Starting phenix.real_space_refine on Mon Feb 19 01:46:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/02_2024/5vc7_8658_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/02_2024/5vc7_8658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/02_2024/5vc7_8658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/02_2024/5vc7_8658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/02_2024/5vc7_8658_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vc7_8658/02_2024/5vc7_8658_trim_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 60 5.16 5 C 14760 2.51 5 N 4050 2.21 5 O 4392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23298 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3821 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 275 Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3821 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 275 Chain: "D" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3821 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 275 Chain: "E" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3821 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 275 Chain: "F" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3821 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 275 Chain: "G" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 3821 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PCIS': 2, 'PTRANS': 33, 'TRANS': 508} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 523 Unresolved non-hydrogen dihedrals: 355 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 5, 'ASP:plan': 17, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 275 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: "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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" 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: "F" 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: "G" 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} Time building chain proxies: 12.06, per 1000 atoms: 0.52 Number of scatterers: 23298 At special positions: 0 Unit cell: (146.45, 137.75, 97.15, 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 60 16.00 P 36 15.00 O 4392 8.00 N 4050 7.00 C 14760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.48 Conformation dependent library (CDL) restraints added in 4.9 seconds 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 12 sheets defined 48.3% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 196 through 211 Proline residue: A 209 - end of helix Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 237 through 248 removed outlier: 3.759A pdb=" N ALA A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 260 No H-bonds generated for 'chain 'A' and resid 257 through 260' Processing helix chain 'A' and resid 268 through 281 removed outlier: 3.592A pdb=" N ILE A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A 276 " --> pdb=" O LEU A 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 320 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 360 through 372 removed outlier: 3.672A pdb=" N LYS A 364 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 371 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 372 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.541A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 421 removed outlier: 3.921A pdb=" N ARG A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG A 416 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 439 through 445 Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 473 through 488 Proline residue: A 486 - end of helix Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 514 through 524 removed outlier: 3.764A pdb=" N LYS A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.625A pdb=" N LEU A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.569A pdb=" N PHE A 553 " --> pdb=" O ILE A 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 572 No H-bonds generated for 'chain 'A' and resid 569 through 572' Processing helix chain 'A' and resid 582 through 585 No H-bonds generated for 'chain 'A' and resid 582 through 585' Processing helix chain 'A' and resid 589 through 598 removed outlier: 3.726A pdb=" N THR A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 616 No H-bonds generated for 'chain 'A' and resid 614 through 616' Processing helix chain 'A' and resid 619 through 622 Processing helix chain 'A' and resid 638 through 651 removed outlier: 4.245A pdb=" N SER A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 672 through 689 removed outlier: 3.615A pdb=" N MET A 684 " --> pdb=" O ARG A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 705 removed outlier: 3.717A pdb=" N ALA A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 723 removed outlier: 3.766A pdb=" N LYS A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 191 No H-bonds generated for 'chain 'C' and resid 189 through 191' Processing helix chain 'C' and resid 196 through 211 Proline residue: C 209 - end of helix Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 237 through 248 removed outlier: 3.760A pdb=" N ALA C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 248 " --> pdb=" O VAL C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 260 No H-bonds generated for 'chain 'C' and resid 257 through 260' Processing helix chain 'C' and resid 268 through 281 removed outlier: 3.593A pdb=" N ILE C 275 " --> pdb=" O LYS C 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE C 276 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 320 Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 360 through 372 removed outlier: 3.672A pdb=" N LYS C 364 " --> pdb=" O ARG C 360 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 371 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 392 removed outlier: 3.540A pdb=" N ALA C 391 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 421 removed outlier: 3.921A pdb=" N ARG C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG C 416 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 439 through 445 Processing helix chain 'C' and resid 466 through 468 No H-bonds generated for 'chain 'C' and resid 466 through 468' Processing helix chain 'C' and resid 473 through 488 Proline residue: C 486 - end of helix Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'C' and resid 514 through 524 removed outlier: 3.763A pdb=" N LYS C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 539 removed outlier: 3.624A pdb=" N LEU C 538 " --> pdb=" O GLY C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.569A pdb=" N PHE C 553 " --> pdb=" O ILE C 549 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 572 No H-bonds generated for 'chain 'C' and resid 569 through 572' Processing helix chain 'C' and resid 582 through 585 No H-bonds generated for 'chain 'C' and resid 582 through 585' Processing helix chain 'C' and resid 589 through 598 removed outlier: 3.726A pdb=" N THR C 594 " --> pdb=" O ASN C 590 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 616 No H-bonds generated for 'chain 'C' and resid 614 through 616' Processing helix chain 'C' and resid 619 through 622 Processing helix chain 'C' and resid 638 through 651 removed outlier: 4.246A pdb=" N SER C 643 " --> pdb=" O GLU C 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS C 646 " --> pdb=" O LEU C 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS C 648 " --> pdb=" O ILE C 644 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN C 651 " --> pdb=" O VAL C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 666 Processing helix chain 'C' and resid 672 through 689 removed outlier: 3.616A pdb=" N MET C 684 " --> pdb=" O ARG C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 705 removed outlier: 3.716A pdb=" N ALA C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 714 through 723 removed outlier: 3.766A pdb=" N LYS C 718 " --> pdb=" O GLU C 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 191 No H-bonds generated for 'chain 'D' and resid 189 through 191' Processing helix chain 'D' and resid 196 through 211 Proline residue: D 209 - end of helix Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 237 through 248 removed outlier: 3.759A pdb=" N ALA D 241 " --> pdb=" O LYS D 237 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA D 243 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER D 248 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 260 No H-bonds generated for 'chain 'D' and resid 257 through 260' Processing helix chain 'D' and resid 268 through 281 removed outlier: 3.592A pdb=" N ILE D 275 " --> pdb=" O LYS D 271 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 320 Processing helix chain 'D' and resid 342 through 344 No H-bonds generated for 'chain 'D' and resid 342 through 344' Processing helix chain 'D' and resid 360 through 372 removed outlier: 3.672A pdb=" N LYS D 364 " --> pdb=" O ARG D 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR D 371 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG D 372 " --> pdb=" O MET D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 392 removed outlier: 3.541A pdb=" N ALA D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 392 " --> pdb=" O GLU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 421 removed outlier: 3.921A pdb=" N ARG D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG D 416 " --> pdb=" O ASN D 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Proline residue: D 419 - end of helix Processing helix chain 'D' and resid 439 through 445 Processing helix chain 'D' and resid 466 through 468 No H-bonds generated for 'chain 'D' and resid 466 through 468' Processing helix chain 'D' and resid 473 through 488 Proline residue: D 486 - end of helix Processing helix chain 'D' and resid 490 through 494 Processing helix chain 'D' and resid 514 through 524 removed outlier: 3.764A pdb=" N LYS D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 539 removed outlier: 3.625A pdb=" N LEU D 538 " --> pdb=" O GLY D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.569A pdb=" N PHE D 553 " --> pdb=" O ILE D 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS D 554 " --> pdb=" O ARG D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 572 No H-bonds generated for 'chain 'D' and resid 569 through 572' Processing helix chain 'D' and resid 582 through 585 No H-bonds generated for 'chain 'D' and resid 582 through 585' Processing helix chain 'D' and resid 589 through 598 removed outlier: 3.726A pdb=" N THR D 594 " --> pdb=" O ASN D 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 616 No H-bonds generated for 'chain 'D' and resid 614 through 616' Processing helix chain 'D' and resid 619 through 622 Processing helix chain 'D' and resid 638 through 651 removed outlier: 4.245A pdb=" N SER D 643 " --> pdb=" O GLU D 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS D 648 " --> pdb=" O ILE D 644 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN D 651 " --> pdb=" O VAL D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 661 through 666 Processing helix chain 'D' and resid 672 through 689 removed outlier: 3.616A pdb=" N MET D 684 " --> pdb=" O ARG D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 705 removed outlier: 3.717A pdb=" N ALA D 704 " --> pdb=" O ASN D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 723 removed outlier: 3.766A pdb=" N LYS D 718 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 191 No H-bonds generated for 'chain 'E' and resid 189 through 191' Processing helix chain 'E' and resid 196 through 211 Proline residue: E 209 - end of helix Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 237 through 248 removed outlier: 3.760A pdb=" N ALA E 241 " --> pdb=" O LYS E 237 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG E 242 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA E 243 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 260 No H-bonds generated for 'chain 'E' and resid 257 through 260' Processing helix chain 'E' and resid 268 through 281 removed outlier: 3.592A pdb=" N ILE E 275 " --> pdb=" O LYS E 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE E 276 " --> pdb=" O LEU E 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU E 280 " --> pdb=" O PHE E 276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 320 Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 360 through 372 removed outlier: 3.672A pdb=" N LYS E 364 " --> pdb=" O ARG E 360 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR E 371 " --> pdb=" O LEU E 367 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG E 372 " --> pdb=" O MET E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 392 removed outlier: 3.540A pdb=" N ALA E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP E 392 " --> pdb=" O GLU E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 421 removed outlier: 3.921A pdb=" N ARG E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG E 416 " --> pdb=" O ASN E 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR E 417 " --> pdb=" O ALA E 413 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 439 through 445 Processing helix chain 'E' and resid 466 through 468 No H-bonds generated for 'chain 'E' and resid 466 through 468' Processing helix chain 'E' and resid 473 through 488 Proline residue: E 486 - end of helix Processing helix chain 'E' and resid 490 through 494 Processing helix chain 'E' and resid 514 through 524 removed outlier: 3.764A pdb=" N LYS E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 539 removed outlier: 3.624A pdb=" N LEU E 538 " --> pdb=" O GLY E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.569A pdb=" N PHE E 553 " --> pdb=" O ILE E 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS E 554 " --> pdb=" O ARG E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 572 No H-bonds generated for 'chain 'E' and resid 569 through 572' Processing helix chain 'E' and resid 582 through 585 No H-bonds generated for 'chain 'E' and resid 582 through 585' Processing helix chain 'E' and resid 589 through 598 removed outlier: 3.725A pdb=" N THR E 594 " --> pdb=" O ASN E 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 614 through 616 No H-bonds generated for 'chain 'E' and resid 614 through 616' Processing helix chain 'E' and resid 619 through 622 Processing helix chain 'E' and resid 638 through 651 removed outlier: 4.246A pdb=" N SER E 643 " --> pdb=" O GLU E 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS E 646 " --> pdb=" O LEU E 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS E 648 " --> pdb=" O ILE E 644 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN E 651 " --> pdb=" O VAL E 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 661 through 666 Processing helix chain 'E' and resid 672 through 689 removed outlier: 3.615A pdb=" N MET E 684 " --> pdb=" O ARG E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 705 removed outlier: 3.716A pdb=" N ALA E 704 " --> pdb=" O ASN E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 714 through 723 removed outlier: 3.766A pdb=" N LYS E 718 " --> pdb=" O GLU E 714 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 191 No H-bonds generated for 'chain 'F' and resid 189 through 191' Processing helix chain 'F' and resid 196 through 211 Proline residue: F 209 - end of helix Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 237 through 248 removed outlier: 3.760A pdb=" N ALA F 241 " --> pdb=" O LYS F 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG F 242 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA F 243 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER F 248 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 260 No H-bonds generated for 'chain 'F' and resid 257 through 260' Processing helix chain 'F' and resid 268 through 281 removed outlier: 3.591A pdb=" N ILE F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N PHE F 276 " --> pdb=" O LEU F 272 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU F 280 " --> pdb=" O PHE F 276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU F 281 " --> pdb=" O SER F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 320 Processing helix chain 'F' and resid 342 through 344 No H-bonds generated for 'chain 'F' and resid 342 through 344' Processing helix chain 'F' and resid 360 through 372 removed outlier: 3.672A pdb=" N LYS F 364 " --> pdb=" O ARG F 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR F 371 " --> pdb=" O LEU F 367 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG F 372 " --> pdb=" O MET F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 392 removed outlier: 3.541A pdb=" N ALA F 391 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP F 392 " --> pdb=" O GLU F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 421 removed outlier: 3.920A pdb=" N ARG F 407 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ARG F 416 " --> pdb=" O ASN F 412 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR F 417 " --> pdb=" O ALA F 413 " (cutoff:3.500A) Proline residue: F 419 - end of helix Processing helix chain 'F' and resid 439 through 445 Processing helix chain 'F' and resid 466 through 468 No H-bonds generated for 'chain 'F' and resid 466 through 468' Processing helix chain 'F' and resid 473 through 488 Proline residue: F 486 - end of helix Processing helix chain 'F' and resid 490 through 494 Processing helix chain 'F' and resid 514 through 524 removed outlier: 3.764A pdb=" N LYS F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 539 removed outlier: 3.625A pdb=" N LEU F 538 " --> pdb=" O GLY F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.569A pdb=" N PHE F 553 " --> pdb=" O ILE F 549 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 554 " --> pdb=" O ARG F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 572 No H-bonds generated for 'chain 'F' and resid 569 through 572' Processing helix chain 'F' and resid 582 through 585 No H-bonds generated for 'chain 'F' and resid 582 through 585' Processing helix chain 'F' and resid 589 through 598 removed outlier: 3.726A pdb=" N THR F 594 " --> pdb=" O ASN F 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP F 597 " --> pdb=" O LEU F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 616 No H-bonds generated for 'chain 'F' and resid 614 through 616' Processing helix chain 'F' and resid 619 through 622 Processing helix chain 'F' and resid 638 through 651 removed outlier: 4.245A pdb=" N SER F 643 " --> pdb=" O GLU F 639 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS F 646 " --> pdb=" O LEU F 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS F 648 " --> pdb=" O ILE F 644 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN F 651 " --> pdb=" O VAL F 647 " (cutoff:3.500A) Processing helix chain 'F' and resid 661 through 666 Processing helix chain 'F' and resid 672 through 689 removed outlier: 3.616A pdb=" N MET F 684 " --> pdb=" O ARG F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 698 through 705 removed outlier: 3.716A pdb=" N ALA F 704 " --> pdb=" O ASN F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 714 through 723 removed outlier: 3.766A pdb=" N LYS F 718 " --> pdb=" O GLU F 714 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 191 No H-bonds generated for 'chain 'G' and resid 189 through 191' Processing helix chain 'G' and resid 196 through 211 Proline residue: G 209 - end of helix Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'G' and resid 237 through 248 removed outlier: 3.760A pdb=" N ALA G 241 " --> pdb=" O LYS G 237 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG G 242 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 243 " --> pdb=" O LEU G 239 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER G 248 " --> pdb=" O VAL G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 260 No H-bonds generated for 'chain 'G' and resid 257 through 260' Processing helix chain 'G' and resid 268 through 281 removed outlier: 3.592A pdb=" N ILE G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE G 276 " --> pdb=" O LEU G 272 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU G 280 " --> pdb=" O PHE G 276 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU G 281 " --> pdb=" O SER G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 320 Processing helix chain 'G' and resid 342 through 344 No H-bonds generated for 'chain 'G' and resid 342 through 344' Processing helix chain 'G' and resid 360 through 372 removed outlier: 3.672A pdb=" N LYS G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR G 371 " --> pdb=" O LEU G 367 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG G 372 " --> pdb=" O MET G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 381 through 392 removed outlier: 3.541A pdb=" N ALA G 391 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP G 392 " --> pdb=" O GLU G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 399 through 421 removed outlier: 3.921A pdb=" N ARG G 407 " --> pdb=" O ALA G 403 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG G 416 " --> pdb=" O ASN G 412 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Proline residue: G 419 - end of helix Processing helix chain 'G' and resid 439 through 445 Processing helix chain 'G' and resid 466 through 468 No H-bonds generated for 'chain 'G' and resid 466 through 468' Processing helix chain 'G' and resid 473 through 488 Proline residue: G 486 - end of helix Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 514 through 524 removed outlier: 3.764A pdb=" N LYS G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 539 removed outlier: 3.625A pdb=" N LEU G 538 " --> pdb=" O GLY G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.569A pdb=" N PHE G 553 " --> pdb=" O ILE G 549 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS G 554 " --> pdb=" O ARG G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 572 No H-bonds generated for 'chain 'G' and resid 569 through 572' Processing helix chain 'G' and resid 582 through 585 No H-bonds generated for 'chain 'G' and resid 582 through 585' Processing helix chain 'G' and resid 589 through 598 removed outlier: 3.726A pdb=" N THR G 594 " --> pdb=" O ASN G 590 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP G 597 " --> pdb=" O LEU G 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 614 through 616 No H-bonds generated for 'chain 'G' and resid 614 through 616' Processing helix chain 'G' and resid 619 through 622 Processing helix chain 'G' and resid 638 through 651 removed outlier: 4.244A pdb=" N SER G 643 " --> pdb=" O GLU G 639 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS G 646 " --> pdb=" O LEU G 642 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS G 648 " --> pdb=" O ILE G 644 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN G 651 " --> pdb=" O VAL G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 661 through 666 Processing helix chain 'G' and resid 672 through 689 removed outlier: 3.615A pdb=" N MET G 684 " --> pdb=" O ARG G 680 " (cutoff:3.500A) Processing helix chain 'G' and resid 698 through 705 removed outlier: 3.715A pdb=" N ALA G 704 " --> pdb=" O ASN G 700 " (cutoff:3.500A) Processing helix chain 'G' and resid 714 through 723 removed outlier: 3.766A pdb=" N LYS G 718 " --> pdb=" O GLU G 714 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 227 through 229 removed outlier: 7.285A pdb=" N ARG A 351 " --> pdb=" O ILE A 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 629 through 633 removed outlier: 4.435A pdb=" N LYS A 629 " --> pdb=" O GLY A 503 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 507 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE A 504 " --> pdb=" O VAL A 605 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 607 " --> pdb=" O PHE A 504 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU A 506 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY A 609 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY A 508 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 611 " --> pdb=" O GLY A 508 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA A 562 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE A 608 " --> pdb=" O ALA A 562 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 564 " --> pdb=" O ILE A 608 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA A 610 " --> pdb=" O VAL A 564 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 566 " --> pdb=" O ALA A 610 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN A 528 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE A 565 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 530 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP A 567 " --> pdb=" O ILE A 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 532 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 227 through 229 removed outlier: 7.286A pdb=" N ARG C 351 " --> pdb=" O ILE C 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 629 through 633 removed outlier: 4.434A pdb=" N LYS C 629 " --> pdb=" O GLY C 503 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR C 507 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE C 504 " --> pdb=" O VAL C 605 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL C 607 " --> pdb=" O PHE C 504 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU C 506 " --> pdb=" O VAL C 607 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY C 609 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLY C 508 " --> pdb=" O GLY C 609 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR C 611 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA C 562 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE C 608 " --> pdb=" O ALA C 562 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 564 " --> pdb=" O ILE C 608 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA C 610 " --> pdb=" O VAL C 564 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 566 " --> pdb=" O ALA C 610 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN C 528 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE C 565 " --> pdb=" O ASN C 528 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 530 " --> pdb=" O PHE C 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP C 567 " --> pdb=" O ILE C 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE C 532 " --> pdb=" O ASP C 567 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 227 through 229 removed outlier: 7.286A pdb=" N ARG D 351 " --> pdb=" O ILE D 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'D' and resid 629 through 633 removed outlier: 4.434A pdb=" N LYS D 629 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 507 " --> pdb=" O ILE D 631 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE D 504 " --> pdb=" O VAL D 605 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL D 607 " --> pdb=" O PHE D 504 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU D 506 " --> pdb=" O VAL D 607 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY D 609 " --> pdb=" O LEU D 506 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY D 508 " --> pdb=" O GLY D 609 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR D 611 " --> pdb=" O GLY D 508 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA D 562 " --> pdb=" O VAL D 606 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE D 608 " --> pdb=" O ALA D 562 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL D 564 " --> pdb=" O ILE D 608 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA D 610 " --> pdb=" O VAL D 564 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU D 566 " --> pdb=" O ALA D 610 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN D 528 " --> pdb=" O ILE D 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE D 565 " --> pdb=" O ASN D 528 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE D 530 " --> pdb=" O PHE D 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP D 567 " --> pdb=" O ILE D 530 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE D 532 " --> pdb=" O ASP D 567 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 227 through 229 removed outlier: 7.285A pdb=" N ARG E 351 " --> pdb=" O ILE E 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 629 through 633 removed outlier: 4.435A pdb=" N LYS E 629 " --> pdb=" O GLY E 503 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR E 507 " --> pdb=" O ILE E 631 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE E 504 " --> pdb=" O VAL E 605 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL E 607 " --> pdb=" O PHE E 504 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LEU E 506 " --> pdb=" O VAL E 607 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY E 609 " --> pdb=" O LEU E 506 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY E 508 " --> pdb=" O GLY E 609 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR E 611 " --> pdb=" O GLY E 508 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA E 562 " --> pdb=" O VAL E 606 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE E 608 " --> pdb=" O ALA E 562 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E 564 " --> pdb=" O ILE E 608 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ALA E 610 " --> pdb=" O VAL E 564 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU E 566 " --> pdb=" O ALA E 610 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN E 528 " --> pdb=" O ILE E 563 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE E 565 " --> pdb=" O ASN E 528 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE E 530 " --> pdb=" O PHE E 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP E 567 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE E 532 " --> pdb=" O ASP E 567 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 227 through 229 removed outlier: 7.285A pdb=" N ARG F 351 " --> pdb=" O ILE F 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'F' and resid 629 through 633 removed outlier: 4.435A pdb=" N LYS F 629 " --> pdb=" O GLY F 503 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR F 507 " --> pdb=" O ILE F 631 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N PHE F 504 " --> pdb=" O VAL F 605 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL F 607 " --> pdb=" O PHE F 504 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU F 506 " --> pdb=" O VAL F 607 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLY F 609 " --> pdb=" O LEU F 506 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY F 508 " --> pdb=" O GLY F 609 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR F 611 " --> pdb=" O GLY F 508 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA F 562 " --> pdb=" O VAL F 606 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE F 608 " --> pdb=" O ALA F 562 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F 564 " --> pdb=" O ILE F 608 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA F 610 " --> pdb=" O VAL F 564 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU F 566 " --> pdb=" O ALA F 610 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ASN F 528 " --> pdb=" O ILE F 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE F 565 " --> pdb=" O ASN F 528 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE F 530 " --> pdb=" O PHE F 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP F 567 " --> pdb=" O ILE F 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE F 532 " --> pdb=" O ASP F 567 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 227 through 229 removed outlier: 7.286A pdb=" N ARG G 351 " --> pdb=" O ILE G 228 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 629 through 633 removed outlier: 4.435A pdb=" N LYS G 629 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR G 507 " --> pdb=" O ILE G 631 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N PHE G 504 " --> pdb=" O VAL G 605 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL G 607 " --> pdb=" O PHE G 504 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU G 506 " --> pdb=" O VAL G 607 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY G 609 " --> pdb=" O LEU G 506 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLY G 508 " --> pdb=" O GLY G 609 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N THR G 611 " --> pdb=" O GLY G 508 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ALA G 562 " --> pdb=" O VAL G 606 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE G 608 " --> pdb=" O ALA G 562 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL G 564 " --> pdb=" O ILE G 608 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA G 610 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU G 566 " --> pdb=" O ALA G 610 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASN G 528 " --> pdb=" O ILE G 563 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N PHE G 565 " --> pdb=" O ASN G 528 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE G 530 " --> pdb=" O PHE G 565 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ASP G 567 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE G 532 " --> pdb=" O ASP G 567 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2142 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: 7.01 Time building geometry restraints manager: 11.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3925 1.32 - 1.44: 5552 1.44 - 1.56: 14073 1.56 - 1.68: 60 1.68 - 1.80: 114 Bond restraints: 23724 Sorted by residual: bond pdb=" C4 ATP C 801 " pdb=" C5 ATP C 801 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.33e+01 bond pdb=" C4 ATP E 801 " pdb=" C5 ATP E 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.29e+01 bond pdb=" C4 ATP D 801 " pdb=" C5 ATP D 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.22e+01 bond pdb=" C4 ATP A 801 " pdb=" C5 ATP A 801 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.18e+01 bond pdb=" C4 ATP G 801 " pdb=" C5 ATP G 801 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.13e+01 ... (remaining 23719 not shown) Histogram of bond angle deviations from ideal: 100.40 - 108.28: 1714 108.28 - 116.16: 14883 116.16 - 124.04: 15378 124.04 - 131.92: 473 131.92 - 139.81: 96 Bond angle restraints: 32544 Sorted by residual: angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 117.17 22.70 1.00e+00 1.00e+00 5.15e+02 angle pdb=" PB ATP F 801 " pdb=" O3B ATP F 801 " pdb=" PG ATP F 801 " ideal model delta sigma weight residual 139.87 117.19 22.68 1.00e+00 1.00e+00 5.14e+02 angle pdb=" PB ATP D 801 " pdb=" O3B ATP D 801 " pdb=" PG ATP D 801 " ideal model delta sigma weight residual 139.87 117.21 22.66 1.00e+00 1.00e+00 5.13e+02 angle pdb=" PB ATP C 801 " pdb=" O3B ATP C 801 " pdb=" PG ATP C 801 " ideal model delta sigma weight residual 139.87 117.22 22.65 1.00e+00 1.00e+00 5.13e+02 angle pdb=" PB ATP E 801 " pdb=" O3B ATP E 801 " pdb=" PG ATP E 801 " ideal model delta sigma weight residual 139.87 117.23 22.64 1.00e+00 1.00e+00 5.12e+02 ... (remaining 32539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 13626 16.47 - 32.94: 630 32.94 - 49.40: 162 49.40 - 65.87: 90 65.87 - 82.34: 48 Dihedral angle restraints: 14556 sinusoidal: 5166 harmonic: 9390 Sorted by residual: dihedral pdb=" CA ILE G 292 " pdb=" C ILE G 292 " pdb=" N ASP G 293 " pdb=" CA ASP G 293 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ILE D 292 " pdb=" C ILE D 292 " pdb=" N ASP D 293 " pdb=" CA ASP D 293 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ILE F 292 " pdb=" C ILE F 292 " pdb=" N ASP F 293 " pdb=" CA ASP F 293 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 14553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3229 0.078 - 0.155: 526 0.155 - 0.233: 142 0.233 - 0.310: 57 0.310 - 0.388: 12 Chirality restraints: 3966 Sorted by residual: chirality pdb=" CA LEU C 210 " pdb=" N LEU C 210 " pdb=" C LEU C 210 " pdb=" CB LEU C 210 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA LEU D 210 " pdb=" N LEU D 210 " pdb=" C LEU D 210 " pdb=" CB LEU D 210 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" CA LEU F 210 " pdb=" N LEU F 210 " pdb=" C LEU F 210 " pdb=" CB LEU F 210 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.74e+00 ... (remaining 3963 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE D 339 " 0.013 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ILE D 339 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE D 339 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP D 340 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 229 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.12e+00 pdb=" C LEU C 229 " -0.043 2.00e-02 2.50e+03 pdb=" O LEU C 229 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR C 230 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 206 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.07e+00 pdb=" C ILE G 206 " -0.043 2.00e-02 2.50e+03 pdb=" O ILE G 206 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU G 207 " 0.014 2.00e-02 2.50e+03 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.92: 192 1.92 - 2.66: 1586 2.66 - 3.41: 39791 3.41 - 4.15: 55012 4.15 - 4.90: 91912 Nonbonded interactions: 188493 Sorted by model distance: nonbonded pdb=" NH2 ARG F 344 " pdb=" OE2 GLU F 352 " model vdw 1.173 2.520 nonbonded pdb=" NH2 ARG C 344 " pdb=" OE2 GLU C 352 " model vdw 1.173 2.520 nonbonded pdb=" NH2 ARG D 344 " pdb=" OE2 GLU D 352 " model vdw 1.174 2.520 nonbonded pdb=" NH2 ARG A 344 " pdb=" OE2 GLU A 352 " model vdw 1.174 2.520 nonbonded pdb=" NH2 ARG E 344 " pdb=" OE2 GLU E 352 " model vdw 1.174 2.520 ... (remaining 188488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.000 Check model and map are aligned: 0.390 Set scattering table: 0.220 Process input model: 64.500 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.180 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 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 : 0.007 0.080 23724 Z= 0.504 Angle : 1.496 22.696 32544 Z= 1.133 Chirality : 0.070 0.388 3966 Planarity : 0.005 0.049 4188 Dihedral : 12.725 82.340 8496 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 117.97 Ramachandran Plot: Outliers : 0.37 % Allowed : 1.48 % Favored : 98.15 % Rotamer: Outliers : 7.14 % Allowed : 6.29 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.13), residues: 3252 helix: -1.83 (0.13), residues: 1374 sheet: -0.36 (0.24), residues: 396 loop : -0.87 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 541 HIS 0.005 0.002 HIS A 648 PHE 0.018 0.001 PHE A 349 TYR 0.017 0.001 TYR A 189 ARG 0.008 0.001 ARG G 641 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 866 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8189 (mt) REVERT: A 287 ILE cc_start: 0.7490 (mm) cc_final: 0.7101 (mm) REVERT: A 315 LEU cc_start: 0.8135 (mp) cc_final: 0.7855 (mt) REVERT: A 474 ASP cc_start: 0.8005 (p0) cc_final: 0.7575 (p0) REVERT: A 532 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7477 (mm) REVERT: A 568 GLU cc_start: 0.8609 (mp0) cc_final: 0.8255 (mt-10) REVERT: A 570 ASP cc_start: 0.8729 (p0) cc_final: 0.8463 (p0) REVERT: A 687 TYR cc_start: 0.8040 (t80) cc_final: 0.7604 (t80) REVERT: C 240 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8314 (mt) REVERT: C 287 ILE cc_start: 0.7505 (mm) cc_final: 0.7040 (mm) REVERT: C 315 LEU cc_start: 0.8214 (mp) cc_final: 0.7929 (mt) REVERT: C 390 MET cc_start: 0.7299 (mtp) cc_final: 0.6769 (mtp) REVERT: C 532 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7679 (mm) REVERT: C 579 THR cc_start: 0.8476 (m) cc_final: 0.8059 (m) REVERT: C 616 ILE cc_start: 0.9212 (mm) cc_final: 0.8819 (mm) REVERT: D 240 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8442 (mt) REVERT: D 287 ILE cc_start: 0.7660 (mm) cc_final: 0.7378 (mm) REVERT: D 315 LEU cc_start: 0.8132 (mp) cc_final: 0.7853 (mt) REVERT: D 570 ASP cc_start: 0.8869 (p0) cc_final: 0.8520 (p0) REVERT: E 240 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8186 (mt) REVERT: E 287 ILE cc_start: 0.7479 (mm) cc_final: 0.7092 (mm) REVERT: E 315 LEU cc_start: 0.8128 (mp) cc_final: 0.7853 (mt) REVERT: E 474 ASP cc_start: 0.8015 (p0) cc_final: 0.7582 (p0) REVERT: E 532 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7491 (mm) REVERT: E 568 GLU cc_start: 0.8617 (mp0) cc_final: 0.8248 (mt-10) REVERT: E 570 ASP cc_start: 0.8735 (p0) cc_final: 0.8474 (p0) REVERT: F 240 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8329 (mt) REVERT: F 287 ILE cc_start: 0.7509 (mm) cc_final: 0.7038 (mm) REVERT: F 315 LEU cc_start: 0.8205 (mp) cc_final: 0.7928 (mt) REVERT: F 390 MET cc_start: 0.7294 (mtp) cc_final: 0.6670 (mtp) REVERT: F 393 TYR cc_start: 0.6187 (m-80) cc_final: 0.5932 (m-80) REVERT: F 532 ILE cc_start: 0.8033 (OUTLIER) cc_final: 0.7690 (mm) REVERT: F 570 ASP cc_start: 0.9122 (p0) cc_final: 0.8775 (p0) REVERT: F 579 THR cc_start: 0.8478 (m) cc_final: 0.8075 (m) REVERT: F 616 ILE cc_start: 0.9205 (mm) cc_final: 0.8814 (mm) REVERT: G 240 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8439 (mt) REVERT: G 287 ILE cc_start: 0.7667 (mm) cc_final: 0.7381 (mm) REVERT: G 315 LEU cc_start: 0.8136 (mp) cc_final: 0.7861 (mt) REVERT: G 485 LEU cc_start: 0.7600 (tt) cc_final: 0.7380 (tp) REVERT: G 570 ASP cc_start: 0.8867 (p0) cc_final: 0.8513 (p0) REVERT: G 648 HIS cc_start: 0.6264 (t-90) cc_final: 0.6061 (t70) outliers start: 150 outliers final: 94 residues processed: 972 average time/residue: 0.3449 time to fit residues: 516.9682 Evaluate side-chains 717 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 613 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 586 GLU Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain C residue 203 ARG Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 586 GLU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain D residue 203 ARG Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 240 ILE Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 352 GLU Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 536 GLU Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 546 GLU Chi-restraints excluded: chain D residue 572 ILE Chi-restraints excluded: chain D residue 586 GLU Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain E residue 203 ARG Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 240 ILE Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 352 GLU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 536 GLU Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 546 GLU Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 586 GLU Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 238 THR Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 352 GLU Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 586 GLU Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain G residue 203 ARG Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain G residue 240 ILE Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 269 GLU Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 536 GLU Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 546 GLU Chi-restraints excluded: chain G residue 572 ILE Chi-restraints excluded: chain G residue 586 GLU Chi-restraints excluded: chain G residue 603 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 7.9990 chunk 245 optimal weight: 0.3980 chunk 136 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 165 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 8.9990 chunk 294 optimal weight: 30.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 700 ASN ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 HIS ** D 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 700 ASN ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 700 ASN ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 700 ASN ** G 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 700 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 23724 Z= 0.339 Angle : 0.889 9.263 32544 Z= 0.454 Chirality : 0.054 0.319 3966 Planarity : 0.008 0.129 4188 Dihedral : 13.690 72.633 4130 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 6.52 % Allowed : 17.71 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.13), residues: 3252 helix: -1.63 (0.11), residues: 1428 sheet: -0.04 (0.24), residues: 390 loop : -0.35 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP A 466 HIS 0.015 0.004 HIS F 326 PHE 0.038 0.004 PHE E 553 TYR 0.032 0.004 TYR C 230 ARG 0.010 0.001 ARG C 680 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 665 time to evaluate : 2.645 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 ILE cc_start: 0.8088 (mp) cc_final: 0.7637 (mt) REVERT: A 216 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: A 314 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8028 (tt) REVERT: A 488 LEU cc_start: 0.8238 (tt) cc_final: 0.8019 (mm) REVERT: A 568 GLU cc_start: 0.8384 (mp0) cc_final: 0.8153 (mt-10) REVERT: A 570 ASP cc_start: 0.8875 (p0) cc_final: 0.8625 (p0) REVERT: A 596 LEU cc_start: 0.8817 (mm) cc_final: 0.8544 (tp) REVERT: C 537 VAL cc_start: 0.8721 (p) cc_final: 0.8491 (p) REVERT: C 570 ASP cc_start: 0.8974 (p0) cc_final: 0.8732 (p0) REVERT: C 596 LEU cc_start: 0.8861 (mm) cc_final: 0.8541 (tp) REVERT: C 613 ARG cc_start: 0.8325 (mtt180) cc_final: 0.8033 (mtp85) REVERT: D 314 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8196 (tp) REVERT: D 398 VAL cc_start: 0.7097 (p) cc_final: 0.6628 (p) REVERT: D 570 ASP cc_start: 0.8934 (p0) cc_final: 0.8702 (p0) REVERT: D 596 LEU cc_start: 0.8787 (mm) cc_final: 0.8561 (tp) REVERT: E 216 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7182 (m-80) REVERT: E 314 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8027 (tt) REVERT: E 353 ILE cc_start: 0.8415 (pt) cc_final: 0.7642 (pt) REVERT: E 474 ASP cc_start: 0.7898 (p0) cc_final: 0.7525 (p0) REVERT: E 488 LEU cc_start: 0.8242 (tt) cc_final: 0.8034 (mm) REVERT: E 568 GLU cc_start: 0.8373 (mp0) cc_final: 0.8133 (mt-10) REVERT: E 570 ASP cc_start: 0.8868 (p0) cc_final: 0.8633 (p0) REVERT: E 596 LEU cc_start: 0.8812 (mm) cc_final: 0.8541 (tp) REVERT: F 314 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8388 (tt) REVERT: F 570 ASP cc_start: 0.8932 (p0) cc_final: 0.8724 (p0) REVERT: F 596 LEU cc_start: 0.8875 (mm) cc_final: 0.8548 (tp) REVERT: F 613 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8001 (mtp85) REVERT: F 616 ILE cc_start: 0.9132 (mm) cc_final: 0.8915 (mm) REVERT: G 314 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8203 (tp) REVERT: G 398 VAL cc_start: 0.7118 (p) cc_final: 0.6667 (p) REVERT: G 474 ASP cc_start: 0.7420 (p0) cc_final: 0.7133 (p0) REVERT: G 570 ASP cc_start: 0.8966 (p0) cc_final: 0.8744 (p0) outliers start: 137 outliers final: 80 residues processed: 753 average time/residue: 0.3035 time to fit residues: 375.3945 Evaluate side-chains 649 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 562 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 PHE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 637 ASP Chi-restraints excluded: chain E residue 216 PHE Chi-restraints excluded: chain E residue 228 ILE Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 448 SER Chi-restraints excluded: chain E residue 531 SER Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 314 LEU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 483 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 536 GLU Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 589 VAL Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 637 ASP Chi-restraints excluded: chain F residue 695 SER Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 603 ASN Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 645 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 294 optimal weight: 20.0000 chunk 318 optimal weight: 4.9990 chunk 262 optimal weight: 0.8980 chunk 292 optimal weight: 0.8980 chunk 100 optimal weight: 0.0370 chunk 236 optimal weight: 1.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 698 GLN ** C 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 698 GLN ** E 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 698 GLN G 698 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23724 Z= 0.248 Angle : 0.739 8.892 32544 Z= 0.368 Chirality : 0.047 0.222 3966 Planarity : 0.006 0.102 4188 Dihedral : 11.822 74.238 3946 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.71 % Allowed : 19.76 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3252 helix: -1.22 (0.12), residues: 1440 sheet: -0.04 (0.24), residues: 396 loop : -0.08 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 541 HIS 0.009 0.002 HIS D 648 PHE 0.021 0.002 PHE A 553 TYR 0.023 0.003 TYR C 265 ARG 0.008 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 750 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 630 time to evaluate : 2.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 488 LEU cc_start: 0.8253 (tt) cc_final: 0.8023 (mm) REVERT: A 568 GLU cc_start: 0.8595 (mp0) cc_final: 0.8341 (mt-10) REVERT: A 570 ASP cc_start: 0.8829 (p0) cc_final: 0.8561 (p0) REVERT: A 596 LEU cc_start: 0.8945 (mm) cc_final: 0.8683 (tp) REVERT: C 368 MET cc_start: 0.8983 (ptp) cc_final: 0.8578 (ptp) REVERT: C 474 ASP cc_start: 0.7792 (p0) cc_final: 0.7264 (p0) REVERT: C 613 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7919 (mtp85) REVERT: D 478 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7946 (tm-30) REVERT: D 498 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7238 (pt) REVERT: D 541 TRP cc_start: 0.7308 (OUTLIER) cc_final: 0.6857 (m100) REVERT: E 488 LEU cc_start: 0.8262 (tt) cc_final: 0.8018 (mm) REVERT: E 568 GLU cc_start: 0.8572 (mp0) cc_final: 0.8333 (mt-10) REVERT: E 570 ASP cc_start: 0.8826 (p0) cc_final: 0.8548 (p0) REVERT: E 596 LEU cc_start: 0.8945 (mm) cc_final: 0.8683 (tp) REVERT: F 368 MET cc_start: 0.8974 (ptp) cc_final: 0.8523 (ptp) REVERT: F 474 ASP cc_start: 0.7716 (p0) cc_final: 0.7218 (p0) REVERT: F 558 GLN cc_start: 0.8735 (mt0) cc_final: 0.8209 (mt0) REVERT: F 570 ASP cc_start: 0.9102 (p0) cc_final: 0.8670 (p0) REVERT: F 613 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8110 (mtp85) REVERT: F 616 ILE cc_start: 0.9095 (mm) cc_final: 0.8864 (mm) REVERT: G 541 TRP cc_start: 0.7304 (OUTLIER) cc_final: 0.6849 (m100) REVERT: G 569 ILE cc_start: 0.8553 (tt) cc_final: 0.8322 (pt) REVERT: G 698 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8105 (mm-40) outliers start: 120 outliers final: 72 residues processed: 689 average time/residue: 0.2875 time to fit residues: 331.4100 Evaluate side-chains 599 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 523 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 541 TRP Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 541 TRP Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 389 GLU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 599 ILE Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 386 PHE Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 588 ILE Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 588 ILE Chi-restraints excluded: chain G residue 603 ASN Chi-restraints excluded: chain G residue 637 ASP Chi-restraints excluded: chain G residue 692 ASP Chi-restraints excluded: chain G residue 698 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.0170 chunk 221 optimal weight: 1.9990 chunk 152 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 313 optimal weight: 0.0050 chunk 154 optimal weight: 2.9990 chunk 280 optimal weight: 0.0470 chunk 84 optimal weight: 0.9980 overall best weight: 0.2930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS C 591 GLN D 591 GLN E 591 GLN E 648 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23724 Z= 0.228 Angle : 0.730 13.482 32544 Z= 0.357 Chirality : 0.046 0.181 3966 Planarity : 0.006 0.087 4188 Dihedral : 11.273 74.891 3926 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 6.00 % Allowed : 22.62 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.14), residues: 3252 helix: -0.95 (0.13), residues: 1398 sheet: -0.05 (0.23), residues: 390 loop : 0.04 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 466 HIS 0.004 0.001 HIS G 648 PHE 0.025 0.002 PHE D 386 TYR 0.020 0.002 TYR A 687 ARG 0.006 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 585 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8184 (mp) REVERT: A 474 ASP cc_start: 0.7615 (p0) cc_final: 0.7287 (p0) REVERT: A 488 LEU cc_start: 0.8236 (tt) cc_final: 0.8020 (mm) REVERT: A 541 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.6609 (m100) REVERT: A 570 ASP cc_start: 0.8759 (p0) cc_final: 0.8474 (p0) REVERT: A 698 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8433 (mm-40) REVERT: C 202 ILE cc_start: 0.8603 (tp) cc_final: 0.7702 (tp) REVERT: C 368 MET cc_start: 0.8939 (ptp) cc_final: 0.8674 (ptm) REVERT: C 474 ASP cc_start: 0.7880 (p0) cc_final: 0.7471 (p0) REVERT: C 558 GLN cc_start: 0.8592 (mt0) cc_final: 0.7982 (mt0) REVERT: C 613 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7275 (ttm110) REVERT: C 617 MET cc_start: 0.8041 (ptp) cc_final: 0.6874 (ptp) REVERT: C 676 GLU cc_start: 0.8004 (tp30) cc_final: 0.7771 (tp30) REVERT: D 478 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7644 (tm-30) REVERT: D 570 ASP cc_start: 0.8573 (p0) cc_final: 0.8325 (p0) REVERT: E 366 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8190 (mp) REVERT: E 474 ASP cc_start: 0.7607 (p0) cc_final: 0.7305 (p0) REVERT: E 488 LEU cc_start: 0.8248 (tt) cc_final: 0.8015 (mm) REVERT: E 541 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.6634 (m100) REVERT: E 570 ASP cc_start: 0.8757 (p0) cc_final: 0.8468 (p0) REVERT: F 368 MET cc_start: 0.8808 (ptp) cc_final: 0.8542 (ptm) REVERT: F 474 ASP cc_start: 0.7785 (p0) cc_final: 0.7448 (p0) REVERT: F 478 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7962 (tm-30) REVERT: F 558 GLN cc_start: 0.8603 (mt0) cc_final: 0.7979 (mt0) REVERT: F 613 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8083 (mtp85) REVERT: F 616 ILE cc_start: 0.9073 (mm) cc_final: 0.8794 (mm) REVERT: G 478 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7705 (tm-30) REVERT: G 541 TRP cc_start: 0.7122 (OUTLIER) cc_final: 0.6917 (m100) REVERT: G 652 MET cc_start: 0.7724 (mmp) cc_final: 0.7419 (mmm) outliers start: 126 outliers final: 83 residues processed: 642 average time/residue: 0.2792 time to fit residues: 302.2836 Evaluate side-chains 615 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 527 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 541 TRP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 588 ILE Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 328 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 541 TRP Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 461 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 588 ILE Chi-restraints excluded: chain G residue 603 ASN Chi-restraints excluded: chain G residue 692 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 0.3980 chunk 177 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 267 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 159 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS D 591 GLN ** D 648 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN G 698 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23724 Z= 0.343 Angle : 0.716 13.056 32544 Z= 0.366 Chirality : 0.045 0.180 3966 Planarity : 0.006 0.088 4188 Dihedral : 11.177 81.765 3918 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 7.29 % Allowed : 23.86 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.14), residues: 3252 helix: -0.67 (0.13), residues: 1434 sheet: -0.37 (0.24), residues: 414 loop : -0.05 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP F 541 HIS 0.008 0.002 HIS F 648 PHE 0.019 0.002 PHE C 386 TYR 0.019 0.003 TYR C 687 ARG 0.009 0.001 ARG E 680 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 512 time to evaluate : 2.542 Fit side-chains revert: symmetry clash REVERT: A 570 ASP cc_start: 0.8740 (p0) cc_final: 0.8441 (p0) REVERT: C 205 MET cc_start: 0.8197 (ppp) cc_final: 0.7815 (ppp) REVERT: C 478 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 558 GLN cc_start: 0.8740 (mt0) cc_final: 0.8124 (mt0) REVERT: C 593 LEU cc_start: 0.8728 (mm) cc_final: 0.8150 (mm) REVERT: C 613 ARG cc_start: 0.8252 (mtt180) cc_final: 0.8021 (mtp85) REVERT: D 208 LEU cc_start: 0.8987 (mt) cc_final: 0.8549 (tp) REVERT: D 478 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 314 LEU cc_start: 0.8235 (tp) cc_final: 0.7987 (tp) REVERT: E 570 ASP cc_start: 0.8731 (p0) cc_final: 0.8418 (p0) REVERT: F 205 MET cc_start: 0.8159 (ppp) cc_final: 0.7806 (ppp) REVERT: F 558 GLN cc_start: 0.8740 (mt0) cc_final: 0.8136 (mt0) REVERT: F 593 LEU cc_start: 0.8681 (mm) cc_final: 0.8154 (mm) REVERT: G 208 LEU cc_start: 0.8983 (mt) cc_final: 0.8522 (tp) outliers start: 153 outliers final: 102 residues processed: 593 average time/residue: 0.2658 time to fit residues: 267.5713 Evaluate side-chains 591 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 489 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 637 ASP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 386 PHE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 589 VAL Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 637 ASP Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 637 ASP Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 454 LEU Chi-restraints excluded: chain F residue 465 HIS Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 541 TRP Chi-restraints excluded: chain F residue 546 GLU Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 603 ASN Chi-restraints excluded: chain G residue 618 ASP Chi-restraints excluded: chain G residue 692 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 313 optimal weight: 0.6980 chunk 260 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 164 optimal weight: 0.0970 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 591 GLN A 648 HIS E 648 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23724 Z= 0.231 Angle : 0.699 9.282 32544 Z= 0.343 Chirality : 0.045 0.215 3966 Planarity : 0.005 0.069 4188 Dihedral : 10.832 80.627 3914 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.67 % Allowed : 26.67 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.14), residues: 3252 helix: -0.57 (0.13), residues: 1410 sheet: -0.42 (0.24), residues: 414 loop : 0.04 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 541 HIS 0.006 0.001 HIS F 648 PHE 0.023 0.002 PHE D 386 TYR 0.022 0.002 TYR A 687 ARG 0.007 0.001 ARG E 680 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 548 time to evaluate : 2.624 Fit side-chains REVERT: A 208 LEU cc_start: 0.9061 (mt) cc_final: 0.8511 (tp) REVERT: A 314 LEU cc_start: 0.8211 (tp) cc_final: 0.7831 (tp) REVERT: A 474 ASP cc_start: 0.7595 (p0) cc_final: 0.7260 (p0) REVERT: A 698 GLN cc_start: 0.8696 (mm-40) cc_final: 0.8458 (mm-40) REVERT: C 205 MET cc_start: 0.8316 (ppp) cc_final: 0.7471 (ptm) REVERT: C 389 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: C 558 GLN cc_start: 0.8664 (mt0) cc_final: 0.8029 (mt0) REVERT: D 208 LEU cc_start: 0.8938 (mt) cc_final: 0.8514 (tp) REVERT: D 478 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7666 (tm-30) REVERT: D 687 TYR cc_start: 0.7578 (t80) cc_final: 0.7304 (t80) REVERT: E 208 LEU cc_start: 0.9058 (mt) cc_final: 0.8505 (tp) REVERT: E 314 LEU cc_start: 0.8222 (tp) cc_final: 0.7838 (tp) REVERT: E 570 ASP cc_start: 0.8702 (p0) cc_final: 0.8488 (p0) REVERT: F 205 MET cc_start: 0.8247 (ppp) cc_final: 0.7436 (ptm) REVERT: F 208 LEU cc_start: 0.8757 (mt) cc_final: 0.8432 (tp) REVERT: F 558 GLN cc_start: 0.8716 (mt0) cc_final: 0.8128 (mt0) REVERT: G 208 LEU cc_start: 0.8928 (mt) cc_final: 0.8504 (tp) REVERT: G 478 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7534 (tm-30) REVERT: G 541 TRP cc_start: 0.6976 (OUTLIER) cc_final: 0.6695 (m100) REVERT: G 687 TYR cc_start: 0.7575 (t80) cc_final: 0.7313 (t80) outliers start: 119 outliers final: 94 residues processed: 601 average time/residue: 0.2802 time to fit residues: 283.2354 Evaluate side-chains 604 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 508 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 531 SER Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 546 GLU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 603 ASN Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 603 ASN Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 465 HIS Chi-restraints excluded: chain F residue 531 SER Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 603 ASN Chi-restraints excluded: chain G residue 618 ASP Chi-restraints excluded: chain G residue 692 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 0.9980 chunk 35 optimal weight: 0.0070 chunk 178 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 263 optimal weight: 20.0000 chunk 175 optimal weight: 0.8980 chunk 312 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 190 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS E 648 HIS E 698 GLN F 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23724 Z= 0.210 Angle : 0.689 8.757 32544 Z= 0.341 Chirality : 0.044 0.221 3966 Planarity : 0.005 0.060 4188 Dihedral : 10.629 80.913 3914 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.24 % Allowed : 27.62 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3252 helix: -0.47 (0.13), residues: 1410 sheet: -0.56 (0.23), residues: 414 loop : 0.04 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 466 HIS 0.005 0.001 HIS F 648 PHE 0.015 0.002 PHE D 386 TYR 0.021 0.002 TYR F 687 ARG 0.008 0.001 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 545 time to evaluate : 2.608 Fit side-chains REVERT: A 208 LEU cc_start: 0.9132 (mt) cc_final: 0.8653 (tp) REVERT: A 314 LEU cc_start: 0.8252 (tp) cc_final: 0.7900 (tp) REVERT: A 698 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8484 (mm110) REVERT: C 205 MET cc_start: 0.8279 (ppp) cc_final: 0.7435 (ptm) REVERT: C 558 GLN cc_start: 0.8688 (mt0) cc_final: 0.8126 (mt0) REVERT: D 208 LEU cc_start: 0.8973 (mt) cc_final: 0.8570 (tp) REVERT: D 687 TYR cc_start: 0.7611 (t80) cc_final: 0.7285 (t80) REVERT: E 205 MET cc_start: 0.8709 (ppp) cc_final: 0.8354 (ppp) REVERT: E 208 LEU cc_start: 0.9118 (mt) cc_final: 0.8627 (tp) REVERT: E 314 LEU cc_start: 0.8267 (tp) cc_final: 0.7897 (tp) REVERT: E 474 ASP cc_start: 0.7509 (p0) cc_final: 0.7217 (p0) REVERT: E 570 ASP cc_start: 0.8692 (p0) cc_final: 0.8459 (p0) REVERT: F 205 MET cc_start: 0.8275 (ppp) cc_final: 0.7473 (ptm) REVERT: F 208 LEU cc_start: 0.8755 (mt) cc_final: 0.8469 (tp) REVERT: F 558 GLN cc_start: 0.8711 (mt0) cc_final: 0.8141 (mt0) REVERT: F 593 LEU cc_start: 0.8574 (mm) cc_final: 0.8153 (mm) REVERT: G 208 LEU cc_start: 0.8971 (mt) cc_final: 0.8568 (tp) REVERT: G 478 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7479 (tm-30) REVERT: G 687 TYR cc_start: 0.7626 (t80) cc_final: 0.7304 (t80) outliers start: 110 outliers final: 91 residues processed: 599 average time/residue: 0.2726 time to fit residues: 279.1584 Evaluate side-chains 611 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 520 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 448 SER Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 386 PHE Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 684 MET Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 465 HIS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 603 ASN Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 386 PHE Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 603 ASN Chi-restraints excluded: chain G residue 684 MET Chi-restraints excluded: chain G residue 692 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 186 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 245 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS E 648 HIS ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23724 Z= 0.234 Angle : 0.676 10.656 32544 Z= 0.336 Chirality : 0.044 0.233 3966 Planarity : 0.004 0.055 4188 Dihedral : 10.529 80.564 3910 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.24 % Allowed : 28.71 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3252 helix: -0.41 (0.13), residues: 1428 sheet: -0.49 (0.24), residues: 408 loop : -0.04 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP E 466 HIS 0.005 0.001 HIS F 648 PHE 0.015 0.002 PHE F 386 TYR 0.027 0.002 TYR F 393 ARG 0.007 0.000 ARG E 680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 541 time to evaluate : 2.897 Fit side-chains REVERT: A 205 MET cc_start: 0.8722 (ppp) cc_final: 0.8462 (ppp) REVERT: A 208 LEU cc_start: 0.9140 (mt) cc_final: 0.8643 (tp) REVERT: A 314 LEU cc_start: 0.8267 (tp) cc_final: 0.7935 (tp) REVERT: A 474 ASP cc_start: 0.7529 (p0) cc_final: 0.7222 (p0) REVERT: A 498 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7448 (mt) REVERT: C 205 MET cc_start: 0.8304 (ppp) cc_final: 0.7440 (ptm) REVERT: C 558 GLN cc_start: 0.8725 (mt0) cc_final: 0.8153 (mt0) REVERT: D 208 LEU cc_start: 0.9019 (mt) cc_final: 0.8568 (tp) REVERT: D 478 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7628 (tm-30) REVERT: D 687 TYR cc_start: 0.7590 (t80) cc_final: 0.7261 (t80) REVERT: E 208 LEU cc_start: 0.9133 (mt) cc_final: 0.8637 (tp) REVERT: E 314 LEU cc_start: 0.8285 (tp) cc_final: 0.7921 (tp) REVERT: E 474 ASP cc_start: 0.7658 (p0) cc_final: 0.7384 (p0) REVERT: E 570 ASP cc_start: 0.8701 (p0) cc_final: 0.8467 (p0) REVERT: E 652 MET cc_start: 0.8103 (tpp) cc_final: 0.7872 (mmm) REVERT: F 205 MET cc_start: 0.8278 (ppp) cc_final: 0.7455 (ptm) REVERT: F 208 LEU cc_start: 0.8781 (mt) cc_final: 0.8495 (tp) REVERT: F 478 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8072 (tm-30) REVERT: F 558 GLN cc_start: 0.8740 (mt0) cc_final: 0.8153 (mt0) REVERT: F 593 LEU cc_start: 0.8547 (mm) cc_final: 0.8196 (mm) REVERT: G 208 LEU cc_start: 0.9018 (mt) cc_final: 0.8565 (tp) REVERT: G 687 TYR cc_start: 0.7601 (t80) cc_final: 0.7271 (t80) outliers start: 110 outliers final: 90 residues processed: 599 average time/residue: 0.2801 time to fit residues: 289.6536 Evaluate side-chains 601 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 510 time to evaluate : 3.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 371 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 260 ILE Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 692 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 465 HIS Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 645 LEU Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 663 ILE Chi-restraints excluded: chain G residue 692 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.1980 chunk 299 optimal weight: 0.9980 chunk 272 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 126 optimal weight: 0.5980 chunk 228 optimal weight: 7.9990 chunk 89 optimal weight: 0.0470 chunk 262 optimal weight: 0.9980 chunk 275 optimal weight: 1.9990 chunk 289 optimal weight: 8.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS E 648 HIS G 698 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23724 Z= 0.204 Angle : 0.706 10.712 32544 Z= 0.344 Chirality : 0.045 0.228 3966 Planarity : 0.004 0.053 4188 Dihedral : 10.337 79.245 3900 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.10 % Allowed : 29.33 % Favored : 65.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3252 helix: -0.40 (0.13), residues: 1428 sheet: -0.47 (0.24), residues: 408 loop : -0.04 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP E 466 HIS 0.003 0.001 HIS F 648 PHE 0.036 0.002 PHE F 386 TYR 0.022 0.002 TYR F 687 ARG 0.006 0.000 ARG F 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 539 time to evaluate : 2.812 Fit side-chains REVERT: A 208 LEU cc_start: 0.9111 (mt) cc_final: 0.8630 (tp) REVERT: A 314 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.8014 (tp) REVERT: A 474 ASP cc_start: 0.7543 (p0) cc_final: 0.7286 (p0) REVERT: C 205 MET cc_start: 0.8280 (ppp) cc_final: 0.7431 (ptm) REVERT: C 366 ILE cc_start: 0.8501 (mp) cc_final: 0.8296 (mp) REVERT: C 558 GLN cc_start: 0.8674 (mt0) cc_final: 0.8131 (mt0) REVERT: C 612 ASN cc_start: 0.7957 (m110) cc_final: 0.7692 (m110) REVERT: D 208 LEU cc_start: 0.8996 (mt) cc_final: 0.8545 (tp) REVERT: D 478 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7574 (tm-30) REVERT: D 613 ARG cc_start: 0.8556 (mtt180) cc_final: 0.7743 (mtp85) REVERT: D 687 TYR cc_start: 0.7556 (t80) cc_final: 0.7183 (t80) REVERT: E 208 LEU cc_start: 0.9105 (mt) cc_final: 0.8625 (tp) REVERT: E 314 LEU cc_start: 0.8280 (tp) cc_final: 0.7898 (tp) REVERT: E 474 ASP cc_start: 0.7533 (p0) cc_final: 0.7309 (p0) REVERT: E 570 ASP cc_start: 0.8658 (p0) cc_final: 0.8399 (p0) REVERT: F 205 MET cc_start: 0.8245 (ppp) cc_final: 0.7443 (ptm) REVERT: F 208 LEU cc_start: 0.8676 (mt) cc_final: 0.8408 (tp) REVERT: F 478 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7981 (tm-30) REVERT: F 558 GLN cc_start: 0.8683 (mt0) cc_final: 0.8117 (mt0) REVERT: F 567 ASP cc_start: 0.7259 (p0) cc_final: 0.7015 (p0) REVERT: F 593 LEU cc_start: 0.8552 (mm) cc_final: 0.8229 (mm) REVERT: G 208 LEU cc_start: 0.8991 (mt) cc_final: 0.8545 (tp) REVERT: G 478 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7464 (tm-30) REVERT: G 613 ARG cc_start: 0.8503 (mtt180) cc_final: 0.7694 (mtp85) REVERT: G 687 TYR cc_start: 0.7581 (t80) cc_final: 0.7218 (t80) outliers start: 107 outliers final: 86 residues processed: 598 average time/residue: 0.2618 time to fit residues: 267.5557 Evaluate side-chains 581 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 494 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 692 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 465 HIS Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 692 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 2.9990 chunk 307 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 322 optimal weight: 0.0060 chunk 297 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 198 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 648 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23724 Z= 0.214 Angle : 0.720 10.376 32544 Z= 0.351 Chirality : 0.045 0.248 3966 Planarity : 0.005 0.054 4188 Dihedral : 10.157 78.045 3894 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.29 % Allowed : 31.00 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3252 helix: -0.40 (0.13), residues: 1428 sheet: -0.59 (0.25), residues: 360 loop : -0.07 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP F 541 HIS 0.014 0.001 HIS A 648 PHE 0.060 0.002 PHE F 386 TYR 0.021 0.002 TYR F 687 ARG 0.006 0.000 ARG C 680 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6504 Ramachandran restraints generated. 3252 Oldfield, 0 Emsley, 3252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 508 time to evaluate : 2.934 Fit side-chains REVERT: A 208 LEU cc_start: 0.9098 (mt) cc_final: 0.8621 (tp) REVERT: A 314 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7860 (tp) REVERT: A 474 ASP cc_start: 0.7482 (p0) cc_final: 0.7214 (p0) REVERT: A 645 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8096 (tp) REVERT: C 205 MET cc_start: 0.8289 (ppp) cc_final: 0.7402 (ptm) REVERT: C 558 GLN cc_start: 0.8711 (mt0) cc_final: 0.8161 (mt0) REVERT: D 208 LEU cc_start: 0.9000 (mt) cc_final: 0.8536 (tp) REVERT: D 478 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7610 (tm-30) REVERT: D 687 TYR cc_start: 0.7549 (t80) cc_final: 0.7271 (t80) REVERT: E 208 LEU cc_start: 0.9089 (mt) cc_final: 0.8613 (tp) REVERT: E 314 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7905 (tp) REVERT: E 474 ASP cc_start: 0.7472 (p0) cc_final: 0.7226 (p0) REVERT: E 570 ASP cc_start: 0.8657 (p0) cc_final: 0.8394 (p0) REVERT: F 205 MET cc_start: 0.8244 (ppp) cc_final: 0.7416 (ptm) REVERT: F 208 LEU cc_start: 0.8679 (mt) cc_final: 0.8404 (tp) REVERT: F 478 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7972 (tm-30) REVERT: F 558 GLN cc_start: 0.8722 (mt0) cc_final: 0.8141 (mt0) REVERT: F 593 LEU cc_start: 0.8569 (mm) cc_final: 0.8258 (mm) REVERT: G 208 LEU cc_start: 0.9002 (mt) cc_final: 0.8537 (tp) REVERT: G 478 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7405 (tm-30) REVERT: G 687 TYR cc_start: 0.7569 (t80) cc_final: 0.7289 (t80) outliers start: 90 outliers final: 83 residues processed: 558 average time/residue: 0.2692 time to fit residues: 257.0345 Evaluate side-chains 575 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 489 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 371 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 648 HIS Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 692 ASP Chi-restraints excluded: chain C residue 199 LEU Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 371 THR Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 572 ILE Chi-restraints excluded: chain C residue 663 ILE Chi-restraints excluded: chain C residue 667 THR Chi-restraints excluded: chain C residue 692 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 437 VAL Chi-restraints excluded: chain D residue 517 LEU Chi-restraints excluded: chain D residue 531 SER Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 663 ILE Chi-restraints excluded: chain D residue 692 ASP Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 261 MET Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 327 VAL Chi-restraints excluded: chain E residue 371 THR Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 569 ILE Chi-restraints excluded: chain E residue 612 ASN Chi-restraints excluded: chain E residue 648 HIS Chi-restraints excluded: chain E residue 667 THR Chi-restraints excluded: chain E residue 692 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 254 SER Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 371 THR Chi-restraints excluded: chain F residue 437 VAL Chi-restraints excluded: chain F residue 465 HIS Chi-restraints excluded: chain F residue 692 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 230 TYR Chi-restraints excluded: chain G residue 260 ILE Chi-restraints excluded: chain G residue 314 LEU Chi-restraints excluded: chain G residue 327 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 405 LEU Chi-restraints excluded: chain G residue 437 VAL Chi-restraints excluded: chain G residue 454 LEU Chi-restraints excluded: chain G residue 531 SER Chi-restraints excluded: chain G residue 541 TRP Chi-restraints excluded: chain G residue 596 LEU Chi-restraints excluded: chain G residue 663 ILE Chi-restraints excluded: chain G residue 692 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 237 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 107 optimal weight: 0.1980 chunk 264 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 648 HIS ** G 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.115779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094841 restraints weight = 60613.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.097947 restraints weight = 35205.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100163 restraints weight = 23795.180| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23724 Z= 0.209 Angle : 0.719 10.196 32544 Z= 0.350 Chirality : 0.045 0.210 3966 Planarity : 0.005 0.054 4188 Dihedral : 9.963 76.931 3890 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.33 % Allowed : 31.48 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.14), residues: 3252 helix: -0.38 (0.13), residues: 1422 sheet: -0.60 (0.25), residues: 360 loop : -0.09 (0.17), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.005 TRP E 466 HIS 0.016 0.001 HIS A 648 PHE 0.050 0.002 PHE F 386 TYR 0.021 0.002 TYR F 687 ARG 0.005 0.000 ARG F 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5721.67 seconds wall clock time: 103 minutes 36.92 seconds (6216.92 seconds total)