 267 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8822 (tptp) REVERT: I 1 MET cc_start: 0.7628 (ttm) cc_final: 0.7220 (ttm) REVERT: I 13 ILE cc_start: 0.8814 (mm) cc_final: 0.8173 (mp) REVERT: I 21 ASP cc_start: 0.8876 (m-30) cc_final: 0.8400 (m-30) REVERT: I 39 ASP cc_start: 0.9436 (p0) cc_final: 0.9052 (p0) outliers start: 63 outliers final: 15 residues processed: 318 average time/residue: 0.6573 time to fit residues: 242.8278 Evaluate side-chains 276 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 255 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 598 ASP Chi-restraints excluded: chain A residue 611 MET Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 695 CYS Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 360 PHE Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 519 MET Chi-restraints excluded: chain H residue 267 LYS Chi-restraints excluded: chain H residue 273 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 344 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN B 603 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS D 401 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 558 ASN E 735 HIS ** F 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 HIS G 548 GLN ** I 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.100624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.067757 restraints weight = 74884.392| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.27 r_work: 0.2947 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 28632 Z= 0.305 Angle : 0.782 17.374 38734 Z= 0.393 Chirality : 0.048 0.269 4314 Planarity : 0.005 0.069 5058 Dihedral : 10.911 131.100 4150 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.96 % Favored : 92.73 % Rotamer: Outliers : 2.60 % Allowed : 13.01 % Favored : 84.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.10 (0.15), residues: 3536 helix: 0.80 (0.13), residues: 1681 sheet: -1.11 (0.25), residues: 385 loop : -0.69 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 349 TYR 0.027 0.002 TYR B 244 PHE 0.023 0.002 PHE A 302 TRP 0.012 0.002 TRP B 551 HIS 0.008 0.002 HIS G 197 Details of bonding type rmsd covalent geometry : bond 0.00715 (28626) covalent geometry : angle 0.77541 (38722) SS BOND : bond 0.03421 ( 6) SS BOND : angle 5.75544 ( 12) hydrogen bonds : bond 0.04718 ( 1266) hydrogen bonds : angle 4.86050 ( 3609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.4978 (OUTLIER) cc_final: 0.4170 (pp) REVERT: A 244 TYR cc_start: 0.7126 (m-10) cc_final: 0.6808 (m-10) REVERT: A 342 ILE cc_start: 0.9176 (mt) cc_final: 0.8972 (mp) REVERT: A 343 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8065 (t) REVERT: A 442 MET cc_start: 0.8903 (mmt) cc_final: 0.8592 (mpp) REVERT: A 466 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: B 277 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9025 (ptpp) REVERT: B 561 GLU cc_start: 0.9189 (tp30) cc_final: 0.8945 (tp30) REVERT: B 760 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8181 (mm-40) REVERT: C 321 GLU cc_start: 0.8902 (mp0) cc_final: 0.8600 (mp0) REVERT: D 427 MET cc_start: 0.8512 (tmm) cc_final: 0.7923 (ppp) REVERT: D 561 GLU cc_start: 0.8949 (pp20) cc_final: 0.8574 (pp20) REVERT: D 740 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7278 (tmm) REVERT: D 757 MET cc_start: 0.9039 (mtp) cc_final: 0.8765 (tpp) REVERT: E 377 ARG cc_start: 0.8462 (ttm170) cc_final: 0.8245 (ttm170) REVERT: E 449 MET cc_start: 0.7148 (tpp) cc_final: 0.6912 (tpp) REVERT: E 678 MET cc_start: 0.6293 (ptt) cc_final: 0.5655 (pmm) REVERT: E 689 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6225 (pp20) REVERT: F 256 ARG cc_start: 0.7502 (tmt170) cc_final: 0.7258 (tmt170) REVERT: F 267 PHE cc_start: 0.8846 (t80) cc_final: 0.8556 (t80) REVERT: F 305 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: F 337 GLN cc_start: 0.8333 (tt0) cc_final: 0.8056 (tm-30) REVERT: F 340 HIS cc_start: 0.6595 (m-70) cc_final: 0.6374 (m90) REVERT: F 344 MET cc_start: 0.8449 (ptm) cc_final: 0.7555 (pmt) REVERT: F 378 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9213 (mm) REVERT: F 454 TRP cc_start: 0.8483 (t-100) cc_final: 0.8061 (t-100) REVERT: G 106 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8684 (p) REVERT: G 154 HIS cc_start: 0.8704 (OUTLIER) cc_final: 0.8473 (m170) REVERT: G 481 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7585 (mp0) REVERT: G 519 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7619 (ppp) REVERT: G 548 GLN cc_start: 0.9069 (mm110) cc_final: 0.8492 (mp10) REVERT: I 1 MET cc_start: 0.7632 (ttm) cc_final: 0.7332 (ttm) REVERT: I 13 ILE cc_start: 0.8828 (mm) cc_final: 0.8269 (mp) REVERT: I 21 ASP cc_start: 0.8986 (m-30) cc_final: 0.8489 (m-30) REVERT: I 39 ASP cc_start: 0.9444 (p0) cc_final: 0.9051 (p0) outliers start: 77 outliers final: 21 residues processed: 292 average time/residue: 0.6458 time to fit residues: 219.5241 Evaluate side-chains 266 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 269 ILE Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 360 PHE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 154 HIS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 519 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 200 optimal weight: 0.4980 chunk 230 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 256 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 298 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 237 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS G 486 HIS I 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.102096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.069155 restraints weight = 74414.084| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.33 r_work: 0.2976 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 28632 Z= 0.187 Angle : 0.718 26.108 38734 Z= 0.358 Chirality : 0.045 0.245 4314 Planarity : 0.004 0.063 5058 Dihedral : 10.656 135.017 4150 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.65 % Favored : 93.04 % Rotamer: Outliers : 2.81 % Allowed : 14.40 % Favored : 82.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: 0.01 (0.15), residues: 3536 helix: 0.90 (0.13), residues: 1687 sheet: -1.10 (0.25), residues: 384 loop : -0.64 (0.17), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 533 TYR 0.022 0.002 TYR A 755 PHE 0.028 0.001 PHE A 302 TRP 0.012 0.001 TRP G 549 HIS 0.009 0.001 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.00435 (28626) covalent geometry : angle 0.71245 (38722) SS BOND : bond 0.02811 ( 6) SS BOND : angle 5.28607 ( 12) hydrogen bonds : bond 0.04192 ( 1266) hydrogen bonds : angle 4.70149 ( 3609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 258 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.4784 (OUTLIER) cc_final: 0.4140 (pp) REVERT: A 244 TYR cc_start: 0.6952 (m-10) cc_final: 0.6686 (m-10) REVERT: A 342 ILE cc_start: 0.9065 (mt) cc_final: 0.8842 (mp) REVERT: A 442 MET cc_start: 0.8850 (mmt) cc_final: 0.8550 (mpp) REVERT: A 546 GLU cc_start: 0.8811 (pt0) cc_final: 0.8397 (pm20) REVERT: B 319 GLU cc_start: 0.7489 (tp30) cc_final: 0.7156 (tp30) REVERT: B 561 GLU cc_start: 0.9179 (tp30) cc_final: 0.8904 (tp30) REVERT: B 662 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7397 (ptp90) REVERT: B 760 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8160 (mm-40) REVERT: C 256 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8562 (mmp80) REVERT: C 321 GLU cc_start: 0.8909 (mp0) cc_final: 0.8612 (mp0) REVERT: C 508 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8469 (mtm) REVERT: D 427 MET cc_start: 0.8534 (tmm) cc_final: 0.7956 (ppp) REVERT: D 550 MET cc_start: 0.7601 (ttt) cc_final: 0.7302 (mmm) REVERT: D 561 GLU cc_start: 0.8936 (pp20) cc_final: 0.8545 (pp20) REVERT: D 740 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7190 (tmm) REVERT: D 757 MET cc_start: 0.9044 (mtp) cc_final: 0.8828 (tpp) REVERT: E 377 ARG cc_start: 0.8573 (ttm170) cc_final: 0.8355 (ttm170) REVERT: E 550 MET cc_start: 0.7741 (mpt) cc_final: 0.6498 (ttp) REVERT: E 678 MET cc_start: 0.6337 (ptt) cc_final: 0.5658 (pmm) REVERT: E 689 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6329 (pp20) REVERT: E 740 MET cc_start: 0.6419 (ppp) cc_final: 0.6002 (ppp) REVERT: F 267 PHE cc_start: 0.8864 (t80) cc_final: 0.8591 (t80) REVERT: F 305 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: F 337 GLN cc_start: 0.8372 (tt0) cc_final: 0.8125 (tm-30) REVERT: F 340 HIS cc_start: 0.6555 (m-70) cc_final: 0.6324 (m90) REVERT: F 344 MET cc_start: 0.8414 (ptm) cc_final: 0.7558 (pmt) REVERT: F 378 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9205 (mm) REVERT: F 454 TRP cc_start: 0.8515 (t-100) cc_final: 0.8087 (t-100) REVERT: G 150 ASP cc_start: 0.8814 (t0) cc_final: 0.7704 (t0) REVERT: G 154 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7812 (m170) REVERT: G 279 ILE cc_start: 0.9298 (tp) cc_final: 0.9073 (pp) REVERT: G 481 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7518 (mp0) REVERT: G 519 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7686 (ppp) REVERT: G 548 GLN cc_start: 0.9082 (mm110) cc_final: 0.8523 (mp10) REVERT: I 1 MET cc_start: 0.7522 (ttm) cc_final: 0.7180 (ttm) REVERT: I 13 ILE cc_start: 0.8858 (mm) cc_final: 0.8322 (mp) REVERT: I 21 ASP cc_start: 0.8947 (m-30) cc_final: 0.8456 (m-30) REVERT: I 39 ASP cc_start: 0.9448 (p0) cc_final: 0.9069 (p0) outliers start: 83 outliers final: 25 residues processed: 306 average time/residue: 0.6677 time to fit residues: 237.3275 Evaluate side-chains 272 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain G residue 154 HIS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 519 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 312 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 494 GLN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS D 558 ASN E 260 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 486 HIS I 31 GLN I 40 GLN I 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.101668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.068666 restraints weight = 74439.937| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.35 r_work: 0.2983 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 28632 Z= 0.181 Angle : 0.706 21.044 38734 Z= 0.352 Chirality : 0.045 0.250 4314 Planarity : 0.004 0.059 5058 Dihedral : 10.454 132.607 4150 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.56 % Favored : 93.16 % Rotamer: Outliers : 2.60 % Allowed : 15.28 % Favored : 82.12 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: 0.14 (0.15), residues: 3536 helix: 1.03 (0.13), residues: 1676 sheet: -1.03 (0.25), residues: 381 loop : -0.60 (0.17), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 533 TYR 0.022 0.002 TYR A 755 PHE 0.019 0.001 PHE A 267 TRP 0.021 0.002 TRP D 551 HIS 0.008 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00422 (28626) covalent geometry : angle 0.69862 (38722) SS BOND : bond 0.03254 ( 6) SS BOND : angle 5.99360 ( 12) hydrogen bonds : bond 0.04103 ( 1266) hydrogen bonds : angle 4.58801 ( 3609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 254 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.4760 (OUTLIER) cc_final: 0.4158 (pp) REVERT: A 244 TYR cc_start: 0.6893 (m-10) cc_final: 0.6650 (m-10) REVERT: A 442 MET cc_start: 0.8823 (mmt) cc_final: 0.8550 (mpp) REVERT: A 546 GLU cc_start: 0.8814 (pt0) cc_final: 0.8524 (pm20) REVERT: B 319 GLU cc_start: 0.7497 (tp30) cc_final: 0.7183 (tp30) REVERT: B 561 GLU cc_start: 0.9182 (tp30) cc_final: 0.8887 (tp30) REVERT: B 662 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7241 (ptp90) REVERT: B 678 MET cc_start: 0.9042 (mmm) cc_final: 0.8370 (ptp) REVERT: B 760 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8266 (mm-40) REVERT: C 256 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8565 (mmp80) REVERT: C 321 GLU cc_start: 0.8919 (mp0) cc_final: 0.8620 (mp0) REVERT: C 508 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: D 427 MET cc_start: 0.8543 (tmm) cc_final: 0.7944 (ppp) REVERT: D 508 MET cc_start: 0.8048 (mmt) cc_final: 0.7546 (mtt) REVERT: D 561 GLU cc_start: 0.8950 (pp20) cc_final: 0.8699 (pp20) REVERT: D 740 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7285 (tmm) REVERT: D 757 MET cc_start: 0.9022 (mtp) cc_final: 0.8816 (tpp) REVERT: E 377 ARG cc_start: 0.8632 (ttm170) cc_final: 0.8240 (ttm170) REVERT: E 453 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8582 (mpp-170) REVERT: E 550 MET cc_start: 0.7719 (mpt) cc_final: 0.6521 (ttp) REVERT: E 678 MET cc_start: 0.6263 (ptt) cc_final: 0.5628 (pmm) REVERT: E 689 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6314 (pp20) REVERT: F 267 PHE cc_start: 0.8879 (t80) cc_final: 0.8633 (t80) REVERT: F 305 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: F 337 GLN cc_start: 0.8377 (tt0) cc_final: 0.8078 (tm-30) REVERT: F 340 HIS cc_start: 0.6549 (m-70) cc_final: 0.6309 (m90) REVERT: F 344 MET cc_start: 0.8442 (ptm) cc_final: 0.7571 (pmt) REVERT: F 378 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9221 (mm) REVERT: F 454 TRP cc_start: 0.8541 (t-100) cc_final: 0.8109 (t-100) REVERT: G 106 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8593 (p) REVERT: G 154 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.8343 (m170) REVERT: G 481 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7513 (mp0) REVERT: G 519 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7719 (ppp) REVERT: G 548 GLN cc_start: 0.9083 (mm110) cc_final: 0.8547 (mp10) REVERT: I 1 MET cc_start: 0.7532 (ttm) cc_final: 0.7319 (ttm) REVERT: I 13 ILE cc_start: 0.8871 (mm) cc_final: 0.8316 (mp) REVERT: I 21 ASP cc_start: 0.8951 (m-30) cc_final: 0.8464 (m-30) REVERT: I 39 ASP cc_start: 0.9414 (p0) cc_final: 0.9012 (p0) outliers start: 77 outliers final: 28 residues processed: 301 average time/residue: 0.6718 time to fit residues: 234.6797 Evaluate side-chains 276 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 561 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 453 ARG Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 382 GLN Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 154 HIS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 519 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 285 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 19 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 199 optimal weight: 0.9980 chunk 284 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 398 GLN I 31 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.102629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.069995 restraints weight = 73751.227| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.31 r_work: 0.3010 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.134 28632 Z= 0.139 Angle : 0.692 21.302 38734 Z= 0.343 Chirality : 0.044 0.244 4314 Planarity : 0.004 0.057 5058 Dihedral : 10.171 131.965 4150 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.48 % Favored : 93.18 % Rotamer: Outliers : 2.43 % Allowed : 15.85 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: 0.16 (0.15), residues: 3536 helix: 1.02 (0.13), residues: 1701 sheet: -1.00 (0.25), residues: 386 loop : -0.59 (0.18), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 635 TYR 0.022 0.001 TYR A 755 PHE 0.022 0.001 PHE G 471 TRP 0.026 0.002 TRP D 551 HIS 0.008 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00320 (28626) covalent geometry : angle 0.68470 (38722) SS BOND : bond 0.02954 ( 6) SS BOND : angle 5.64687 ( 12) hydrogen bonds : bond 0.03824 ( 1266) hydrogen bonds : angle 4.51100 ( 3609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 254 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.4617 (OUTLIER) cc_final: 0.4117 (pp) REVERT: A 546 GLU cc_start: 0.8839 (pt0) cc_final: 0.8524 (pm20) REVERT: B 319 GLU cc_start: 0.7466 (tp30) cc_final: 0.7116 (tp30) REVERT: B 561 GLU cc_start: 0.9181 (tp30) cc_final: 0.8853 (tp30) REVERT: B 760 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8216 (mm-40) REVERT: B 772 ARG cc_start: 0.7427 (tpm170) cc_final: 0.6957 (tpm170) REVERT: C 256 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8538 (mmp80) REVERT: C 321 GLU cc_start: 0.8925 (mp0) cc_final: 0.8620 (mp0) REVERT: D 273 GLU cc_start: 0.8890 (tt0) cc_final: 0.8596 (tt0) REVERT: D 427 MET cc_start: 0.8563 (tmm) cc_final: 0.7974 (ppp) REVERT: D 561 GLU cc_start: 0.8962 (pp20) cc_final: 0.8730 (pp20) REVERT: D 740 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7324 (tmm) REVERT: D 757 MET cc_start: 0.9026 (mtp) cc_final: 0.8808 (tpp) REVERT: E 377 ARG cc_start: 0.8699 (ttm170) cc_final: 0.8268 (ttm170) REVERT: E 550 MET cc_start: 0.7685 (mpt) cc_final: 0.6341 (ttp) REVERT: E 678 MET cc_start: 0.6242 (ptt) cc_final: 0.5619 (pmm) REVERT: E 689 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6367 (pt0) REVERT: E 740 MET cc_start: 0.6454 (ppp) cc_final: 0.6077 (ppp) REVERT: F 267 PHE cc_start: 0.8819 (t80) cc_final: 0.8583 (t80) REVERT: F 305 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: F 337 GLN cc_start: 0.8373 (tt0) cc_final: 0.8050 (tm-30) REVERT: F 340 HIS cc_start: 0.6581 (m-70) cc_final: 0.6333 (m90) REVERT: F 344 MET cc_start: 0.8468 (ptm) cc_final: 0.7720 (pmt) REVERT: F 378 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9175 (mm) REVERT: F 454 TRP cc_start: 0.8515 (t-100) cc_final: 0.8081 (t-100) REVERT: G 106 VAL cc_start: 0.8733 (OUTLIER) cc_final: 0.8456 (p) REVERT: G 150 ASP cc_start: 0.8823 (t0) cc_final: 0.7796 (t0) REVERT: G 154 HIS cc_start: 0.8475 (OUTLIER) cc_final: 0.7648 (m170) REVERT: G 481 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7516 (mp0) REVERT: G 519 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7752 (ppp) REVERT: G 525 ILE cc_start: 0.8411 (tt) cc_final: 0.8206 (pp) REVERT: G 544 LYS cc_start: 0.8230 (tptm) cc_final: 0.7984 (tptp) REVERT: G 548 GLN cc_start: 0.9102 (mm110) cc_final: 0.8588 (mp10) REVERT: I 1 MET cc_start: 0.7634 (ttm) cc_final: 0.7330 (ttm) REVERT: I 13 ILE cc_start: 0.8862 (mm) cc_final: 0.8339 (mp) REVERT: I 21 ASP cc_start: 0.8904 (m-30) cc_final: 0.8396 (m-30) REVERT: I 39 ASP cc_start: 0.9412 (p0) cc_final: 0.9034 (p0) outliers start: 72 outliers final: 24 residues processed: 298 average time/residue: 0.6402 time to fit residues: 221.3823 Evaluate side-chains 267 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain D residue 740 MET Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 303 ILE Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 154 HIS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 519 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 69 optimal weight: 0.8980 chunk 338 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 336 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 4 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 189 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN D 340 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 398 GLN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.103032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070467 restraints weight = 74394.729| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 3.33 r_work: 0.3022 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 28632 Z= 0.140 Angle : 0.726 25.024 38734 Z= 0.357 Chirality : 0.044 0.256 4314 Planarity : 0.004 0.055 5058 Dihedral : 9.995 130.491 4150 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.33 % Favored : 93.35 % Rotamer: Outliers : 1.82 % Allowed : 16.80 % Favored : 81.38 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: 0.21 (0.15), residues: 3536 helix: 1.06 (0.13), residues: 1698 sheet: -0.92 (0.25), residues: 379 loop : -0.58 (0.17), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 533 TYR 0.026 0.001 TYR A 755 PHE 0.029 0.001 PHE E 539 TRP 0.026 0.002 TRP D 551 HIS 0.008 0.001 HIS A 340 Details of bonding type rmsd covalent geometry : bond 0.00328 (28626) covalent geometry : angle 0.71729 (38722) SS BOND : bond 0.02953 ( 6) SS BOND : angle 6.29736 ( 12) hydrogen bonds : bond 0.03660 ( 1266) hydrogen bonds : angle 4.57025 ( 3609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 260 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.4588 (OUTLIER) cc_final: 0.4185 (pp) REVERT: A 546 GLU cc_start: 0.8857 (pt0) cc_final: 0.8487 (pm20) REVERT: B 319 GLU cc_start: 0.7458 (tp30) cc_final: 0.7100 (tp30) REVERT: B 437 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7474 (mm) REVERT: B 561 GLU cc_start: 0.9177 (tp30) cc_final: 0.8837 (tp30) REVERT: B 678 MET cc_start: 0.9021 (mmm) cc_final: 0.8408 (ptp) REVERT: B 760 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8236 (mm-40) REVERT: C 256 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8532 (mmp80) REVERT: C 321 GLU cc_start: 0.8926 (mp0) cc_final: 0.8624 (mp0) REVERT: C 508 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7815 (mtm) REVERT: C 695 CYS cc_start: 0.5379 (t) cc_final: 0.4790 (t) REVERT: C 757 MET cc_start: 0.9048 (ttp) cc_final: 0.8663 (ptt) REVERT: C 760 GLN cc_start: 0.9055 (tp40) cc_final: 0.8624 (mm-40) REVERT: D 273 GLU cc_start: 0.8913 (tt0) cc_final: 0.8618 (tt0) REVERT: D 388 MET cc_start: 0.8711 (ptm) cc_final: 0.8501 (ptp) REVERT: D 427 MET cc_start: 0.8560 (tmm) cc_final: 0.7967 (ppp) REVERT: D 508 MET cc_start: 0.7881 (mmt) cc_final: 0.7573 (mtt) REVERT: D 550 MET cc_start: 0.7161 (tpt) cc_final: 0.6920 (tpt) REVERT: D 561 GLU cc_start: 0.8978 (pp20) cc_final: 0.8557 (pp20) REVERT: D 757 MET cc_start: 0.9036 (mtp) cc_final: 0.8810 (tpp) REVERT: E 377 ARG cc_start: 0.8734 (ttm170) cc_final: 0.8356 (ttm170) REVERT: E 388 MET cc_start: 0.0812 (pmm) cc_final: 0.0341 (pmt) REVERT: E 404 HIS cc_start: 0.8740 (OUTLIER) cc_final: 0.8262 (m90) REVERT: E 550 MET cc_start: 0.7509 (mpt) cc_final: 0.6266 (ttp) REVERT: E 678 MET cc_start: 0.6227 (ptt) cc_final: 0.5612 (pmm) REVERT: E 689 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6368 (pt0) REVERT: E 740 MET cc_start: 0.6428 (ppp) cc_final: 0.6148 (ppp) REVERT: F 305 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: F 337 GLN cc_start: 0.8379 (tt0) cc_final: 0.8055 (tm-30) REVERT: F 340 HIS cc_start: 0.6709 (m-70) cc_final: 0.6452 (m90) REVERT: F 344 MET cc_start: 0.8479 (ptm) cc_final: 0.7746 (pmt) REVERT: F 378 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9235 (mm) REVERT: F 454 TRP cc_start: 0.8526 (t-100) cc_final: 0.8085 (t-100) REVERT: G 106 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8422 (p) REVERT: G 150 ASP cc_start: 0.8860 (t0) cc_final: 0.7809 (t0) REVERT: G 154 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.7585 (m170) REVERT: G 481 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7581 (mp0) REVERT: G 519 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7694 (ppp) REVERT: G 525 ILE cc_start: 0.8419 (tt) cc_final: 0.8196 (pp) REVERT: G 544 LYS cc_start: 0.8211 (tptm) cc_final: 0.7996 (tptp) REVERT: G 548 GLN cc_start: 0.9108 (mm110) cc_final: 0.8584 (mp10) REVERT: I 1 MET cc_start: 0.7660 (ttm) cc_final: 0.7356 (ttm) REVERT: I 13 ILE cc_start: 0.8851 (mm) cc_final: 0.8342 (mp) REVERT: I 21 ASP cc_start: 0.8906 (m-30) cc_final: 0.8404 (m-30) REVERT: I 39 ASP cc_start: 0.9421 (p0) cc_final: 0.9072 (p0) outliers start: 54 outliers final: 20 residues processed: 289 average time/residue: 0.6710 time to fit residues: 224.4277 Evaluate side-chains 273 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 242 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 508 MET Chi-restraints excluded: chain C residue 742 PHE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain D residue 678 MET Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 154 HIS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 519 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 297 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 276 optimal weight: 0.1980 chunk 246 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 208 optimal weight: 1.9990 chunk 235 optimal weight: 0.0570 chunk 47 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN C 421 GLN D 340 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 398 GLN F 401 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.103447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.070826 restraints weight = 74230.882| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.34 r_work: 0.3020 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 28632 Z= 0.142 Angle : 0.755 29.828 38734 Z= 0.373 Chirality : 0.044 0.270 4314 Planarity : 0.004 0.056 5058 Dihedral : 9.854 130.616 4150 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.28 % Favored : 93.41 % Rotamer: Outliers : 1.69 % Allowed : 17.37 % Favored : 80.94 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: 0.24 (0.15), residues: 3536 helix: 1.11 (0.13), residues: 1687 sheet: -0.87 (0.25), residues: 385 loop : -0.59 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 256 TYR 0.022 0.001 TYR A 755 PHE 0.022 0.001 PHE F 266 TRP 0.028 0.002 TRP D 551 HIS 0.007 0.001 HIS A 404 Details of bonding type rmsd covalent geometry : bond 0.00322 (28626) covalent geometry : angle 0.74838 (38722) SS BOND : bond 0.03493 ( 6) SS BOND : angle 5.70390 ( 12) hydrogen bonds : bond 0.03685 ( 1266) hydrogen bonds : angle 4.53298 ( 3609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.4476 (OUTLIER) cc_final: 0.3971 (pp) REVERT: A 256 ARG cc_start: 0.5149 (ptm-80) cc_final: 0.4697 (ptm-80) REVERT: A 546 GLU cc_start: 0.8831 (pt0) cc_final: 0.8562 (pm20) REVERT: B 319 GLU cc_start: 0.7484 (tp30) cc_final: 0.7148 (tp30) REVERT: B 546 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8326 (pm20) REVERT: B 561 GLU cc_start: 0.9182 (tp30) cc_final: 0.8840 (tp30) REVERT: B 678 MET cc_start: 0.9037 (mmm) cc_final: 0.8380 (ptp) REVERT: B 760 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8275 (mm-40) REVERT: B 772 ARG cc_start: 0.7435 (tpm170) cc_final: 0.6969 (tpm170) REVERT: C 256 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8532 (mmp80) REVERT: C 321 GLU cc_start: 0.8938 (mp0) cc_final: 0.8635 (mp0) REVERT: C 695 CYS cc_start: 0.5371 (t) cc_final: 0.4796 (t) REVERT: C 740 MET cc_start: 0.8980 (mtm) cc_final: 0.8730 (mpp) REVERT: C 757 MET cc_start: 0.9040 (ttp) cc_final: 0.8627 (ptt) REVERT: C 760 GLN cc_start: 0.9051 (tp40) cc_final: 0.8613 (mm-40) REVERT: D 273 GLU cc_start: 0.8870 (tt0) cc_final: 0.8581 (tt0) REVERT: D 388 MET cc_start: 0.8705 (ptm) cc_final: 0.8494 (ptp) REVERT: D 427 MET cc_start: 0.8567 (tmm) cc_final: 0.7986 (ppp) REVERT: D 508 MET cc_start: 0.7905 (mmt) cc_final: 0.7681 (mtt) REVERT: D 561 GLU cc_start: 0.8985 (pp20) cc_final: 0.8737 (pp20) REVERT: D 740 MET cc_start: 0.7793 (tmm) cc_final: 0.7511 (tmm) REVERT: D 757 MET cc_start: 0.9044 (mtp) cc_final: 0.8817 (tpp) REVERT: E 377 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8393 (ttm170) REVERT: E 388 MET cc_start: 0.0948 (pmm) cc_final: 0.0529 (pmt) REVERT: E 404 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8245 (m-70) REVERT: E 550 MET cc_start: 0.7533 (mpt) cc_final: 0.6287 (ttp) REVERT: E 689 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.6381 (pt0) REVERT: E 740 MET cc_start: 0.6512 (ppp) cc_final: 0.6274 (ppp) REVERT: F 305 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: F 337 GLN cc_start: 0.8367 (tt0) cc_final: 0.8055 (tm-30) REVERT: F 340 HIS cc_start: 0.6800 (m-70) cc_final: 0.6545 (m90) REVERT: F 344 MET cc_start: 0.8481 (ptm) cc_final: 0.7708 (pmt) REVERT: F 378 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9215 (mm) REVERT: F 454 TRP cc_start: 0.8544 (t-100) cc_final: 0.8102 (t-100) REVERT: G 106 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8379 (p) REVERT: G 150 ASP cc_start: 0.8862 (t0) cc_final: 0.7853 (t0) REVERT: G 154 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7545 (m170) REVERT: G 481 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7757 (pm20) REVERT: G 525 ILE cc_start: 0.8440 (tt) cc_final: 0.8209 (pp) REVERT: G 548 GLN cc_start: 0.9114 (mm110) cc_final: 0.8599 (mp10) REVERT: I 1 MET cc_start: 0.7688 (ttm) cc_final: 0.7312 (ttm) REVERT: I 13 ILE cc_start: 0.8866 (mm) cc_final: 0.8359 (mp) REVERT: I 21 ASP cc_start: 0.8923 (m-30) cc_final: 0.8428 (m-30) REVERT: I 39 ASP cc_start: 0.9367 (p0) cc_final: 0.9050 (p0) outliers start: 50 outliers final: 22 residues processed: 280 average time/residue: 0.6500 time to fit residues: 212.3348 Evaluate side-chains 268 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 300 ILE Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 154 HIS Chi-restraints excluded: chain G residue 155 LEU Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 323 optimal weight: 2.9990 chunk 268 optimal weight: 3.9990 chunk 265 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 345 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 339 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN D 270 ASN D 340 HIS ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 HIS F 398 GLN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.101186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.068677 restraints weight = 74590.978| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 3.29 r_work: 0.2975 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 28632 Z= 0.234 Angle : 0.801 30.623 38734 Z= 0.397 Chirality : 0.046 0.268 4314 Planarity : 0.004 0.055 5058 Dihedral : 10.004 132.703 4150 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.53 % Favored : 93.18 % Rotamer: Outliers : 1.32 % Allowed : 17.91 % Favored : 80.77 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: 0.24 (0.15), residues: 3536 helix: 1.12 (0.13), residues: 1674 sheet: -0.91 (0.25), residues: 387 loop : -0.57 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.033 0.002 TYR A 755 PHE 0.026 0.002 PHE F 302 TRP 0.024 0.002 TRP D 551 HIS 0.010 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00548 (28626) covalent geometry : angle 0.79462 (38722) SS BOND : bond 0.03669 ( 6) SS BOND : angle 5.62651 ( 12) hydrogen bonds : bond 0.03990 ( 1266) hydrogen bonds : angle 4.62616 ( 3609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7072 Ramachandran restraints generated. 3536 Oldfield, 0 Emsley, 3536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.4730 (OUTLIER) cc_final: 0.4102 (pp) REVERT: A 546 GLU cc_start: 0.8769 (pt0) cc_final: 0.8480 (pm20) REVERT: A 757 MET cc_start: 0.9080 (ptp) cc_final: 0.8855 (pmm) REVERT: B 319 GLU cc_start: 0.7624 (tp30) cc_final: 0.7312 (tp30) REVERT: B 561 GLU cc_start: 0.9224 (tp30) cc_final: 0.8894 (tp30) REVERT: B 678 MET cc_start: 0.9062 (mmm) cc_final: 0.8371 (ptp) REVERT: B 760 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8257 (mp10) REVERT: B 772 ARG cc_start: 0.7441 (tpm170) cc_final: 0.7026 (tpm170) REVERT: C 256 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8492 (mmp80) REVERT: C 321 GLU cc_start: 0.8942 (mp0) cc_final: 0.8618 (mp0) REVERT: C 508 MET cc_start: 0.8055 (mtp) cc_final: 0.7763 (mtm) REVERT: C 695 CYS cc_start: 0.5535 (t) cc_final: 0.4985 (t) REVERT: C 757 MET cc_start: 0.9052 (ttp) cc_final: 0.8634 (ptt) REVERT: D 273 GLU cc_start: 0.8917 (tt0) cc_final: 0.8607 (tt0) REVERT: D 291 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8286 (mp0) REVERT: D 427 MET cc_start: 0.8575 (tmm) cc_final: 0.7992 (ppp) REVERT: D 508 MET cc_start: 0.8091 (mmt) cc_final: 0.7696 (mtt) REVERT: D 561 GLU cc_start: 0.8976 (pp20) cc_final: 0.8555 (pp20) REVERT: D 740 MET cc_start: 0.7761 (tmm) cc_final: 0.7428 (tmm) REVERT: D 757 MET cc_start: 0.9032 (mtp) cc_final: 0.8822 (tpp) REVERT: E 388 MET cc_start: 0.1140 (pmm) cc_final: 0.0814 (pmt) REVERT: E 404 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8224 (m-70) REVERT: E 550 MET cc_start: 0.7447 (mpt) cc_final: 0.6172 (ttp) REVERT: E 678 MET cc_start: 0.6223 (ptt) cc_final: 0.5477 (pmm) REVERT: E 689 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6430 (pt0) REVERT: E 740 MET cc_start: 0.6489 (ppp) cc_final: 0.6124 (ppp) REVERT: F 305 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: F 337 GLN cc_start: 0.8395 (tt0) cc_final: 0.8060 (tm-30) REVERT: F 340 HIS cc_start: 0.6856 (m-70) cc_final: 0.6588 (m90) REVERT: F 344 MET cc_start: 0.8572 (ptm) cc_final: 0.7685 (pmt) REVERT: F 378 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9201 (mm) REVERT: F 454 TRP cc_start: 0.8556 (t-100) cc_final: 0.8105 (t-100) REVERT: G 150 ASP cc_start: 0.8868 (t0) cc_final: 0.7903 (t0) REVERT: G 154 HIS cc_start: 0.8492 (OUTLIER) cc_final: 0.7668 (m170) REVERT: G 481 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7782 (pm20) REVERT: G 525 ILE cc_start: 0.8479 (tt) cc_final: 0.8225 (pp) REVERT: G 548 GLN cc_start: 0.9142 (mm110) cc_final: 0.8614 (mp10) REVERT: I 1 MET cc_start: 0.7669 (ttm) cc_final: 0.7384 (ttm) REVERT: I 13 ILE cc_start: 0.8840 (mm) cc_final: 0.8367 (mp) REVERT: I 21 ASP cc_start: 0.8985 (m-30) cc_final: 0.8496 (m-30) REVERT: I 39 ASP cc_start: 0.9392 (p0) cc_final: 0.9058 (p0) outliers start: 39 outliers final: 22 residues processed: 265 average time/residue: 0.6576 time to fit residues: 202.0998 Evaluate side-chains 261 residues out of total 2995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 402 GLU Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 404 HIS Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 382 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 404 HIS Chi-restraints excluded: chain E residue 689 GLU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain F residue 302 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 154 HIS Chi-restraints excluded: chain G residue 198 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 177 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 239 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 240 optimal weight: 10.0000 chunk 310 optimal weight: 0.8980 chunk 233 optimal weight: 0.9990 chunk 280 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 HIS E 260 ASN ** E 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 GLN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.103255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.070515 restraints weight = 74304.509| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.36 r_work: 0.3016 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 28632 Z= 0.144 Angle : 0.773 29.637 38734 Z= 0.381 Chirality : 0.045 0.264 4314 Planarity : 0.004 0.055 5058 Dihedral : 9.785 133.157 4150 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.14 % Favored : 93.55 % Rotamer: Outliers : 1.39 % Allowed : 18.01 % Favored : 80.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 4.32 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: 0.26 (0.15), residues: 3536 helix: 1.11 (0.13), residues: 1689 sheet: -0.80 (0.25), residues: 385 loop : -0.57 (0.18), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 256 TYR 0.026 0.001 TYR A 755 PHE 0.031 0.001 PHE F 267 TRP 0.026 0.002 TRP D 551 HIS 0.008 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00327 (28626) covalent geometry : angle 0.76727 (38722) SS BOND : bond 0.03394 ( 6) SS BOND : angle 5.53417 ( 12) hydrogen bonds : bond 0.03752 ( 1266) hydrogen bonds : angle 4.56085 ( 3609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9173.57 seconds wall clock time: 156 minutes 46.81 seconds (9406.81 seconds total)