Starting phenix.real_space_refine on Tue Sep 15 12:07:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ray_4787/09_2026/6ray_4787.map" } resolution = 4.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 29 5.49 5 S 208 5.16 5 C 24484 2.51 5 N 6871 2.21 5 O 7479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 328 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39071 Number of models: 1 Model: "" Number of chains: 18 Chain: "3" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4685 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 577} Chain breaks: 8 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "4" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4901 Classifications: {'peptide': 617} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 25, 'TRANS': 591} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "7" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4577 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 562} Unresolved chain links: 1 Chain breaks: 11 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "6" Number of atoms: 4748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4748 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 580} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "5" Number of atoms: 4505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4505 Classifications: {'peptide': 577} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 25, 'TRANS': 551} Chain breaks: 10 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4555 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 552} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1504 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1422 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1377 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 161} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1627 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'HIS:plan': 2, 'ILE%COO:oxt': 1} Unresolved non-hydrogen planarities: 32 Chain: "2" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4731 Classifications: {'peptide': 600} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 571} Chain breaks: 5 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 261 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "6" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.63, per 1000 atoms: 0.20 Number of scatterers: 39071 At special positions: 0 Unit cell: (204.12, 189, 155.52, 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 208 16.00 P 29 15.00 O 7479 8.00 N 6871 7.00 C 24484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 192 " - pdb=" SG CYS 5 202 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.5 seconds 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9300 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 31 sheets defined 35.3% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain '3' and resid 7 through 18 removed outlier: 4.032A pdb=" N ASP 3 11 " --> pdb=" O GLN 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 22 through 28 Processing helix chain '3' and resid 47 through 55 removed outlier: 3.824A pdb=" N LEU 3 51 " --> pdb=" O ASN 3 47 " (cutoff:3.500A) Processing helix chain '3' and resid 55 through 65 removed outlier: 4.212A pdb=" N LEU 3 62 " --> pdb=" O ARG 3 58 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU 3 63 " --> pdb=" O ALA 3 59 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 85 Processing helix chain '3' and resid 86 through 90 removed outlier: 3.660A pdb=" N ALA 3 89 " --> pdb=" O PRO 3 86 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS 3 90 " --> pdb=" O GLY 3 87 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 86 through 90' Processing helix chain '3' and resid 201 through 205 removed outlier: 3.612A pdb=" N LYS 3 204 " --> pdb=" O MET 3 201 " (cutoff:3.500A) Processing helix chain '3' and resid 274 through 284 removed outlier: 4.348A pdb=" N ILE 3 278 " --> pdb=" O SER 3 274 " (cutoff:3.500A) Processing helix chain '3' and resid 287 through 289 No H-bonds generated for 'chain '3' and resid 287 through 289' Processing helix chain '3' and resid 290 through 296 Processing helix chain '3' and resid 309 through 317 removed outlier: 4.749A pdb=" N CYS 3 314 " --> pdb=" O GLN 3 310 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU 3 315 " --> pdb=" O ALA 3 311 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 355 Processing helix chain '3' and resid 410 through 423 removed outlier: 3.869A pdb=" N ARG 3 414 " --> pdb=" O SER 3 410 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR 3 415 " --> pdb=" O ASP 3 411 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA 3 416 " --> pdb=" O ILE 3 412 " (cutoff:3.500A) Processing helix chain '3' and resid 486 through 503 removed outlier: 4.578A pdb=" N GLN 3 490 " --> pdb=" O SER 3 486 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET 3 491 " --> pdb=" O ASP 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 558 through 563 Processing helix chain '3' and resid 564 through 566 No H-bonds generated for 'chain '3' and resid 564 through 566' Processing helix chain '3' and resid 568 through 572 removed outlier: 3.767A pdb=" N MET 3 572 " --> pdb=" O ALA 3 569 " (cutoff:3.500A) Processing helix chain '3' and resid 579 through 595 removed outlier: 4.076A pdb=" N ALA 3 583 " --> pdb=" O GLN 3 579 " (cutoff:3.500A) Processing helix chain '3' and resid 600 through 604 Processing helix chain '3' and resid 609 through 624 removed outlier: 3.637A pdb=" N GLU 3 613 " --> pdb=" O ALA 3 609 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR 3 614 " --> pdb=" O ARG 3 610 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE 3 616 " --> pdb=" O LEU 3 612 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER 3 619 " --> pdb=" O LEU 3 615 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA 3 621 " --> pdb=" O ARG 3 617 " (cutoff:3.500A) Processing helix chain '3' and resid 632 through 639 Processing helix chain '3' and resid 640 through 647 removed outlier: 3.908A pdb=" N TYR 3 647 " --> pdb=" O VAL 3 643 " (cutoff:3.500A) Processing helix chain '4' and resid 160 through 174 removed outlier: 3.851A pdb=" N CYS 4 164 " --> pdb=" O VAL 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 177 through 182 Processing helix chain '4' and resid 194 through 205 Processing helix chain '4' and resid 215 through 220 removed outlier: 3.674A pdb=" N LYS 4 219 " --> pdb=" O ALA 4 216 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR 4 220 " --> pdb=" O HIS 4 217 " (cutoff:3.500A) Processing helix chain '4' and resid 223 through 232 Processing helix chain '4' and resid 236 through 252 removed outlier: 4.679A pdb=" N PHE 4 249 " --> pdb=" O ASN 4 245 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU 4 250 " --> pdb=" O GLU 4 246 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG 4 251 " --> pdb=" O MET 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 447 through 455 Processing helix chain '4' and resid 456 through 458 No H-bonds generated for 'chain '4' and resid 456 through 458' Processing helix chain '4' and resid 459 through 469 removed outlier: 4.793A pdb=" N ALA 4 465 " --> pdb=" O TYR 4 461 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA 4 469 " --> pdb=" O ALA 4 465 " (cutoff:3.500A) Processing helix chain '4' and resid 475 through 477 No H-bonds generated for 'chain '4' and resid 475 through 477' Processing helix chain '4' and resid 478 through 487 removed outlier: 4.673A pdb=" N LEU 4 484 " --> pdb=" O LYS 4 480 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN 4 485 " --> pdb=" O GLY 4 481 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE 4 487 " --> pdb=" O LEU 4 483 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 529 removed outlier: 3.626A pdb=" N MET 4 521 " --> pdb=" O SER 4 517 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU 4 522 " --> pdb=" O LYS 4 518 " (cutoff:3.500A) Processing helix chain '4' and resid 577 through 581 removed outlier: 4.001A pdb=" N LYS 4 580 " --> pdb=" O GLU 4 577 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET 4 581 " --> pdb=" O PHE 4 578 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 577 through 581' Processing helix chain '4' and resid 631 through 636 Processing helix chain '4' and resid 657 through 670 removed outlier: 4.443A pdb=" N ASP 4 661 " --> pdb=" O ASP 4 657 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ARG 4 663 " --> pdb=" O ILE 4 659 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU 4 664 " --> pdb=" O PHE 4 660 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER 4 670 " --> pdb=" O SER 4 666 " (cutoff:3.500A) Processing helix chain '4' and resid 670 through 675 removed outlier: 4.072A pdb=" N THR 4 675 " --> pdb=" O LEU 4 671 " (cutoff:3.500A) Processing helix chain '4' and resid 689 through 696 Processing helix chain '4' and resid 709 through 721 removed outlier: 3.845A pdb=" N GLN 4 714 " --> pdb=" O GLN 4 710 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL 4 717 " --> pdb=" O ILE 4 713 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP 4 718 " --> pdb=" O GLN 4 714 " (cutoff:3.500A) Processing helix chain '4' and resid 722 through 724 No H-bonds generated for 'chain '4' and resid 722 through 724' Processing helix chain '4' and resid 734 through 749 removed outlier: 3.748A pdb=" N SER 4 738 " --> pdb=" O ARG 4 734 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 4 745 " --> pdb=" O ARG 4 741 " (cutoff:3.500A) Processing helix chain '4' and resid 757 through 768 removed outlier: 4.461A pdb=" N GLU 4 761 " --> pdb=" O LEU 4 757 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 19 removed outlier: 3.573A pdb=" N GLU 7 11 " --> pdb=" O ALA 7 7 " (cutoff:3.500A) Processing helix chain '7' and resid 31 through 41 Processing helix chain '7' and resid 51 through 59 removed outlier: 3.824A pdb=" N LEU 7 55 " --> pdb=" O ASP 7 51 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU 7 57 " --> pdb=" O ASP 7 53 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE 7 58 " --> pdb=" O ASP 7 54 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN 7 59 " --> pdb=" O LEU 7 55 " (cutoff:3.500A) Processing helix chain '7' and resid 71 through 83 removed outlier: 3.668A pdb=" N ILE 7 81 " --> pdb=" O PHE 7 77 " (cutoff:3.500A) Processing helix chain '7' and resid 99 through 107 removed outlier: 3.934A pdb=" N GLU 7 104 " --> pdb=" O ASP 7 100 " (cutoff:3.500A) Processing helix chain '7' and resid 223 through 227 Processing helix chain '7' and resid 260 through 262 No H-bonds generated for 'chain '7' and resid 260 through 262' Processing helix chain '7' and resid 323 through 330 removed outlier: 3.700A pdb=" N GLN 7 329 " --> pdb=" O GLU 7 325 " (cutoff:3.500A) Processing helix chain '7' and resid 334 through 340 removed outlier: 3.786A pdb=" N THR 7 338 " --> pdb=" O GLU 7 334 " (cutoff:3.500A) Processing helix chain '7' and resid 347 through 360 removed outlier: 3.559A pdb=" N LYS 7 351 " --> pdb=" O HIS 7 347 " (cutoff:3.500A) Processing helix chain '7' and resid 365 through 369 removed outlier: 4.252A pdb=" N GLY 7 368 " --> pdb=" O ARG 7 365 " (cutoff:3.500A) Processing helix chain '7' and resid 386 through 398 removed outlier: 4.318A pdb=" N LEU 7 390 " --> pdb=" O ALA 7 386 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU 7 391 " --> pdb=" O LYS 7 387 " (cutoff:3.500A) Processing helix chain '7' and resid 432 through 437 Processing helix chain '7' and resid 446 through 450 Processing helix chain '7' and resid 454 through 463 removed outlier: 3.655A pdb=" N VAL 7 461 " --> pdb=" O ALA 7 457 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU 7 463 " --> pdb=" O HIS 7 459 " (cutoff:3.500A) Processing helix chain '7' and resid 508 through 514 removed outlier: 3.832A pdb=" N LEU 7 512 " --> pdb=" O PRO 7 508 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG 7 514 " --> pdb=" O ALA 7 510 " (cutoff:3.500A) Processing helix chain '7' and resid 528 through 543 removed outlier: 3.535A pdb=" N ILE 7 537 " --> pdb=" O LEU 7 533 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL 7 540 " --> pdb=" O HIS 7 536 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS 7 541 " --> pdb=" O ILE 7 537 " (cutoff:3.500A) Processing helix chain '7' and resid 555 through 565 removed outlier: 3.692A pdb=" N LEU 7 565 " --> pdb=" O ARG 7 561 " (cutoff:3.500A) Processing helix chain '7' and resid 575 through 592 removed outlier: 3.801A pdb=" N ASP 7 579 " --> pdb=" O ASP 7 575 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR 7 580 " --> pdb=" O GLU 7 576 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL 7 582 " --> pdb=" O THR 7 578 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU 7 587 " --> pdb=" O GLY 7 583 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU 7 588 " --> pdb=" O ALA 7 584 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG 7 589 " --> pdb=" O TYR 7 585 " (cutoff:3.500A) Processing helix chain '7' and resid 602 through 617 removed outlier: 4.549A pdb=" N LEU 7 606 " --> pdb=" O SER 7 602 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU 7 607 " --> pdb=" O ALA 7 603 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE 7 609 " --> pdb=" O ASN 7 605 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA 7 617 " --> pdb=" O SER 7 613 " (cutoff:3.500A) Processing helix chain '7' and resid 626 through 641 removed outlier: 3.708A pdb=" N VAL 7 630 " --> pdb=" O GLU 7 626 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU 7 632 " --> pdb=" O ASP 7 628 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA 7 633 " --> pdb=" O ASP 7 629 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS 7 641 " --> pdb=" O LEU 7 637 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 30 removed outlier: 4.512A pdb=" N PHE 6 28 " --> pdb=" O LEU 6 24 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU 6 29 " --> pdb=" O PHE 6 25 " (cutoff:3.500A) Processing helix chain '6' and resid 43 through 47 Processing helix chain '6' and resid 60 through 65 Processing helix chain '6' and resid 69 through 74 Processing helix chain '6' and resid 76 through 94 Proline residue: 6 82 - end of helix Processing helix chain '6' and resid 121 through 125 Processing helix chain '6' and resid 223 through 227 removed outlier: 3.571A pdb=" N LEU 6 226 " --> pdb=" O ARG 6 223 " (cutoff:3.500A) Processing helix chain '6' and resid 325 through 330 Processing helix chain '6' and resid 331 through 333 No H-bonds generated for 'chain '6' and resid 331 through 333' Processing helix chain '6' and resid 336 through 345 Processing helix chain '6' and resid 355 through 360 Processing helix chain '6' and resid 361 through 364 Processing helix chain '6' and resid 397 through 405 removed outlier: 3.550A pdb=" N SER 6 402 " --> pdb=" O LEU 6 398 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER 6 405 " --> pdb=" O VAL 6 401 " (cutoff:3.500A) Processing helix chain '6' and resid 460 through 469 removed outlier: 3.546A pdb=" N ALA 6 464 " --> pdb=" O ARG 6 460 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU 6 467 " --> pdb=" O VAL 6 463 " (cutoff:3.500A) Processing helix chain '6' and resid 507 through 513 Processing helix chain '6' and resid 517 through 522 Processing helix chain '6' and resid 533 through 545 removed outlier: 3.517A pdb=" N ASP 6 537 " --> pdb=" O ASN 6 533 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE 6 540 " --> pdb=" O VAL 6 536 " (cutoff:3.500A) Processing helix chain '6' and resid 560 through 571 removed outlier: 4.409A pdb=" N THR 6 569 " --> pdb=" O LEU 6 565 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N PHE 6 570 " --> pdb=" O ARG 6 566 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 585 Processing helix chain '6' and resid 585 through 598 removed outlier: 3.862A pdb=" N ARG 6 596 " --> pdb=" O HIS 6 592 " (cutoff:3.500A) Processing helix chain '6' and resid 610 through 627 Processing helix chain '6' and resid 634 through 645 removed outlier: 3.604A pdb=" N LYS 6 638 " --> pdb=" O GLU 6 634 " (cutoff:3.500A) Processing helix chain '6' and resid 646 through 652 removed outlier: 3.530A pdb=" N GLU 6 652 " --> pdb=" O ILE 6 649 " (cutoff:3.500A) Processing helix chain '5' and resid 27 through 32 Processing helix chain '5' and resid 32 through 41 Processing helix chain '5' and resid 52 through 58 Processing helix chain '5' and resid 71 through 76 Processing helix chain '5' and resid 79 through 84 removed outlier: 4.000A pdb=" N ASN 5 84 " --> pdb=" O ALA 5 80 " (cutoff:3.500A) Processing helix chain '5' and resid 86 through 106 removed outlier: 4.069A pdb=" N GLU 5 92 " --> pdb=" O THR 5 88 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP 5 103 " --> pdb=" O ARG 5 99 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU 5 104 " --> pdb=" O GLU 5 100 " (cutoff:3.500A) Processing helix chain '5' and resid 136 through 140 Processing helix chain '5' and resid 211 through 214 Processing helix chain '5' and resid 313 through 324 removed outlier: 3.612A pdb=" N MET 5 322 " --> pdb=" O HIS 5 318 " (cutoff:3.500A) Processing helix chain '5' and resid 330 through 335 removed outlier: 4.007A pdb=" N GLN 5 334 " --> pdb=" O ARG 5 331 " (cutoff:3.500A) Processing helix chain '5' and resid 343 through 351 removed outlier: 3.875A pdb=" N ALA 5 349 " --> pdb=" O ASP 5 345 " (cutoff:3.500A) Processing helix chain '5' and resid 383 through 390 removed outlier: 3.583A pdb=" N LEU 5 388 " --> pdb=" O LYS 5 384 " (cutoff:3.500A) Processing helix chain '5' and resid 452 through 460 removed outlier: 4.502A pdb=" N HIS 5 456 " --> pdb=" O ARG 5 452 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA 5 458 " --> pdb=" O ALA 5 454 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU 5 460 " --> pdb=" O HIS 5 456 " (cutoff:3.500A) Processing helix chain '5' and resid 489 through 495 Processing helix chain '5' and resid 505 through 509 removed outlier: 3.545A pdb=" N LEU 5 508 " --> pdb=" O PRO 5 505 " (cutoff:3.500A) Processing helix chain '5' and resid 522 through 532 removed outlier: 3.671A pdb=" N ILE 5 527 " --> pdb=" O GLU 5 523 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR 5 528 " --> pdb=" O SER 5 524 " (cutoff:3.500A) Processing helix chain '5' and resid 533 through 538 Processing helix chain '5' and resid 554 through 566 Processing helix chain '5' and resid 608 through 613 Processing helix chain '5' and resid 616 through 626 removed outlier: 4.035A pdb=" N ALA 5 623 " --> pdb=" O SER 5 619 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS 5 624 " --> pdb=" O GLU 5 620 " (cutoff:3.500A) Processing helix chain '5' and resid 637 through 648 removed outlier: 4.253A pdb=" N VAL 5 645 " --> pdb=" O ARG 5 641 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER 5 646 " --> pdb=" O LEU 5 642 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU 5 648 " --> pdb=" O GLN 5 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 14 Processing helix chain 'A' and resid 27 through 43 removed outlier: 4.206A pdb=" N ILE A 35 " --> pdb=" O CYS A 31 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.647A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS A 59 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.564A pdb=" N PHE A 134 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 198 removed outlier: 4.399A pdb=" N GLN A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 197 " --> pdb=" O TRP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 224 removed outlier: 3.877A pdb=" N LYS A 224 " --> pdb=" O GLU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 removed outlier: 3.551A pdb=" N LEU A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TRP A 234 " --> pdb=" O MET A 230 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A 239 " --> pdb=" O TRP A 235 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 266 removed outlier: 3.689A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.820A pdb=" N SER A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ARG A 304 " --> pdb=" O THR A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 removed outlier: 4.019A pdb=" N GLN A 312 " --> pdb=" O TYR A 308 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 332 removed outlier: 4.238A pdb=" N GLU A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.514A pdb=" N GLN A 340 " --> pdb=" O HIS A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.563A pdb=" N ARG A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER A 355 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 3.867A pdb=" N LEU A 393 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 394' Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.702A pdb=" N SER A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 439 removed outlier: 3.594A pdb=" N SER A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ILE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.636A pdb=" N GLU A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.717A pdb=" N LEU A 478 " --> pdb=" O TYR A 474 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N LEU A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 3.879A pdb=" N ALA A 534 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 542 removed outlier: 3.581A pdb=" N ALA A 539 " --> pdb=" O PHE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 570 Processing helix chain 'H' and resid 10 through 18 removed outlier: 3.706A pdb=" N PHE H 13 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU H 16 " --> pdb=" O PHE H 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS H 17 " --> pdb=" O ASP H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 40 Processing helix chain 'H' and resid 44 through 49 Processing helix chain 'H' and resid 60 through 62 No H-bonds generated for 'chain 'H' and resid 60 through 62' Processing helix chain 'H' and resid 63 through 99 removed outlier: 3.932A pdb=" N PHE H 69 " --> pdb=" O PRO H 65 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU H 74 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG H 79 " --> pdb=" O GLN H 75 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU H 85 " --> pdb=" O LEU H 81 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG H 88 " --> pdb=" O TYR H 84 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ARG H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE H 92 " --> pdb=" O ARG H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'L' and resid 4 through 10 Processing helix chain 'L' and resid 49 through 54 Processing helix chain 'L' and resid 73 through 78 Processing helix chain 'L' and resid 79 through 81 No H-bonds generated for 'chain 'L' and resid 79 through 81' Processing helix chain 'L' and resid 94 through 103 Processing helix chain 'L' and resid 104 through 106 No H-bonds generated for 'chain 'L' and resid 104 through 106' Processing helix chain 'L' and resid 111 through 133 removed outlier: 3.667A pdb=" N LYS L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ILE L 123 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 128 " --> pdb=" O ARG L 124 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 156 Processing helix chain 'L' and resid 160 through 169 removed outlier: 3.852A pdb=" N ASP L 165 " --> pdb=" O PRO L 161 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS L 166 " --> pdb=" O TYR L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 60 removed outlier: 3.812A pdb=" N LYS M 60 " --> pdb=" O TRP M 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 57 through 60' Processing helix chain 'M' and resid 78 through 86 removed outlier: 4.624A pdb=" N VAL M 84 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 112 removed outlier: 4.232A pdb=" N TYR M 111 " --> pdb=" O TYR M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 117 through 126 removed outlier: 3.733A pdb=" N ILE M 121 " --> pdb=" O ILE M 117 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE M 122 " --> pdb=" O GLY M 118 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU M 123 " --> pdb=" O ARG M 119 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR M 124 " --> pdb=" O ILE M 120 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU M 125 " --> pdb=" O ILE M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 Processing helix chain 'M' and resid 152 through 172 removed outlier: 3.834A pdb=" N LEU M 156 " --> pdb=" O ILE M 152 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN M 164 " --> pdb=" O GLY M 160 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU M 169 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 171 " --> pdb=" O TYR M 167 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN M 172 " --> pdb=" O ILE M 168 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 41 removed outlier: 3.926A pdb=" N GLU N 40 " --> pdb=" O GLN N 36 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE N 41 " --> pdb=" O LYS N 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 36 through 41' Processing helix chain 'N' and resid 43 through 51 removed outlier: 4.461A pdb=" N GLU N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET N 50 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS N 51 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 79 removed outlier: 5.094A pdb=" N VAL N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL N 70 " --> pdb=" O MET N 66 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA N 71 " --> pdb=" O VAL N 67 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET N 73 " --> pdb=" O GLN N 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN N 76 " --> pdb=" O HIS N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 97 removed outlier: 3.529A pdb=" N HIS N 90 " --> pdb=" O ARG N 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER N 91 " --> pdb=" O ALA N 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 115 removed outlier: 3.975A pdb=" N MET N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER N 103 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU N 105 " --> pdb=" O MET N 101 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS N 107 " --> pdb=" O SER N 103 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG N 108 " --> pdb=" O TYR N 104 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN N 110 " --> pdb=" O ARG N 106 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE N 112 " --> pdb=" O ARG N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 124 removed outlier: 3.579A pdb=" N GLN N 122 " --> pdb=" O HIS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 135 No H-bonds generated for 'chain 'N' and resid 134 through 135' Processing helix chain 'N' and resid 137 through 137 No H-bonds generated for 'chain 'N' and resid 137 through 137' Processing helix chain 'N' and resid 138 through 151 removed outlier: 3.958A pdb=" N GLN N 142 " --> pdb=" O THR N 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU N 143 " --> pdb=" O LYS N 139 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER N 146 " --> pdb=" O GLN N 142 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR N 151 " --> pdb=" O ASN N 147 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 155 Processing helix chain 'N' and resid 218 through 223 Processing helix chain '2' and resid 176 through 186 removed outlier: 3.938A pdb=" N ASN 2 182 " --> pdb=" O THR 2 178 " (cutoff:3.500A) Processing helix chain '2' and resid 198 through 211 removed outlier: 3.897A pdb=" N ASP 2 202 " --> pdb=" O TYR 2 198 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE 2 204 " --> pdb=" O TYR 2 200 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ARG 2 205 " --> pdb=" O ARG 2 201 " (cutoff:3.500A) Processing helix chain '2' and resid 219 through 226 Processing helix chain '2' and resid 236 through 256 removed outlier: 3.795A pdb=" N MET 2 240 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU 2 241 " --> pdb=" O PRO 2 237 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL 2 247 " --> pdb=" O ILE 2 243 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER 2 254 " --> pdb=" O ASP 2 250 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE 2 255 " --> pdb=" O MET 2 251 " (cutoff:3.500A) Processing helix chain '2' and resid 457 through 465 removed outlier: 4.765A pdb=" N VAL 2 463 " --> pdb=" O VAL 2 459 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER 2 465 " --> pdb=" O ARG 2 461 " (cutoff:3.500A) Processing helix chain '2' and resid 473 through 484 removed outlier: 3.874A pdb=" N LYS 2 477 " --> pdb=" O HIS 2 473 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU 2 482 " --> pdb=" O ARG 2 478 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA 2 483 " --> pdb=" O ALA 2 479 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU 2 484 " --> pdb=" O LEU 2 480 " (cutoff:3.500A) Processing helix chain '2' and resid 519 through 525 removed outlier: 3.699A pdb=" N LYS 2 523 " --> pdb=" O LYS 2 519 " (cutoff:3.500A) Processing helix chain '2' and resid 578 through 592 removed outlier: 3.886A pdb=" N SER 2 584 " --> pdb=" O GLN 2 580 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE 2 585 " --> pdb=" O ASP 2 581 " (cutoff:3.500A) Processing helix chain '2' and resid 635 through 640 removed outlier: 3.826A pdb=" N LEU 2 639 " --> pdb=" O SER 2 635 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER 2 640 " --> pdb=" O GLU 2 636 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 635 through 640' Processing helix chain '2' and resid 653 through 668 removed outlier: 3.759A pdb=" N ASP 2 657 " --> pdb=" O ASP 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 697 through 708 removed outlier: 3.727A pdb=" N ILE 2 701 " --> pdb=" O LEU 2 697 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS 2 705 " --> pdb=" O ILE 2 701 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU 2 706 " --> pdb=" O VAL 2 702 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE 2 708 " --> pdb=" O ALA 2 704 " (cutoff:3.500A) Processing helix chain '2' and resid 717 through 730 removed outlier: 4.337A pdb=" N LEU 2 727 " --> pdb=" O MET 2 723 " (cutoff:3.500A) Processing helix chain '2' and resid 741 through 757 removed outlier: 4.328A pdb=" N VAL 2 747 " --> pdb=" O HIS 2 743 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU 2 752 " --> pdb=" O ILE 2 748 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA 2 753 " --> pdb=" O ARG 2 749 " (cutoff:3.500A) Processing helix chain '2' and resid 764 through 779 removed outlier: 4.604A pdb=" N VAL 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET 2 774 " --> pdb=" O MET 2 770 " (cutoff:3.500A) Processing helix chain '2' and resid 780 through 783 removed outlier: 3.768A pdb=" N GLN 2 783 " --> pdb=" O ILE 2 780 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 780 through 783' Processing helix chain '2' and resid 788 through 795 Processing sheet with id=AA1, first strand: chain '3' and resid 107 through 108 removed outlier: 4.093A pdb=" N GLU 3 125 " --> pdb=" O VAL 3 108 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN 3 194 " --> pdb=" O CYS 3 218 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU 3 196 " --> pdb=" O ILE 3 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '3' and resid 135 through 138 removed outlier: 3.670A pdb=" N ILE 3 234 " --> pdb=" O VAL 3 124 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY 3 126 " --> pdb=" O VAL 3 232 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL 3 235 " --> pdb=" O ASN 3 260 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN 3 260 " --> pdb=" O VAL 3 235 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL 3 256 " --> pdb=" O ARG 3 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 140 through 143 Processing sheet with id=AA4, first strand: chain '4' and resid 372 through 376 removed outlier: 3.602A pdb=" N GLY 4 290 " --> pdb=" O VAL 4 391 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU 4 402 " --> pdb=" O VAL 4 414 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL 4 414 " --> pdb=" O LEU 4 402 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '4' and resid 304 through 306 Processing sheet with id=AA6, first strand: chain '7' and resid 176 through 179 removed outlier: 7.399A pdb=" N LYS 7 228 " --> pdb=" O VAL 7 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '7' and resid 232 through 235 removed outlier: 3.743A pdb=" N CYS 7 257 " --> pdb=" O GLN 7 233 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL 7 235 " --> pdb=" O ILE 7 255 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '7' and resid 272 through 273 Processing sheet with id=AA9, first strand: chain '7' and resid 401 through 403 removed outlier: 7.127A pdb=" N GLN 7 402 " --> pdb=" O CYS 7 443 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU 7 485 " --> pdb=" O CYS 7 442 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ILE 7 377 " --> pdb=" O ALA 7 486 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ALA 7 488 " --> pdb=" O ILE 7 377 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU 7 379 " --> pdb=" O ALA 7 488 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '6' and resid 56 through 58 removed outlier: 6.586A pdb=" N VAL 6 57 " --> pdb=" O THR 6 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '6' and resid 136 through 139 removed outlier: 5.042A pdb=" N ARG 6 137 " --> pdb=" O ARG 6 201 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG 6 201 " --> pdb=" O ARG 6 137 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS 6 199 " --> pdb=" O HIS 6 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN 6 198 " --> pdb=" O LEU 6 222 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU 6 222 " --> pdb=" O GLN 6 198 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE 6 220 " --> pdb=" O ILE 6 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '6' and resid 408 through 412 removed outlier: 3.897A pdb=" N THR 6 411 " --> pdb=" O CYS 6 450 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain '5' and resid 146 through 147 removed outlier: 3.733A pdb=" N ILE 5 146 " --> pdb=" O ILE 5 260 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE 5 260 " --> pdb=" O ILE 5 146 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN 5 261 " --> pdb=" O GLY 5 294 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY 5 294 " --> pdb=" O GLN 5 261 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 149 through 150 removed outlier: 3.559A pdb=" N LEU 5 224 " --> pdb=" O LEU 5 240 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU 5 240 " --> pdb=" O LEU 5 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 164 through 165 removed outlier: 4.458A pdb=" N SER 5 164 " --> pdb=" O MET 5 210 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 374 through 377 removed outlier: 3.839A pdb=" N PHE 5 515 " --> pdb=" O LEU 5 375 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU 5 377 " --> pdb=" O PHE 5 515 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '5' and resid 439 through 442 removed outlier: 6.082A pdb=" N VAL 5 439 " --> pdb=" O LEU 5 482 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA 5 484 " --> pdb=" O VAL 5 439 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE 5 441 " --> pdb=" O ALA 5 484 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 18 through 19 removed outlier: 3.986A pdb=" N VAL A 73 " --> pdb=" O ILE A 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 284 through 289 removed outlier: 4.039A pdb=" N THR A 284 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR A 375 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 501 through 505 Processing sheet with id=AC4, first strand: chain 'L' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'M' and resid 22 through 23 Processing sheet with id=AC6, first strand: chain 'N' and resid 183 through 184 removed outlier: 3.780A pdb=" N GLN N 226 " --> pdb=" O LYS N 184 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '2' and resid 215 through 218 removed outlier: 6.899A pdb=" N PHE 2 215 " --> pdb=" O ARG 2 269 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER 2 271 " --> pdb=" O PHE 2 215 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL 2 217 " --> pdb=" O SER 2 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '2' and resid 296 through 297 Processing sheet with id=AC9, first strand: chain '2' and resid 303 through 305 Processing sheet with id=AD1, first strand: chain '2' and resid 380 through 382 removed outlier: 6.779A pdb=" N ASP 2 380 " --> pdb=" O ILE 2 424 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE 2 425 " --> pdb=" O ILE 2 402 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE 2 402 " --> pdb=" O ILE 2 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '2' and resid 397 through 399 Processing sheet with id=AD3, first strand: chain '2' and resid 506 through 507 removed outlier: 3.990A pdb=" N CYS 2 507 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain '2' and resid 529 through 530 removed outlier: 3.574A pdb=" N LEU 2 570 " --> pdb=" O VAL 2 529 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2523 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: 9.40 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 6662 1.31 - 1.44: 9992 1.44 - 1.57: 22634 1.57 - 1.70: 120 1.70 - 1.83: 336 Bond restraints: 39744 Sorted by residual: bond pdb=" C THR 7 254 " pdb=" N ILE 7 255 " ideal model delta sigma weight residual 1.331 1.667 -0.336 1.32e-02 5.74e+03 6.50e+02 bond pdb=" C VAL 4 588 " pdb=" N LEU 4 589 " ideal model delta sigma weight residual 1.332 1.659 -0.326 1.40e-02 5.10e+03 5.44e+02 bond pdb=" C PHE 6 108 " pdb=" N THR 6 109 " ideal model delta sigma weight residual 1.328 1.523 -0.194 1.23e-02 6.61e+03 2.50e+02 bond pdb=" C PRO 7 267 " pdb=" N GLY 7 268 " ideal model delta sigma weight residual 1.331 1.536 -0.205 1.46e-02 4.69e+03 1.98e+02 bond pdb=" C THR 4 271 " pdb=" N ARG 4 272 " ideal model delta sigma weight residual 1.332 1.487 -0.155 1.29e-02 6.01e+03 1.44e+02 ... (remaining 39739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.82: 53319 6.82 - 13.64: 352 13.64 - 20.46: 47 20.46 - 27.27: 17 27.27 - 34.09: 2 Bond angle restraints: 53737 Sorted by residual: angle pdb=" PB ATP 3 901 " pdb=" O3B ATP 3 901 " pdb=" PG ATP 3 901 " ideal model delta sigma weight residual 139.87 115.04 24.83 1.00e+00 1.00e+00 6.16e+02 angle pdb=" PB ATP 2 901 " pdb=" O3B ATP 2 901 " pdb=" PG ATP 2 901 " ideal model delta sigma weight residual 139.87 116.06 23.81 1.00e+00 1.00e+00 5.67e+02 angle pdb=" PA ATP 3 901 " pdb=" O3A ATP 3 901 " pdb=" PB ATP 3 901 " ideal model delta sigma weight residual 136.83 113.35 23.48 1.00e+00 1.00e+00 5.51e+02 angle pdb=" PB ATP 4 901 " pdb=" O3B ATP 4 901 " pdb=" PG ATP 4 901 " ideal model delta sigma weight residual 139.87 117.24 22.63 1.00e+00 1.00e+00 5.12e+02 angle pdb=" PB ATP 6 901 " pdb=" O3B ATP 6 901 " pdb=" PG ATP 6 901 " ideal model delta sigma weight residual 139.87 118.05 21.82 1.00e+00 1.00e+00 4.76e+02 ... (remaining 53732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 23377 35.47 - 70.94: 864 70.94 - 106.41: 77 106.41 - 141.88: 7 141.88 - 177.36: 2 Dihedral angle restraints: 24327 sinusoidal: 10042 harmonic: 14285 Sorted by residual: dihedral pdb=" C PRO 5 419 " pdb=" N PRO 5 419 " pdb=" CA PRO 5 419 " pdb=" CB PRO 5 419 " ideal model delta harmonic sigma weight residual -120.70 -153.65 32.95 0 2.50e+00 1.60e-01 1.74e+02 dihedral pdb=" CD ARG 6 427 " pdb=" NE ARG 6 427 " pdb=" CZ ARG 6 427 " pdb=" NH1 ARG 6 427 " ideal model delta sinusoidal sigma weight residual 0.00 119.81 -119.81 1 1.00e+01 1.00e-02 1.44e+02 dihedral pdb=" N PRO 5 419 " pdb=" C PRO 5 419 " pdb=" CA PRO 5 419 " pdb=" CB PRO 5 419 " ideal model delta harmonic sigma weight residual 115.10 145.01 -29.91 0 2.50e+00 1.60e-01 1.43e+02 ... (remaining 24324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.584: 6042 0.584 - 1.168: 9 1.168 - 1.752: 17 1.752 - 2.336: 14 2.336 - 2.920: 1 Chirality restraints: 6083 Sorted by residual: chirality pdb=" CB VAL 4 652 " pdb=" CA VAL 4 652 " pdb=" CG1 VAL 4 652 " pdb=" CG2 VAL 4 652 " both_signs ideal model delta sigma weight residual False -2.63 0.29 -2.92 2.00e-01 2.50e+01 2.13e+02 chirality pdb=" CB ILE 4 472 " pdb=" CA ILE 4 472 " pdb=" CG1 ILE 4 472 " pdb=" CG2 ILE 4 472 " both_signs ideal model delta sigma weight residual False 2.64 0.31 2.33 2.00e-01 2.50e+01 1.36e+02 chirality pdb=" CB ILE 2 310 " pdb=" CA ILE 2 310 " pdb=" CG1 ILE 2 310 " pdb=" CG2 ILE 2 310 " both_signs ideal model delta sigma weight residual False 2.64 0.49 2.15 2.00e-01 2.50e+01 1.16e+02 ... (remaining 6080 not shown) Planarity restraints: 6914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 510 " 0.443 9.50e-02 1.11e+02 2.26e-01 1.69e+02 pdb=" NE ARG 5 510 " -0.102 2.00e-02 2.50e+03 pdb=" CZ ARG 5 510 " 0.202 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 510 " -0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 510 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 641 " 0.459 9.50e-02 1.11e+02 2.29e-01 1.54e+02 pdb=" NE ARG 2 641 " -0.099 2.00e-02 2.50e+03 pdb=" CZ ARG 2 641 " 0.190 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 641 " -0.061 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 641 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP 7 629 " 0.070 2.00e-02 2.50e+03 1.22e-01 1.49e+02 pdb=" C ASP 7 629 " -0.211 2.00e-02 2.50e+03 pdb=" O ASP 7 629 " 0.067 2.00e-02 2.50e+03 pdb=" N VAL 7 630 " 0.075 2.00e-02 2.50e+03 ... (remaining 6911 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 13 2.08 - 2.78: 9308 2.78 - 3.49: 57745 3.49 - 4.19: 91190 4.19 - 4.90: 145685 Nonbonded interactions: 303941 Sorted by model distance: nonbonded pdb=" OD2 ASP 3 397 " pdb=" CG1 VAL 7 246 " model vdw 1.371 3.460 nonbonded pdb=" O VAL 5 425 " pdb=" CG2 VAL 5 425 " model vdw 1.780 3.460 nonbonded pdb=" NZ LYS 5 384 " pdb=" OD1 ASN 5 486 " model vdw 1.918 3.120 nonbonded pdb=" OG SER 4 519 " pdb=" O1G ATP 4 901 " model vdw 1.923 3.040 nonbonded pdb=" CZ ARG 7 219 " pdb=" CG ARG 6 263 " model vdw 1.957 2.936 ... (remaining 303936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.700 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 36.610 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.130 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: 0.020 Load rotamer database and sin/cos tables:2.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 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 : 0.013 0.761 39752 Z= 0.795 Angle : 1.772 34.092 53739 Z= 1.014 Chirality : 0.162 2.920 6083 Planarity : 0.018 0.488 6914 Dihedral : 18.464 177.356 15024 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.77 % Allowed : 17.40 % Favored : 81.82 % Rotamer: Outliers : 7.45 % Allowed : 16.00 % Favored : 76.55 % Cbeta Deviations : 0.84 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.99 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.68 (0.09), residues: 4775 helix: -3.73 (0.09), residues: 1355 sheet: -3.86 (0.19), residues: 398 loop : -4.01 (0.09), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.208 0.005 ARG 5 510 TYR 0.053 0.005 TYR L 30 PHE 0.061 0.005 PHE 5 219 TRP 0.037 0.005 TRP 2 554 HIS 0.043 0.005 HIS L 91 Details of bonding type rmsd/Z covalent geometry : bond 0.01255 / 0.63 (39744) covalent geometry : angle 1.77163 / 1.01 (53737) SS BOND : bond 0.00533 / 0.28 ( 1) SS BOND : angle 3.80806 / 2.20 ( 2) hydrogen bonds : bond 0.26014 / 17.45 ( 889) hydrogen bonds : angle 10.43663 / 7.10 ( 2523) Misc. bond : bond 0.36657 / 14.87 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 314 poor density : 1127 time to evaluate : 1.493 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. 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: 3 70 GLN cc_start: 0.8515 (mt0) cc_final: 0.8221 (mm-40) REVERT: 3 79 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8175 (tm-30) REVERT: 3 118 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6339 (mt) REVERT: 3 130 LYS cc_start: 0.5206 (mtpt) cc_final: 0.4135 (mptt) REVERT: 3 197 THR cc_start: 0.3487 (p) cc_final: 0.3231 (p) REVERT: 3 218 CYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7950 (t) REVERT: 3 230 ASP cc_start: 0.6160 (t0) cc_final: 0.5902 (t0) REVERT: 3 239 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6202 (mtp-110) REVERT: 3 409 MET cc_start: 0.6561 (ttt) cc_final: 0.6354 (ttt) REVERT: 3 419 GLU cc_start: 0.7525 (tt0) cc_final: 0.7147 (tm-30) REVERT: 3 448 ASN cc_start: 0.6314 (t0) cc_final: 0.5962 (m-40) REVERT: 3 628 SER cc_start: 0.6688 (m) cc_final: 0.6473 (m) REVERT: 4 210 TYR cc_start: 0.6703 (m-80) cc_final: 0.5932 (m-80) REVERT: 4 285 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7442 (pt) REVERT: 4 299 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7652 (tp) REVERT: 4 306 PHE cc_start: 0.6009 (t80) cc_final: 0.5753 (t80) REVERT: 4 324 ARG cc_start: 0.6508 (mpp-170) cc_final: 0.6095 (mmm160) REVERT: 4 356 LYS cc_start: 0.8021 (ttmm) cc_final: 0.7693 (tttp) REVERT: 4 363 ASP cc_start: 0.7143 (m-30) cc_final: 0.6823 (t0) REVERT: 4 371 HIS cc_start: 0.6506 (m-70) cc_final: 0.5641 (m-70) REVERT: 4 372 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8224 (p0) REVERT: 4 373 VAL cc_start: 0.5951 (OUTLIER) cc_final: 0.5739 (p) REVERT: 4 428 ASP cc_start: -0.0269 (OUTLIER) cc_final: -0.1925 (p0) REVERT: 4 527 ASN cc_start: 0.8221 (t0) cc_final: 0.7862 (t0) REVERT: 4 533 GLN cc_start: 0.6019 (OUTLIER) cc_final: 0.4651 (tm-30) REVERT: 4 615 ILE cc_start: 0.8954 (tt) cc_final: 0.8668 (mp) REVERT: 4 620 ASN cc_start: 0.5935 (p0) cc_final: 0.5610 (p0) REVERT: 4 713 ILE cc_start: 0.7621 (mt) cc_final: 0.7299 (mm) REVERT: 7 64 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8427 (pm20) REVERT: 7 79 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6270 (p0) REVERT: 7 200 PHE cc_start: 0.7623 (t80) cc_final: 0.7342 (t80) REVERT: 7 221 TYR cc_start: 0.7458 (m-80) cc_final: 0.7089 (m-10) REVERT: 7 242 ASP cc_start: 0.8049 (t70) cc_final: 0.7716 (t0) REVERT: 7 298 LEU cc_start: 0.7618 (tp) cc_final: 0.7326 (tt) REVERT: 7 304 ILE cc_start: 0.2501 (OUTLIER) cc_final: 0.1802 (tt) REVERT: 7 387 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8442 (pttm) REVERT: 7 465 GLN cc_start: 0.6669 (OUTLIER) cc_final: 0.6408 (tt0) REVERT: 7 522 GLN cc_start: 0.2387 (OUTLIER) cc_final: 0.1982 (tp-100) REVERT: 7 541 HIS cc_start: 0.6251 (m90) cc_final: 0.5380 (m90) REVERT: 7 559 MET cc_start: 0.6862 (mtp) cc_final: 0.6267 (mtp) REVERT: 7 561 ARG cc_start: 0.8056 (mtt90) cc_final: 0.7755 (mtp85) REVERT: 7 630 VAL cc_start: 0.8768 (t) cc_final: 0.8567 (p) REVERT: 7 639 MET cc_start: 0.7220 (tpp) cc_final: 0.6461 (tpp) REVERT: 6 69 LEU cc_start: 0.5867 (mp) cc_final: 0.5619 (mt) REVERT: 6 76 GLU cc_start: 0.3532 (mt-10) cc_final: 0.3126 (mp0) REVERT: 6 86 GLN cc_start: 0.9411 (tt0) cc_final: 0.9170 (tm-30) REVERT: 6 131 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6944 (tp) REVERT: 6 223 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6341 (ptt-90) REVERT: 6 235 ARG cc_start: 0.7600 (mmt-90) cc_final: 0.7126 (mmt-90) REVERT: 6 355 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7577 (pm20) REVERT: 6 389 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: 6 404 PHE cc_start: 0.5840 (t80) cc_final: 0.5444 (t80) REVERT: 6 432 PHE cc_start: -0.0085 (OUTLIER) cc_final: -0.0327 (m-80) REVERT: 6 442 MET cc_start: 0.6171 (ttt) cc_final: 0.5112 (mmm) REVERT: 6 443 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7288 (pp) REVERT: 6 486 ASN cc_start: 0.7547 (p0) cc_final: 0.6779 (p0) REVERT: 6 506 LYS cc_start: 0.5456 (mtpt) cc_final: 0.5249 (mmtp) REVERT: 6 537 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7382 (t0) REVERT: 5 32 LYS cc_start: 0.7994 (mmmm) cc_final: 0.7527 (mmtm) REVERT: 5 37 PHE cc_start: 0.7209 (t80) cc_final: 0.6587 (t80) REVERT: 5 52 ASP cc_start: 0.9097 (m-30) cc_final: 0.8728 (p0) REVERT: 5 62 ARG cc_start: 0.7585 (mmt-90) cc_final: 0.7213 (ttm110) REVERT: 5 66 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8307 (pm20) REVERT: 5 69 MET cc_start: 0.2054 (ptt) cc_final: 0.1571 (mmm) REVERT: 5 216 CYS cc_start: 0.6715 (p) cc_final: 0.6442 (p) REVERT: 5 322 MET cc_start: 0.6314 (mtt) cc_final: 0.5909 (tpt) REVERT: 5 416 MET cc_start: 0.5639 (ppp) cc_final: 0.5128 (ppp) REVERT: 5 418 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5761 (p0) REVERT: 5 426 MET cc_start: 0.4370 (ptm) cc_final: 0.3761 (ppp) REVERT: 5 459 MET cc_start: 0.5427 (mpp) cc_final: 0.5141 (ptt) REVERT: 5 474 THR cc_start: 0.7615 (m) cc_final: 0.7182 (p) REVERT: 5 515 PHE cc_start: 0.6154 (m-80) cc_final: 0.3485 (m-80) REVERT: 5 556 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7683 (t) REVERT: 5 612 LEU cc_start: 0.7831 (tt) cc_final: 0.7508 (tt) REVERT: 5 641 ARG cc_start: 0.8676 (mtt90) cc_final: 0.7509 (tmm-80) REVERT: A 20 LEU cc_start: 0.9163 (tt) cc_final: 0.8936 (tt) REVERT: A 77 CYS cc_start: 0.1151 (OUTLIER) cc_final: 0.0539 (t) REVERT: A 99 ASP cc_start: 0.6148 (t70) cc_final: 0.5796 (t0) REVERT: A 100 SER cc_start: 0.6360 (m) cc_final: 0.6049 (t) REVERT: A 229 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7232 (t0) REVERT: A 259 GLU cc_start: 0.9001 (tt0) cc_final: 0.8741 (tm-30) REVERT: A 276 ASN cc_start: 0.7836 (p0) cc_final: 0.6901 (t0) REVERT: A 331 MET cc_start: 0.8246 (ttp) cc_final: 0.8014 (tpt) REVERT: A 378 TYR cc_start: 0.8003 (m-10) cc_final: 0.7640 (m-10) REVERT: A 383 ARG cc_start: 0.7938 (mmt-90) cc_final: 0.7219 (mtp85) REVERT: A 396 ILE cc_start: 0.5058 (OUTLIER) cc_final: 0.4272 (mt) REVERT: A 418 SER cc_start: 0.7422 (OUTLIER) cc_final: 0.7159 (p) REVERT: A 568 ASP cc_start: 0.8846 (m-30) cc_final: 0.8129 (t0) REVERT: H 35 ARG cc_start: 0.9244 (mmp80) cc_final: 0.8640 (mmp80) REVERT: H 36 GLN cc_start: 0.9374 (tp-100) cc_final: 0.9055 (tm-30) REVERT: H 120 ASN cc_start: 0.7235 (OUTLIER) cc_final: 0.6835 (t0) REVERT: L 73 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8514 (mt-10) REVERT: L 109 ARG cc_start: 0.7481 (mmt180) cc_final: 0.6938 (ttt90) REVERT: M 59 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7918 (tt) REVERT: M 126 ARG cc_start: 0.7683 (tpt-90) cc_final: 0.7463 (tpt170) REVERT: M 169 GLU cc_start: 0.8144 (mp0) cc_final: 0.6796 (tp30) REVERT: N 30 MET cc_start: 0.3466 (mtt) cc_final: 0.3223 (ptp) REVERT: N 48 ASN cc_start: 0.6563 (p0) cc_final: 0.6242 (p0) REVERT: N 115 PHE cc_start: 0.7144 (t80) cc_final: 0.6845 (t80) REVERT: 2 206 ARG cc_start: 0.8100 (mtm180) cc_final: 0.7451 (mtm110) REVERT: 2 212 MET cc_start: 0.7557 (tpp) cc_final: 0.7020 (tpp) REVERT: 2 351 GLU cc_start: 0.5799 (pt0) cc_final: 0.5282 (pt0) REVERT: 2 422 THR cc_start: 0.4890 (OUTLIER) cc_final: 0.4073 (p) REVERT: 2 518 LEU cc_start: 0.3951 (OUTLIER) cc_final: 0.3707 (pp) REVERT: 2 572 ASP cc_start: 0.7669 (m-30) cc_final: 0.7331 (m-30) REVERT: 2 609 CYS cc_start: 0.2940 (OUTLIER) cc_final: 0.1333 (m) REVERT: 2 716 ASP cc_start: 0.7661 (m-30) cc_final: 0.7099 (t0) REVERT: 2 742 ARG cc_start: 0.9116 (mtt90) cc_final: 0.8892 (mtp180) REVERT: 2 745 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8926 (tm-30) REVERT: 2 797 LYS cc_start: 0.3376 (mttt) cc_final: 0.3172 (mttt) outliers start: 314 outliers final: 91 residues processed: 1354 average time/residue: 0.2571 time to fit residues: 552.5108 Evaluate side-chains 853 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 733 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 470 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 381 GLN 3 546 HIS 3 567 HIS 4 204 HIS 4 223 GLN 4 228 GLN 4 326 ASN 4 441 HIS 4 507 HIS ** 4 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 181 ASN 6 198 GLN 6 364 GLN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 513 GLN 5 128 ASN ** 5 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 456 HIS ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 GLN A 182 GLN A 296 HIS ** L 166 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN N 69 GLN N 142 GLN N 164 GLN N 180 HIS 2 211 ASN 2 227 HIS 2 352 GLN 2 364 GLN 2 450 GLN 2 496 HIS ** 2 758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.218971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.203505 restraints weight = 113055.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.204388 restraints weight = 100624.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.204954 restraints weight = 86588.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.205685 restraints weight = 74087.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.205761 restraints weight = 70790.595| |-----------------------------------------------------------------------------| r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5682 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 39752 Z= 0.216 Angle : 0.990 13.897 53739 Z= 0.515 Chirality : 0.055 0.441 6083 Planarity : 0.010 0.436 6914 Dihedral : 12.084 171.822 5485 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.36 % Favored : 86.58 % Rotamer: Outliers : 0.62 % Allowed : 7.90 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.67 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.92 (0.10), residues: 4775 helix: -2.99 (0.10), residues: 1448 sheet: -3.42 (0.21), residues: 409 loop : -3.58 (0.10), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG 7 219 TYR 0.038 0.003 TYR N 99 PHE 0.044 0.003 PHE A 482 TRP 0.025 0.002 TRP 7 519 HIS 0.018 0.002 HIS 7 459 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (39744) covalent geometry : angle 0.98969 / 0.51 (53737) SS BOND : bond 0.00362 / 0.19 ( 1) SS BOND : angle 3.41710 / 2.00 ( 2) hydrogen bonds : bond 0.05978 / 3.88 ( 889) hydrogen bonds : angle 7.74393 / 5.34 ( 2523) Misc. bond : bond 0.00816 / 0.40 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 982 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 956 time to evaluate : 1.459 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 47 ASN cc_start: 0.8038 (t0) cc_final: 0.7535 (t0) REVERT: 3 124 VAL cc_start: 0.6340 (t) cc_final: 0.5894 (m) REVERT: 3 130 LYS cc_start: 0.6493 (mtpt) cc_final: 0.5575 (mptt) REVERT: 3 238 TYR cc_start: 0.6178 (t80) cc_final: 0.5419 (t80) REVERT: 3 448 ASN cc_start: 0.6749 (t0) cc_final: 0.6371 (m-40) REVERT: 3 572 MET cc_start: 0.3577 (mmp) cc_final: 0.3163 (tpt) REVERT: 3 627 MET cc_start: 0.6254 (ptp) cc_final: 0.5045 (ptp) REVERT: 4 713 ILE cc_start: 0.7553 (mt) cc_final: 0.7199 (mm) REVERT: 7 174 LYS cc_start: 0.8360 (mmtm) cc_final: 0.8091 (mmmm) REVERT: 7 176 MET cc_start: 0.3788 (ttp) cc_final: 0.3514 (ttp) REVERT: 7 293 LEU cc_start: 0.7303 (mm) cc_final: 0.7049 (mm) REVERT: 7 369 MET cc_start: 0.6272 (tpt) cc_final: 0.4466 (mpp) REVERT: 7 397 LEU cc_start: 0.8700 (tt) cc_final: 0.8374 (tt) REVERT: 7 559 MET cc_start: 0.6901 (mtp) cc_final: 0.6657 (mtp) REVERT: 7 639 MET cc_start: 0.6898 (tpp) cc_final: 0.6203 (tpp) REVERT: 6 19 ILE cc_start: 0.7702 (mt) cc_final: 0.7227 (mt) REVERT: 6 69 LEU cc_start: 0.3739 (mp) cc_final: 0.3038 (mp) REVERT: 6 186 MET cc_start: 0.3750 (tpt) cc_final: 0.3299 (tpt) REVERT: 6 227 VAL cc_start: 0.8533 (t) cc_final: 0.8323 (p) REVERT: 6 442 MET cc_start: 0.4478 (ttt) cc_final: 0.3759 (mmp) REVERT: 6 486 ASN cc_start: 0.6668 (p0) cc_final: 0.5305 (p0) REVERT: 6 585 MET cc_start: 0.6592 (mmm) cc_final: 0.5384 (mmm) REVERT: 5 37 PHE cc_start: 0.7713 (t80) cc_final: 0.7266 (t80) REVERT: 5 39 ARG cc_start: 0.7636 (mtt180) cc_final: 0.7061 (mpp80) REVERT: 5 62 ARG cc_start: 0.7484 (mmt-90) cc_final: 0.7152 (mmt-90) REVERT: 5 260 ILE cc_start: 0.8000 (pt) cc_final: 0.7405 (pt) REVERT: 5 416 MET cc_start: 0.4902 (ppp) cc_final: 0.3834 (ptt) REVERT: 5 426 MET cc_start: 0.5725 (ptm) cc_final: 0.5442 (ppp) REVERT: 5 641 ARG cc_start: 0.7573 (mtt90) cc_final: 0.7169 (tmm-80) REVERT: A 9 ASP cc_start: 0.6884 (p0) cc_final: 0.6659 (p0) REVERT: A 267 ARG cc_start: 0.7007 (tpt90) cc_final: 0.6270 (mmp80) REVERT: A 276 ASN cc_start: 0.7721 (p0) cc_final: 0.6471 (t0) REVERT: A 281 SER cc_start: 0.6237 (m) cc_final: 0.5734 (p) REVERT: A 287 ASN cc_start: 0.5818 (t0) cc_final: 0.5149 (m-40) REVERT: A 348 VAL cc_start: 0.8549 (m) cc_final: 0.8322 (t) REVERT: A 349 LEU cc_start: 0.7229 (mp) cc_final: 0.6897 (mt) REVERT: A 376 LEU cc_start: 0.5338 (tp) cc_final: 0.5059 (tp) REVERT: A 378 TYR cc_start: 0.7817 (m-10) cc_final: 0.7540 (m-10) REVERT: A 408 ASP cc_start: 0.6817 (m-30) cc_final: 0.6595 (m-30) REVERT: A 424 LEU cc_start: 0.8333 (pp) cc_final: 0.8116 (pp) REVERT: A 568 ASP cc_start: 0.7732 (m-30) cc_final: 0.6883 (t0) REVERT: H 199 HIS cc_start: 0.6746 (p90) cc_final: 0.5220 (t-90) REVERT: L 75 LYS cc_start: 0.8302 (pptt) cc_final: 0.7995 (pptt) REVERT: L 109 ARG cc_start: 0.6910 (mmt180) cc_final: 0.6449 (ttm170) REVERT: L 123 ILE cc_start: 0.7931 (pt) cc_final: 0.7489 (pt) REVERT: L 125 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7328 (mp0) REVERT: L 159 ILE cc_start: 0.7157 (mp) cc_final: 0.6875 (mt) REVERT: M 169 GLU cc_start: 0.6966 (mp0) cc_final: 0.6516 (tp30) REVERT: N 48 ASN cc_start: 0.6589 (p0) cc_final: 0.6351 (p0) REVERT: N 73 MET cc_start: 0.6813 (tpp) cc_final: 0.6516 (tpp) REVERT: N 88 VAL cc_start: 0.7133 (t) cc_final: 0.6608 (p) REVERT: N 94 LEU cc_start: 0.8050 (tp) cc_final: 0.7115 (tp) REVERT: N 110 GLN cc_start: 0.6885 (tm-30) cc_final: 0.6659 (tm-30) REVERT: 2 277 GLU cc_start: 0.7524 (mp0) cc_final: 0.5625 (tm-30) REVERT: 2 294 LEU cc_start: 0.7082 (pt) cc_final: 0.6605 (pt) REVERT: 2 589 MET cc_start: 0.0997 (mtm) cc_final: 0.0483 (mtp) REVERT: 2 723 MET cc_start: 0.8414 (mmp) cc_final: 0.7867 (mmp) outliers start: 26 outliers final: 6 residues processed: 976 average time/residue: 0.2510 time to fit residues: 393.0958 Evaluate side-chains 693 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 687 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 74 optimal weight: 4.9990 chunk 462 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 323 optimal weight: 8.9990 chunk 55 optimal weight: 0.0980 chunk 354 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 451 optimal weight: 8.9990 chunk 474 optimal weight: 0.0270 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 GLN 3 579 GLN 4 204 HIS 4 500 GLN 4 625 GLN 4 656 GLN ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 536 HIS 6 67 GLN 6 285 ASN 6 296 GLN 6 320 GLN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 499 ASN 6 584 HIS ** 6 636 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 128 ASN 5 456 HIS 5 537 HIS 5 563 HIS A 44 HIS A 264 HIS A 325 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS H 36 GLN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 115 HIS M 131 HIS M 164 ASN N 162 ASN 2 211 ASN 2 450 GLN ** 2 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 758 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4809 r_free = 0.4809 target = 0.220501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.204689 restraints weight = 110368.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.206034 restraints weight = 98496.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.206443 restraints weight = 81160.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.206738 restraints weight = 72529.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.206975 restraints weight = 69408.390| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 39752 Z= 0.170 Angle : 0.859 12.861 53739 Z= 0.444 Chirality : 0.049 0.244 6083 Planarity : 0.007 0.181 6914 Dihedral : 11.324 171.337 5485 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.11 % Favored : 86.83 % Rotamer: Outliers : 0.28 % Allowed : 5.53 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.07 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.57 (0.10), residues: 4775 helix: -2.61 (0.11), residues: 1484 sheet: -3.07 (0.21), residues: 420 loop : -3.44 (0.10), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG 6 223 TYR 0.039 0.002 TYR 6 105 PHE 0.038 0.002 PHE A 482 TRP 0.014 0.001 TRP A 193 HIS 0.019 0.001 HIS H 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (39744) covalent geometry : angle 0.85851 / 0.44 (53737) SS BOND : bond 0.00204 / 0.11 ( 1) SS BOND : angle 2.20426 / 1.30 ( 2) hydrogen bonds : bond 0.05358 / 3.53 ( 889) hydrogen bonds : angle 7.15927 / 4.97 ( 2523) Misc. bond : bond 0.00484 / 0.23 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 859 time to evaluate : 1.455 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.6324 (t) cc_final: 0.5881 (m) REVERT: 3 130 LYS cc_start: 0.6646 (mtpt) cc_final: 0.5674 (mptt) REVERT: 3 220 ASP cc_start: 0.7619 (m-30) cc_final: 0.7238 (m-30) REVERT: 3 293 LEU cc_start: 0.7620 (tt) cc_final: 0.6698 (tt) REVERT: 3 572 MET cc_start: 0.4281 (mmp) cc_final: 0.2964 (tpt) REVERT: 3 579 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5796 (mm110) REVERT: 3 627 MET cc_start: 0.6326 (ptp) cc_final: 0.5420 (ptm) REVERT: 4 247 MET cc_start: 0.7962 (ttt) cc_final: 0.6924 (tpp) REVERT: 4 421 VAL cc_start: 0.7469 (t) cc_final: 0.6840 (t) REVERT: 4 660 PHE cc_start: 0.5852 (m-80) cc_final: 0.5293 (m-80) REVERT: 4 698 GLU cc_start: 0.6650 (tt0) cc_final: 0.5963 (tt0) REVERT: 4 762 GLU cc_start: 0.6551 (mm-30) cc_final: 0.6339 (mm-30) REVERT: 7 200 PHE cc_start: 0.7627 (t80) cc_final: 0.6902 (t80) REVERT: 7 221 TYR cc_start: 0.5962 (m-10) cc_final: 0.5712 (m-10) REVERT: 7 261 VAL cc_start: 0.8220 (t) cc_final: 0.7339 (t) REVERT: 7 369 MET cc_start: 0.6956 (tpt) cc_final: 0.4838 (mpp) REVERT: 7 397 LEU cc_start: 0.8681 (tt) cc_final: 0.8370 (tt) REVERT: 7 559 MET cc_start: 0.7083 (mtp) cc_final: 0.6794 (mtp) REVERT: 6 356 VAL cc_start: 0.7473 (m) cc_final: 0.7174 (m) REVERT: 6 459 GLN cc_start: 0.8122 (mp10) cc_final: 0.7897 (mp10) REVERT: 6 486 ASN cc_start: 0.6866 (p0) cc_final: 0.5844 (p0) REVERT: 6 503 ASP cc_start: 0.7234 (t70) cc_final: 0.6955 (t0) REVERT: 6 650 ARG cc_start: 0.7985 (tpt170) cc_final: 0.7763 (tpt90) REVERT: 5 62 ARG cc_start: 0.7476 (mmt-90) cc_final: 0.6977 (mmt-90) REVERT: 5 260 ILE cc_start: 0.7924 (pt) cc_final: 0.7518 (pt) REVERT: 5 314 ASP cc_start: 0.7435 (t70) cc_final: 0.7165 (t70) REVERT: 5 416 MET cc_start: 0.5143 (ppp) cc_final: 0.3897 (ptt) REVERT: 5 641 ARG cc_start: 0.7615 (mtt90) cc_final: 0.7271 (tmm-80) REVERT: A 275 GLN cc_start: 0.7108 (pm20) cc_final: 0.6724 (tp40) REVERT: A 276 ASN cc_start: 0.7803 (p0) cc_final: 0.6596 (t0) REVERT: A 281 SER cc_start: 0.6110 (m) cc_final: 0.5866 (p) REVERT: A 378 TYR cc_start: 0.7862 (m-10) cc_final: 0.7641 (m-10) REVERT: A 424 LEU cc_start: 0.8591 (pp) cc_final: 0.8370 (pp) REVERT: A 568 ASP cc_start: 0.7826 (m-30) cc_final: 0.6863 (t0) REVERT: H 145 ASN cc_start: 0.2274 (m-40) cc_final: 0.1631 (t0) REVERT: H 199 HIS cc_start: 0.6538 (p90) cc_final: 0.5918 (t-90) REVERT: L 75 LYS cc_start: 0.8297 (pptt) cc_final: 0.8056 (pptt) REVERT: L 84 PHE cc_start: 0.5041 (m-10) cc_final: 0.4420 (m-10) REVERT: L 109 ARG cc_start: 0.6901 (mmt180) cc_final: 0.6067 (ttt90) REVERT: L 159 ILE cc_start: 0.7405 (mp) cc_final: 0.7096 (mt) REVERT: M 162 ARG cc_start: 0.8678 (ttp-170) cc_final: 0.8412 (ttp-170) REVERT: M 166 GLN cc_start: 0.8434 (mp10) cc_final: 0.8090 (mp10) REVERT: M 169 GLU cc_start: 0.7202 (mp0) cc_final: 0.6914 (tp30) REVERT: 2 277 GLU cc_start: 0.7382 (mp0) cc_final: 0.7011 (mp0) REVERT: 2 294 LEU cc_start: 0.7163 (pt) cc_final: 0.6711 (pt) REVERT: 2 435 LYS cc_start: 0.8426 (tttt) cc_final: 0.8102 (tttm) REVERT: 2 663 PHE cc_start: 0.6148 (m-80) cc_final: 0.5867 (m-10) REVERT: 2 723 MET cc_start: 0.8553 (mmp) cc_final: 0.8196 (mmp) REVERT: 2 797 LYS cc_start: 0.4619 (mttt) cc_final: 0.4321 (mttt) outliers start: 12 outliers final: 4 residues processed: 867 average time/residue: 0.2408 time to fit residues: 337.6345 Evaluate side-chains 659 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 654 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 178 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 376 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 312 optimal weight: 20.0000 chunk 235 optimal weight: 2.9990 chunk 209 optimal weight: 0.2980 chunk 460 optimal weight: 6.9990 chunk 473 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 441 HIS ** 4 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 240 HIS ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 389 GLN ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 533 ASN 6 589 ASN 6 636 HIS 6 645 ASN ** 5 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 128 ASN 5 261 GLN 5 563 HIS A 264 HIS ** A 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 154 HIS M 164 ASN N 117 GLN 2 211 ASN 2 450 GLN 2 516 GLN ** 2 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 606 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.216661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.201099 restraints weight = 111226.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.201792 restraints weight = 99691.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.202127 restraints weight = 84663.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.202341 restraints weight = 76288.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.202526 restraints weight = 74983.605| |-----------------------------------------------------------------------------| r_work (final): 0.4613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 39752 Z= 0.189 Angle : 0.842 11.397 53739 Z= 0.437 Chirality : 0.049 0.234 6083 Planarity : 0.006 0.073 6914 Dihedral : 10.892 172.397 5485 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.70 % Favored : 86.26 % Rotamer: Outliers : 0.28 % Allowed : 6.15 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.10), residues: 4775 helix: -2.37 (0.12), residues: 1475 sheet: -3.03 (0.20), residues: 452 loop : -3.25 (0.10), residues: 2848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 5 361 TYR 0.039 0.002 TYR 7 33 PHE 0.040 0.002 PHE A 482 TRP 0.013 0.002 TRP L 47 HIS 0.009 0.002 HIS H 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (39744) covalent geometry : angle 0.84173 / 0.44 (53737) SS BOND : bond 0.01028 / 0.54 ( 1) SS BOND : angle 2.68518 / 1.58 ( 2) hydrogen bonds : bond 0.04972 / 3.28 ( 889) hydrogen bonds : angle 6.81897 / 4.75 ( 2523) Misc. bond : bond 0.00219 / 0.09 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 824 time to evaluate : 1.570 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.6637 (t) cc_final: 0.6134 (m) REVERT: 3 130 LYS cc_start: 0.6631 (mtpt) cc_final: 0.5647 (mptt) REVERT: 3 219 ASP cc_start: 0.7833 (t0) cc_final: 0.7507 (t0) REVERT: 3 220 ASP cc_start: 0.7720 (m-30) cc_final: 0.7388 (m-30) REVERT: 3 572 MET cc_start: 0.4510 (mmp) cc_final: 0.3075 (tpt) REVERT: 3 627 MET cc_start: 0.6429 (ptp) cc_final: 0.5760 (ptm) REVERT: 4 247 MET cc_start: 0.8090 (ttt) cc_final: 0.6979 (tpp) REVERT: 4 356 LYS cc_start: 0.8323 (ttmm) cc_final: 0.8122 (ttpt) REVERT: 4 363 ASP cc_start: 0.7009 (t0) cc_final: 0.6780 (t0) REVERT: 4 500 GLN cc_start: 0.6792 (tp-100) cc_final: 0.6552 (tp-100) REVERT: 4 698 GLU cc_start: 0.6887 (tt0) cc_final: 0.5585 (tt0) REVERT: 7 157 ILE cc_start: 0.7669 (mm) cc_final: 0.7326 (mm) REVERT: 7 369 MET cc_start: 0.6755 (tpt) cc_final: 0.4951 (mpp) REVERT: 7 397 LEU cc_start: 0.8625 (tt) cc_final: 0.8330 (tt) REVERT: 7 419 MET cc_start: 0.2627 (ttt) cc_final: 0.2423 (ttt) REVERT: 7 559 MET cc_start: 0.7117 (mtp) cc_final: 0.6822 (mtp) REVERT: 6 186 MET cc_start: 0.3860 (tpt) cc_final: 0.3564 (tpt) REVERT: 6 459 GLN cc_start: 0.7961 (mp10) cc_final: 0.7452 (mp10) REVERT: 6 503 ASP cc_start: 0.7151 (t70) cc_final: 0.6851 (t0) REVERT: 6 636 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.5586 (m90) REVERT: 6 638 LYS cc_start: 0.7882 (ptmm) cc_final: 0.7656 (ptpp) REVERT: 6 643 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.6713 (pt) REVERT: 6 650 ARG cc_start: 0.8042 (tpt170) cc_final: 0.7659 (tpt90) REVERT: 5 62 ARG cc_start: 0.7595 (mmt-90) cc_final: 0.7169 (ttm-80) REVERT: 5 361 ARG cc_start: 0.8564 (mmp-170) cc_final: 0.8294 (mmp80) REVERT: 5 426 MET cc_start: 0.5871 (ppp) cc_final: 0.5380 (ppp) REVERT: 5 459 MET cc_start: 0.7335 (ppp) cc_final: 0.6841 (ppp) REVERT: 5 641 ARG cc_start: 0.7693 (mtt90) cc_final: 0.7302 (tmm-80) REVERT: A 59 LYS cc_start: 0.0949 (tptt) cc_final: 0.0648 (tptt) REVERT: A 276 ASN cc_start: 0.8035 (p0) cc_final: 0.6892 (t0) REVERT: A 378 TYR cc_start: 0.7718 (m-10) cc_final: 0.7468 (m-10) REVERT: A 568 ASP cc_start: 0.7880 (m-30) cc_final: 0.6837 (t0) REVERT: H 46 GLU cc_start: 0.8190 (mp0) cc_final: 0.7933 (mp0) REVERT: H 199 HIS cc_start: 0.6382 (p90) cc_final: 0.6119 (t-90) REVERT: L 14 MET cc_start: 0.3214 (mtm) cc_final: 0.2993 (mtm) REVERT: L 159 ILE cc_start: 0.7473 (mp) cc_final: 0.7174 (mt) REVERT: M 126 ARG cc_start: 0.6979 (tpt-90) cc_final: 0.6270 (tpt90) REVERT: M 162 ARG cc_start: 0.8788 (ttp-170) cc_final: 0.8372 (ttp-170) REVERT: M 166 GLN cc_start: 0.8377 (mp10) cc_final: 0.8090 (mp10) REVERT: N 92 MET cc_start: 0.7046 (ttm) cc_final: 0.6554 (ttm) REVERT: 2 277 GLU cc_start: 0.7391 (mp0) cc_final: 0.6969 (mp0) REVERT: 2 294 LEU cc_start: 0.7372 (pt) cc_final: 0.6934 (pt) REVERT: 2 384 LEU cc_start: 0.7323 (tt) cc_final: 0.6951 (mm) REVERT: 2 435 LYS cc_start: 0.8394 (tttt) cc_final: 0.8104 (tttm) outliers start: 12 outliers final: 4 residues processed: 832 average time/residue: 0.2447 time to fit residues: 330.1602 Evaluate side-chains 649 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 643 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 181 optimal weight: 10.0000 chunk 141 optimal weight: 0.0870 chunk 264 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 15 optimal weight: 0.0370 chunk 309 optimal weight: 1.9990 chunk 371 optimal weight: 5.9990 chunk 281 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 chunk 283 optimal weight: 0.0050 chunk 194 optimal weight: 0.0470 overall best weight: 0.1748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 500 GLN 4 595 GLN ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 389 GLN ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 383 ASN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 241 GLN 5 261 GLN 5 456 HIS ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS A 420 GLN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS L 154 HIS M 164 ASN 2 211 ASN 2 450 GLN 2 548 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.222072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.205231 restraints weight = 110864.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.206301 restraints weight = 95128.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.206975 restraints weight = 84485.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.207497 restraints weight = 70827.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.207786 restraints weight = 67384.611| |-----------------------------------------------------------------------------| r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5665 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39752 Z= 0.143 Angle : 0.776 11.883 53739 Z= 0.398 Chirality : 0.047 0.238 6083 Planarity : 0.006 0.063 6914 Dihedral : 10.545 172.523 5485 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.00 % Favored : 87.98 % Rotamer: Outliers : 0.17 % Allowed : 3.47 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.11), residues: 4775 helix: -2.21 (0.12), residues: 1506 sheet: -2.83 (0.20), residues: 480 loop : -3.18 (0.10), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 7 219 TYR 0.026 0.002 TYR 7 33 PHE 0.039 0.002 PHE 7 77 TRP 0.012 0.001 TRP A 193 HIS 0.009 0.001 HIS 5 456 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (39744) covalent geometry : angle 0.77631 / 0.40 (53737) SS BOND : bond 0.00245 / 0.13 ( 1) SS BOND : angle 2.57412 / 1.51 ( 2) hydrogen bonds : bond 0.04339 / 2.84 ( 889) hydrogen bonds : angle 6.49357 / 4.52 ( 2523) Misc. bond : bond 0.00308 / 0.15 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 828 time to evaluate : 1.562 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.6763 (t) cc_final: 0.6218 (m) REVERT: 3 130 LYS cc_start: 0.6410 (mtpt) cc_final: 0.5554 (mptt) REVERT: 3 572 MET cc_start: 0.4253 (mmp) cc_final: 0.2932 (tpt) REVERT: 3 627 MET cc_start: 0.6647 (ptp) cc_final: 0.6123 (ptm) REVERT: 4 593 MET cc_start: 0.6192 (mmp) cc_final: 0.5664 (mmp) REVERT: 4 713 ILE cc_start: 0.8251 (mm) cc_final: 0.7904 (mm) REVERT: 7 131 MET cc_start: 0.6373 (ptp) cc_final: 0.6131 (ptm) REVERT: 7 200 PHE cc_start: 0.7354 (t80) cc_final: 0.6689 (t80) REVERT: 7 369 MET cc_start: 0.6593 (tpt) cc_final: 0.5082 (mpp) REVERT: 7 559 MET cc_start: 0.7126 (mtp) cc_final: 0.6739 (mtp) REVERT: 7 561 ARG cc_start: 0.6663 (mtp85) cc_final: 0.6429 (mtt-85) REVERT: 6 459 GLN cc_start: 0.7730 (mp10) cc_final: 0.7277 (mp10) REVERT: 6 503 ASP cc_start: 0.7023 (t70) cc_final: 0.6717 (t0) REVERT: 6 548 HIS cc_start: 0.4730 (m90) cc_final: 0.4348 (m170) REVERT: 5 62 ARG cc_start: 0.7261 (mmt-90) cc_final: 0.6972 (mmt-90) REVERT: 5 116 MET cc_start: 0.5671 (ttp) cc_final: 0.4999 (tmm) REVERT: 5 314 ASP cc_start: 0.7532 (t70) cc_final: 0.7323 (t70) REVERT: 5 426 MET cc_start: 0.6162 (ppp) cc_final: 0.5950 (ppp) REVERT: 5 513 MET cc_start: 0.4139 (mmm) cc_final: 0.3874 (mtt) REVERT: A 9 ASP cc_start: 0.6295 (p0) cc_final: 0.6007 (p0) REVERT: A 18 ARG cc_start: 0.4750 (ptp-170) cc_final: 0.3991 (ptp-170) REVERT: A 59 LYS cc_start: 0.1018 (tptt) cc_final: 0.0796 (tptt) REVERT: A 276 ASN cc_start: 0.7329 (p0) cc_final: 0.6596 (t0) REVERT: A 331 MET cc_start: 0.7617 (ppp) cc_final: 0.7259 (ppp) REVERT: A 347 LEU cc_start: 0.8338 (pp) cc_final: 0.7867 (tp) REVERT: A 349 LEU cc_start: 0.7928 (mp) cc_final: 0.7658 (mt) REVERT: A 478 LEU cc_start: 0.7607 (mt) cc_final: 0.7303 (mt) REVERT: A 514 CYS cc_start: 0.5651 (m) cc_final: 0.5230 (t) REVERT: A 568 ASP cc_start: 0.8164 (m-30) cc_final: 0.7049 (t0) REVERT: L 125 GLU cc_start: 0.7815 (mp0) cc_final: 0.7416 (mp0) REVERT: L 159 ILE cc_start: 0.7199 (mp) cc_final: 0.6722 (mt) REVERT: M 126 ARG cc_start: 0.6596 (tpt-90) cc_final: 0.6164 (tpt90) REVERT: N 62 MET cc_start: 0.6481 (tpp) cc_final: 0.6190 (tpp) REVERT: N 92 MET cc_start: 0.6557 (ttm) cc_final: 0.5938 (ttm) REVERT: 2 294 LEU cc_start: 0.7113 (pt) cc_final: 0.6708 (pt) REVERT: 2 348 ILE cc_start: 0.8409 (pt) cc_final: 0.7885 (pt) REVERT: 2 384 LEU cc_start: 0.7130 (tt) cc_final: 0.6835 (mm) REVERT: 2 723 MET cc_start: 0.8399 (mmp) cc_final: 0.8192 (mmp) outliers start: 7 outliers final: 3 residues processed: 833 average time/residue: 0.2477 time to fit residues: 335.2607 Evaluate side-chains 653 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 650 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 351 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 147 optimal weight: 0.4980 chunk 262 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 204 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 423 GLN ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 345 ASN 4 596 GLN ** 4 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 383 ASN ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 645 ASN 5 128 ASN 5 563 HIS ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN H 48 ASN H 195 GLN L 154 HIS M 164 ASN 2 450 GLN 2 516 GLN 2 758 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.221417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.204445 restraints weight = 110921.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.205802 restraints weight = 93615.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.206142 restraints weight = 77501.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.206587 restraints weight = 72160.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.206843 restraints weight = 66186.611| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39752 Z= 0.138 Angle : 0.757 13.543 53739 Z= 0.385 Chirality : 0.047 0.237 6083 Planarity : 0.008 0.466 6914 Dihedral : 10.399 173.739 5485 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.40 % Favored : 87.58 % Rotamer: Outliers : 0.14 % Allowed : 3.11 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.97 (0.11), residues: 4775 helix: -2.03 (0.12), residues: 1518 sheet: -2.65 (0.22), residues: 460 loop : -3.12 (0.10), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG 2 698 TYR 0.025 0.002 TYR 7 33 PHE 0.035 0.002 PHE A 482 TRP 0.017 0.002 TRP H 97 HIS 0.013 0.001 HIS 5 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (39744) covalent geometry : angle 0.75598 / 0.39 (53737) SS BOND : bond 0.04797 / 2.52 ( 1) SS BOND : angle 4.77582 / 2.81 ( 2) hydrogen bonds : bond 0.04122 / 2.68 ( 889) hydrogen bonds : angle 6.33638 / 4.41 ( 2523) Misc. bond : bond 0.00057 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 782 time to evaluate : 1.538 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.6937 (t) cc_final: 0.6453 (m) REVERT: 3 130 LYS cc_start: 0.6389 (mtpt) cc_final: 0.5491 (mptt) REVERT: 3 215 ASP cc_start: 0.8769 (p0) cc_final: 0.8540 (p0) REVERT: 3 219 ASP cc_start: 0.7602 (t0) cc_final: 0.7060 (t0) REVERT: 3 220 ASP cc_start: 0.7615 (m-30) cc_final: 0.6955 (p0) REVERT: 3 405 GLU cc_start: 0.6427 (mp0) cc_final: 0.6068 (mp0) REVERT: 3 462 GLU cc_start: 0.5321 (mm-30) cc_final: 0.4804 (mm-30) REVERT: 3 572 MET cc_start: 0.4408 (mmp) cc_final: 0.2980 (tpt) REVERT: 3 624 ARG cc_start: 0.5381 (ttt180) cc_final: 0.5171 (ttt90) REVERT: 3 627 MET cc_start: 0.6771 (ptp) cc_final: 0.6050 (ptm) REVERT: 4 363 ASP cc_start: 0.6772 (t0) cc_final: 0.6455 (t0) REVERT: 4 698 GLU cc_start: 0.6675 (tt0) cc_final: 0.6313 (tt0) REVERT: 4 713 ILE cc_start: 0.8312 (mm) cc_final: 0.7948 (mm) REVERT: 7 369 MET cc_start: 0.6597 (tpt) cc_final: 0.5157 (mpp) REVERT: 7 559 MET cc_start: 0.7127 (mtp) cc_final: 0.6760 (mtp) REVERT: 6 235 ARG cc_start: 0.6190 (tpp-160) cc_final: 0.5606 (tpp-160) REVERT: 6 321 MET cc_start: 0.4219 (ptp) cc_final: 0.3739 (ptp) REVERT: 6 459 GLN cc_start: 0.7921 (mp10) cc_final: 0.7327 (mp10) REVERT: 6 503 ASP cc_start: 0.7040 (t70) cc_final: 0.6743 (t0) REVERT: 6 548 HIS cc_start: 0.5044 (m90) cc_final: 0.4651 (m170) REVERT: 6 585 MET cc_start: 0.7526 (mpp) cc_final: 0.6857 (mmm) REVERT: 5 62 ARG cc_start: 0.7395 (mmt-90) cc_final: 0.7021 (mtt90) REVERT: 5 116 MET cc_start: 0.5549 (ttp) cc_final: 0.5143 (ttp) REVERT: 5 353 MET cc_start: 0.8230 (tpt) cc_final: 0.7987 (tpt) REVERT: 5 426 MET cc_start: 0.6214 (ppp) cc_final: 0.5898 (ppp) REVERT: 5 456 HIS cc_start: 0.7234 (t-90) cc_final: 0.6649 (t-170) REVERT: A 276 ASN cc_start: 0.7289 (p0) cc_final: 0.6382 (t0) REVERT: A 347 LEU cc_start: 0.8006 (pp) cc_final: 0.7753 (tp) REVERT: A 349 LEU cc_start: 0.7829 (mp) cc_final: 0.7569 (mt) REVERT: A 478 LEU cc_start: 0.7832 (mt) cc_final: 0.7552 (mt) REVERT: A 514 CYS cc_start: 0.5551 (m) cc_final: 0.5031 (t) REVERT: A 568 ASP cc_start: 0.8271 (m-30) cc_final: 0.7144 (t0) REVERT: L 125 GLU cc_start: 0.7833 (mp0) cc_final: 0.7551 (mp0) REVERT: L 159 ILE cc_start: 0.7412 (mp) cc_final: 0.7116 (mt) REVERT: M 126 ARG cc_start: 0.6630 (tpt-90) cc_final: 0.6126 (tpt90) REVERT: 2 294 LEU cc_start: 0.7180 (pt) cc_final: 0.6819 (pt) REVERT: 2 348 ILE cc_start: 0.8428 (pt) cc_final: 0.7831 (pt) REVERT: 2 624 PRO cc_start: 0.6537 (Cg_exo) cc_final: 0.5613 (Cg_endo) outliers start: 6 outliers final: 4 residues processed: 784 average time/residue: 0.2414 time to fit residues: 308.7842 Evaluate side-chains 638 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 634 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 284 optimal weight: 0.0470 chunk 426 optimal weight: 2.9990 chunk 340 optimal weight: 9.9990 chunk 380 optimal weight: 0.0770 chunk 413 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 365 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 415 optimal weight: 3.9990 chunk 317 optimal weight: 2.9990 chunk 194 optimal weight: 0.0060 overall best weight: 0.3452 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 567 HIS 4 204 HIS ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 472 GLN 6 589 ASN 6 592 HIS 5 128 ASN ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 ASN H 195 GLN M 164 ASN 2 450 GLN 2 516 GLN 2 666 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.222622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.204566 restraints weight = 107636.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.206221 restraints weight = 86701.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.207623 restraints weight = 69780.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.208065 restraints weight = 58395.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.208286 restraints weight = 55042.104| |-----------------------------------------------------------------------------| r_work (final): 0.4672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5676 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 39752 Z= 0.135 Angle : 0.753 13.502 53739 Z= 0.382 Chirality : 0.046 0.224 6083 Planarity : 0.005 0.146 6914 Dihedral : 10.359 174.010 5485 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.66 % Favored : 88.31 % Rotamer: Outliers : 0.09 % Allowed : 2.59 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.11), residues: 4775 helix: -1.83 (0.12), residues: 1499 sheet: -2.42 (0.23), residues: 436 loop : -3.05 (0.10), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.001 ARG 6 263 TYR 0.030 0.002 TYR H 84 PHE 0.037 0.002 PHE 7 77 TRP 0.016 0.001 TRP H 97 HIS 0.010 0.001 HIS 6 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (39744) covalent geometry : angle 0.75292 / 0.38 (53737) SS BOND : bond 0.00170 / 0.09 ( 1) SS BOND : angle 3.15173 / 1.85 ( 2) hydrogen bonds : bond 0.03982 / 2.63 ( 889) hydrogen bonds : angle 6.18518 / 4.30 ( 2523) Misc. bond : bond 0.00097 / 0.05 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 785 time to evaluate : 1.495 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.7207 (t) cc_final: 0.6759 (m) REVERT: 3 130 LYS cc_start: 0.6314 (mtpt) cc_final: 0.5437 (mptt) REVERT: 3 215 ASP cc_start: 0.8711 (p0) cc_final: 0.8504 (p0) REVERT: 3 220 ASP cc_start: 0.7570 (m-30) cc_final: 0.7345 (m-30) REVERT: 3 405 GLU cc_start: 0.6599 (mp0) cc_final: 0.5980 (mp0) REVERT: 3 462 GLU cc_start: 0.5337 (mm-30) cc_final: 0.4951 (mm-30) REVERT: 3 572 MET cc_start: 0.4427 (mmp) cc_final: 0.3150 (tpt) REVERT: 3 627 MET cc_start: 0.6751 (ptp) cc_final: 0.5938 (ptm) REVERT: 4 363 ASP cc_start: 0.6931 (t0) cc_final: 0.6700 (t0) REVERT: 4 380 ASP cc_start: 0.7351 (p0) cc_final: 0.6398 (p0) REVERT: 4 698 GLU cc_start: 0.6432 (tt0) cc_final: 0.6032 (tt0) REVERT: 4 713 ILE cc_start: 0.8317 (mm) cc_final: 0.7979 (mm) REVERT: 7 369 MET cc_start: 0.6712 (tpt) cc_final: 0.5540 (mpp) REVERT: 7 559 MET cc_start: 0.6980 (mtp) cc_final: 0.6645 (mtp) REVERT: 6 235 ARG cc_start: 0.5987 (tpp-160) cc_final: 0.5301 (tpp-160) REVERT: 6 321 MET cc_start: 0.3977 (ptp) cc_final: 0.3559 (ptp) REVERT: 6 459 GLN cc_start: 0.7764 (mp10) cc_final: 0.7321 (mp10) REVERT: 6 503 ASP cc_start: 0.6979 (t70) cc_final: 0.6713 (t0) REVERT: 6 548 HIS cc_start: 0.4865 (m90) cc_final: 0.4546 (m170) REVERT: 5 47 PHE cc_start: 0.1460 (m-80) cc_final: 0.0742 (m-80) REVERT: 5 314 ASP cc_start: 0.7481 (t70) cc_final: 0.7279 (t70) REVERT: 5 353 MET cc_start: 0.8233 (tpt) cc_final: 0.7929 (tpt) REVERT: 5 416 MET cc_start: 0.5574 (ppp) cc_final: 0.4179 (ptm) REVERT: 5 426 MET cc_start: 0.6170 (ppp) cc_final: 0.5840 (ppp) REVERT: 5 456 HIS cc_start: 0.7338 (t-90) cc_final: 0.6587 (t-170) REVERT: A 45 MET cc_start: 0.3554 (mtp) cc_final: 0.3238 (ttt) REVERT: A 230 MET cc_start: 0.7207 (mmp) cc_final: 0.6988 (mmp) REVERT: A 276 ASN cc_start: 0.7133 (p0) cc_final: 0.6565 (t0) REVERT: A 331 MET cc_start: 0.7276 (ppp) cc_final: 0.6691 (ppp) REVERT: A 347 LEU cc_start: 0.7951 (pp) cc_final: 0.7702 (tp) REVERT: A 478 LEU cc_start: 0.7938 (mt) cc_final: 0.7486 (mt) REVERT: A 514 CYS cc_start: 0.5611 (m) cc_final: 0.5336 (t) REVERT: A 547 LEU cc_start: 0.7760 (mp) cc_final: 0.7443 (mp) REVERT: A 568 ASP cc_start: 0.8171 (m-30) cc_final: 0.7082 (t0) REVERT: L 125 GLU cc_start: 0.7782 (mp0) cc_final: 0.7547 (mp0) REVERT: L 159 ILE cc_start: 0.7559 (mp) cc_final: 0.7190 (mt) REVERT: M 126 ARG cc_start: 0.6562 (tpt-90) cc_final: 0.6094 (tpt90) REVERT: 2 212 MET cc_start: 0.7323 (mmp) cc_final: 0.7113 (mmp) REVERT: 2 294 LEU cc_start: 0.7103 (pt) cc_final: 0.6714 (pt) REVERT: 2 348 ILE cc_start: 0.8428 (pt) cc_final: 0.7857 (pt) REVERT: 2 624 PRO cc_start: 0.6763 (Cg_exo) cc_final: 0.5822 (Cg_endo) outliers start: 4 outliers final: 3 residues processed: 787 average time/residue: 0.2423 time to fit residues: 310.7869 Evaluate side-chains 635 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 632 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 445 optimal weight: 5.9990 chunk 459 optimal weight: 0.1980 chunk 247 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 323 optimal weight: 0.0010 chunk 225 optimal weight: 0.6980 chunk 370 optimal weight: 0.0060 chunk 53 optimal weight: 0.5980 chunk 260 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS 4 500 GLN ** 4 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 645 ASN 5 60 ASN 5 563 HIS ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN A 206 GLN A 264 HIS A 444 GLN H 48 ASN H 71 HIS M 164 ASN N 117 GLN 2 450 GLN 2 516 GLN 2 548 ASN 2 668 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.222892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.204896 restraints weight = 107085.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.205921 restraints weight = 86083.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.207055 restraints weight = 74804.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.207822 restraints weight = 62536.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.208148 restraints weight = 58283.681| |-----------------------------------------------------------------------------| r_work (final): 0.4664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.6547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39752 Z= 0.130 Angle : 0.748 14.130 53739 Z= 0.377 Chirality : 0.046 0.234 6083 Planarity : 0.005 0.077 6914 Dihedral : 10.257 174.564 5485 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.41 % Favored : 88.57 % Rotamer: Outliers : 0.14 % Allowed : 1.50 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.11), residues: 4775 helix: -1.80 (0.12), residues: 1497 sheet: -2.40 (0.23), residues: 454 loop : -2.99 (0.10), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 7 219 TYR 0.035 0.002 TYR H 84 PHE 0.029 0.001 PHE A 482 TRP 0.023 0.001 TRP L 47 HIS 0.007 0.001 HIS A 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (39744) covalent geometry : angle 0.74736 / 0.38 (53737) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 2.59823 / 1.53 ( 2) hydrogen bonds : bond 0.03848 / 2.52 ( 889) hydrogen bonds : angle 6.03859 / 4.21 ( 2523) Misc. bond : bond 0.00042 / 0.03 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 758 time to evaluate : 1.666 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 TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.7280 (t) cc_final: 0.6770 (m) REVERT: 3 130 LYS cc_start: 0.6548 (mtpt) cc_final: 0.5595 (mptt) REVERT: 3 220 ASP cc_start: 0.7581 (m-30) cc_final: 0.7200 (m-30) REVERT: 3 405 GLU cc_start: 0.6429 (mp0) cc_final: 0.5641 (mp0) REVERT: 3 421 MET cc_start: 0.7419 (mmt) cc_final: 0.6874 (mmt) REVERT: 3 572 MET cc_start: 0.4467 (mmp) cc_final: 0.3119 (tpt) REVERT: 3 627 MET cc_start: 0.6661 (ptp) cc_final: 0.5788 (ptm) REVERT: 3 628 SER cc_start: 0.7411 (m) cc_final: 0.7022 (p) REVERT: 4 403 LYS cc_start: 0.6077 (ttpt) cc_final: 0.5752 (tppt) REVERT: 4 698 GLU cc_start: 0.6502 (tt0) cc_final: 0.6071 (tt0) REVERT: 4 713 ILE cc_start: 0.8321 (mm) cc_final: 0.7975 (mm) REVERT: 7 369 MET cc_start: 0.6767 (tpt) cc_final: 0.5420 (mpp) REVERT: 7 559 MET cc_start: 0.7104 (mtp) cc_final: 0.6816 (mtp) REVERT: 6 186 MET cc_start: 0.4000 (tpt) cc_final: 0.3275 (mmm) REVERT: 6 219 GLU cc_start: 0.7994 (mp0) cc_final: 0.7680 (mp0) REVERT: 6 459 GLN cc_start: 0.7817 (mp10) cc_final: 0.7207 (mp10) REVERT: 6 503 ASP cc_start: 0.6897 (t70) cc_final: 0.6627 (t0) REVERT: 6 548 HIS cc_start: 0.5061 (m90) cc_final: 0.4722 (m170) REVERT: 6 638 LYS cc_start: 0.7569 (pttm) cc_final: 0.7216 (pttp) REVERT: 5 47 PHE cc_start: 0.1134 (m-80) cc_final: 0.0506 (m-80) REVERT: 5 62 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7325 (mmt-90) REVERT: 5 416 MET cc_start: 0.5519 (ppp) cc_final: 0.4265 (ptt) REVERT: 5 426 MET cc_start: 0.6140 (ppp) cc_final: 0.5789 (ppp) REVERT: 5 456 HIS cc_start: 0.7398 (t-90) cc_final: 0.6753 (t-170) REVERT: 5 459 MET cc_start: 0.7094 (ppp) cc_final: 0.6858 (ppp) REVERT: 5 474 THR cc_start: 0.7549 (m) cc_final: 0.6555 (p) REVERT: A 230 MET cc_start: 0.7248 (mmp) cc_final: 0.6979 (mmp) REVERT: A 276 ASN cc_start: 0.7290 (p0) cc_final: 0.6642 (t0) REVERT: A 331 MET cc_start: 0.7326 (ppp) cc_final: 0.6806 (ppp) REVERT: A 349 LEU cc_start: 0.7702 (mt) cc_final: 0.7500 (mt) REVERT: A 478 LEU cc_start: 0.7860 (mt) cc_final: 0.7460 (mt) REVERT: A 514 CYS cc_start: 0.5837 (m) cc_final: 0.5402 (t) REVERT: A 547 LEU cc_start: 0.7761 (mp) cc_final: 0.7483 (mp) REVERT: A 568 ASP cc_start: 0.8125 (m-30) cc_final: 0.6989 (t0) REVERT: L 46 LEU cc_start: 0.6012 (mm) cc_final: 0.5663 (mm) REVERT: L 125 GLU cc_start: 0.7632 (mp0) cc_final: 0.7351 (mp0) REVERT: L 146 ASP cc_start: 0.4397 (t70) cc_final: 0.4113 (t70) REVERT: L 159 ILE cc_start: 0.7509 (mp) cc_final: 0.7052 (mt) REVERT: M 126 ARG cc_start: 0.6571 (tpt-90) cc_final: 0.6130 (tpt90) REVERT: M 162 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.8217 (ttp-170) REVERT: 2 294 LEU cc_start: 0.6990 (pt) cc_final: 0.6665 (pt) REVERT: 2 348 ILE cc_start: 0.8457 (pt) cc_final: 0.7843 (pt) REVERT: 2 358 TYR cc_start: 0.5070 (t80) cc_final: 0.4309 (t80) REVERT: 2 624 PRO cc_start: 0.6645 (Cg_exo) cc_final: 0.5711 (Cg_endo) outliers start: 6 outliers final: 3 residues processed: 761 average time/residue: 0.2369 time to fit residues: 294.8988 Evaluate side-chains 625 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 622 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 chunk 458 optimal weight: 0.9990 chunk 6 optimal weight: 0.0270 chunk 405 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 370 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 chunk 468 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 466 HIS ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS H 48 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 127 GLN M 164 ASN 2 227 HIS 2 450 GLN 2 516 GLN 2 548 ASN 2 606 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.223740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.207150 restraints weight = 111589.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.208064 restraints weight = 95819.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.208777 restraints weight = 81058.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.209733 restraints weight = 70243.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.209769 restraints weight = 65526.410| |-----------------------------------------------------------------------------| r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 39752 Z= 0.130 Angle : 0.754 15.781 53739 Z= 0.380 Chirality : 0.046 0.212 6083 Planarity : 0.005 0.071 6914 Dihedral : 10.147 174.867 5485 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.89 % Favored : 89.09 % Rotamer: Outliers : 0.14 % Allowed : 1.04 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.11), residues: 4775 helix: -1.65 (0.13), residues: 1479 sheet: -2.48 (0.22), residues: 465 loop : -2.89 (0.10), residues: 2831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 4 227 TYR 0.025 0.001 TYR L 30 PHE 0.039 0.002 PHE 7 77 TRP 0.016 0.001 TRP L 47 HIS 0.012 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (39744) covalent geometry : angle 0.75407 / 0.38 (53737) SS BOND : bond 0.00002 / 0.00 ( 1) SS BOND : angle 2.35614 / 1.38 ( 2) hydrogen bonds : bond 0.03867 / 2.60 ( 889) hydrogen bonds : angle 5.92898 / 4.14 ( 2523) Misc. bond : bond 0.00074 / 0.04 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 764 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.7241 (t) cc_final: 0.6753 (m) REVERT: 3 130 LYS cc_start: 0.6265 (mtpt) cc_final: 0.5271 (mptt) REVERT: 3 197 THR cc_start: 0.4291 (p) cc_final: 0.4062 (p) REVERT: 3 220 ASP cc_start: 0.7425 (m-30) cc_final: 0.7129 (m-30) REVERT: 3 405 GLU cc_start: 0.6686 (mp0) cc_final: 0.6383 (mp0) REVERT: 3 572 MET cc_start: 0.4472 (mmp) cc_final: 0.3051 (tpt) REVERT: 3 627 MET cc_start: 0.6986 (ptp) cc_final: 0.6135 (ptm) REVERT: 3 628 SER cc_start: 0.7392 (m) cc_final: 0.6947 (p) REVERT: 4 380 ASP cc_start: 0.7337 (p0) cc_final: 0.6331 (p0) REVERT: 4 403 LYS cc_start: 0.6101 (ttpt) cc_final: 0.5729 (tppt) REVERT: 4 415 TYR cc_start: 0.5874 (m-80) cc_final: 0.5260 (m-80) REVERT: 4 698 GLU cc_start: 0.6570 (tt0) cc_final: 0.6144 (tt0) REVERT: 4 713 ILE cc_start: 0.8273 (mm) cc_final: 0.7959 (mm) REVERT: 7 174 LYS cc_start: 0.8139 (tptm) cc_final: 0.7732 (mmmm) REVERT: 7 369 MET cc_start: 0.5569 (tpt) cc_final: 0.4714 (mpp) REVERT: 6 186 MET cc_start: 0.3915 (tpt) cc_final: 0.3232 (mmm) REVERT: 6 219 GLU cc_start: 0.7846 (mp0) cc_final: 0.7641 (mp0) REVERT: 6 459 GLN cc_start: 0.7855 (mp10) cc_final: 0.7180 (mp10) REVERT: 6 503 ASP cc_start: 0.6826 (t70) cc_final: 0.6558 (t0) REVERT: 6 548 HIS cc_start: 0.4887 (m90) cc_final: 0.4586 (m170) REVERT: 6 638 LYS cc_start: 0.7478 (pttm) cc_final: 0.6880 (ptmm) REVERT: 5 32 LYS cc_start: 0.7063 (mmtm) cc_final: 0.6719 (mmtm) REVERT: 5 47 PHE cc_start: 0.0878 (m-80) cc_final: 0.0353 (m-80) REVERT: 5 62 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7482 (mmt-90) REVERT: 5 416 MET cc_start: 0.5244 (ppp) cc_final: 0.3887 (ptm) REVERT: 5 426 MET cc_start: 0.6172 (ppp) cc_final: 0.5836 (ppp) REVERT: 5 456 HIS cc_start: 0.7324 (t-90) cc_final: 0.6776 (t-170) REVERT: 5 474 THR cc_start: 0.7502 (m) cc_final: 0.6471 (p) REVERT: 5 561 TYR cc_start: 0.6786 (t80) cc_final: 0.6318 (t80) REVERT: A 230 MET cc_start: 0.7239 (mmp) cc_final: 0.7002 (mmp) REVERT: A 259 GLU cc_start: 0.8613 (pt0) cc_final: 0.8361 (tm-30) REVERT: A 276 ASN cc_start: 0.6612 (p0) cc_final: 0.6247 (t0) REVERT: A 331 MET cc_start: 0.7498 (ppp) cc_final: 0.6972 (ppp) REVERT: A 349 LEU cc_start: 0.7687 (mt) cc_final: 0.7402 (mt) REVERT: A 513 MET cc_start: 0.2413 (mmp) cc_final: 0.2039 (mmt) REVERT: A 547 LEU cc_start: 0.7766 (mp) cc_final: 0.7470 (mp) REVERT: A 568 ASP cc_start: 0.8068 (m-30) cc_final: 0.6977 (t0) REVERT: H 42 LYS cc_start: 0.7230 (mttt) cc_final: 0.6577 (mtpp) REVERT: L 46 LEU cc_start: 0.6007 (mm) cc_final: 0.5567 (mm) REVERT: L 125 GLU cc_start: 0.7656 (mp0) cc_final: 0.7282 (mp0) REVERT: L 155 SER cc_start: 0.8278 (m) cc_final: 0.7552 (t) REVERT: L 159 ILE cc_start: 0.7547 (mp) cc_final: 0.7157 (mt) REVERT: 2 294 LEU cc_start: 0.6886 (pt) cc_final: 0.6513 (pt) REVERT: 2 348 ILE cc_start: 0.8493 (pt) cc_final: 0.7905 (pt) REVERT: 2 358 TYR cc_start: 0.4966 (t80) cc_final: 0.4259 (t80) REVERT: 2 624 PRO cc_start: 0.6421 (Cg_exo) cc_final: 0.5542 (Cg_endo) outliers start: 6 outliers final: 4 residues processed: 768 average time/residue: 0.2399 time to fit residues: 300.9999 Evaluate side-chains 618 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 614 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 351 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 384 optimal weight: 0.9990 chunk 321 optimal weight: 0.5980 chunk 474 optimal weight: 9.9990 chunk 352 optimal weight: 0.4980 chunk 381 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 465 GLN 6 645 ASN 5 563 HIS ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** A 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN ** N 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 267 HIS 2 450 GLN 2 516 GLN 2 548 ASN 2 606 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.218602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.201486 restraints weight = 112137.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.202384 restraints weight = 92411.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.203074 restraints weight = 77590.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.203962 restraints weight = 71766.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.204146 restraints weight = 66321.799| |-----------------------------------------------------------------------------| r_work (final): 0.4623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5769 moved from start: 0.6918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 39752 Z= 0.144 Angle : 0.765 13.586 53739 Z= 0.388 Chirality : 0.047 0.255 6083 Planarity : 0.005 0.099 6914 Dihedral : 10.112 175.358 5485 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.71 % Favored : 88.25 % Rotamer: Outliers : 0.12 % Allowed : 0.55 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.11), residues: 4775 helix: -1.61 (0.13), residues: 1481 sheet: -2.45 (0.22), residues: 462 loop : -2.85 (0.11), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 76 TYR 0.028 0.002 TYR H 84 PHE 0.035 0.002 PHE 3 253 TRP 0.021 0.002 TRP L 47 HIS 0.018 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (39744) covalent geometry : angle 0.76429 / 0.39 (53737) SS BOND : bond 0.00186 / 0.10 ( 1) SS BOND : angle 5.46705 / 3.20 ( 2) hydrogen bonds : bond 0.03886 / 2.58 ( 889) hydrogen bonds : angle 5.90940 / 4.13 ( 2523) Misc. bond : bond 0.00073 / 0.04 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9550 Ramachandran restraints generated. 4775 Oldfield, 0 Emsley, 4775 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 755 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 7 108 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU 7 110 " (corrupted residue). Skipping it. 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 TARDY: cannot create tardy model for: "GLN 6 653 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 5 652 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE H 201 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR M 174 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE N 228 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: 3 124 VAL cc_start: 0.7463 (t) cc_final: 0.6877 (m) REVERT: 3 130 LYS cc_start: 0.6536 (mtpt) cc_final: 0.5595 (mptt) REVERT: 3 279 MET cc_start: 0.7807 (mpp) cc_final: 0.7584 (mpp) REVERT: 3 293 LEU cc_start: 0.7608 (tt) cc_final: 0.7042 (tt) REVERT: 3 405 GLU cc_start: 0.6634 (mp0) cc_final: 0.5735 (mp0) REVERT: 3 628 SER cc_start: 0.7481 (m) cc_final: 0.6992 (p) REVERT: 4 274 MET cc_start: 0.6067 (ttm) cc_final: 0.5788 (mtp) REVERT: 4 282 MET cc_start: 0.7911 (tpp) cc_final: 0.7671 (tpp) REVERT: 4 380 ASP cc_start: 0.7570 (p0) cc_final: 0.6572 (p0) REVERT: 4 403 LYS cc_start: 0.6043 (ttpt) cc_final: 0.5663 (tppt) REVERT: 4 415 TYR cc_start: 0.6108 (m-80) cc_final: 0.5458 (m-80) REVERT: 4 698 GLU cc_start: 0.6726 (tt0) cc_final: 0.6110 (tt0) REVERT: 4 713 ILE cc_start: 0.8459 (mm) cc_final: 0.8136 (mm) REVERT: 7 369 MET cc_start: 0.5760 (tpt) cc_final: 0.4932 (mpp) REVERT: 6 186 MET cc_start: 0.4094 (tpt) cc_final: 0.3369 (mmm) REVERT: 6 219 GLU cc_start: 0.7920 (mp0) cc_final: 0.7695 (mp0) REVERT: 6 459 GLN cc_start: 0.7905 (mp10) cc_final: 0.7282 (mp10) REVERT: 6 503 ASP cc_start: 0.7025 (t70) cc_final: 0.6726 (t0) REVERT: 6 548 HIS cc_start: 0.5049 (m90) cc_final: 0.4691 (m170) REVERT: 5 32 LYS cc_start: 0.7034 (mmtm) cc_final: 0.6750 (mmtm) REVERT: 5 47 PHE cc_start: 0.0717 (m-80) cc_final: -0.0059 (m-80) REVERT: 5 246 ARG cc_start: 0.6650 (tpm170) cc_final: 0.6434 (tpm170) REVERT: 5 416 MET cc_start: 0.5113 (ppp) cc_final: 0.3881 (ptm) REVERT: 5 426 MET cc_start: 0.6488 (ppp) cc_final: 0.6144 (ppp) REVERT: 5 456 HIS cc_start: 0.7245 (t-90) cc_final: 0.6731 (t-170) REVERT: 5 474 THR cc_start: 0.7424 (m) cc_final: 0.6425 (p) REVERT: A 230 MET cc_start: 0.7418 (mmp) cc_final: 0.6644 (mtm) REVERT: A 259 GLU cc_start: 0.8546 (pt0) cc_final: 0.7801 (mm-30) REVERT: A 331 MET cc_start: 0.7849 (ppp) cc_final: 0.7364 (ppp) REVERT: A 513 MET cc_start: 0.3150 (mmp) cc_final: 0.2493 (mmt) REVERT: A 547 LEU cc_start: 0.7838 (mp) cc_final: 0.7594 (mp) REVERT: A 568 ASP cc_start: 0.8347 (m-30) cc_final: 0.7195 (t0) REVERT: H 42 LYS cc_start: 0.7606 (mttt) cc_final: 0.7102 (mtpp) REVERT: L 46 LEU cc_start: 0.6670 (mm) cc_final: 0.6325 (mm) REVERT: L 125 GLU cc_start: 0.7628 (mp0) cc_final: 0.7254 (mp0) REVERT: L 155 SER cc_start: 0.8315 (m) cc_final: 0.7541 (t) REVERT: L 159 ILE cc_start: 0.7795 (mp) cc_final: 0.7347 (mt) REVERT: M 102 TYR cc_start: 0.6298 (m-10) cc_final: 0.5616 (m-10) REVERT: N 226 GLN cc_start: 0.7231 (mp10) cc_final: 0.6787 (mp10) REVERT: 2 240 MET cc_start: 0.5098 (mmm) cc_final: 0.4713 (mmm) REVERT: 2 294 LEU cc_start: 0.6934 (pt) cc_final: 0.6551 (pt) REVERT: 2 348 ILE cc_start: 0.8472 (pt) cc_final: 0.8193 (pt) REVERT: 2 624 PRO cc_start: 0.6487 (Cg_exo) cc_final: 0.5624 (Cg_endo) REVERT: 2 740 THR cc_start: 0.7176 (t) cc_final: 0.6690 (m) REVERT: 2 774 MET cc_start: 0.3295 (mmm) cc_final: 0.2871 (mtt) outliers start: 5 outliers final: 3 residues processed: 758 average time/residue: 0.2339 time to fit residues: 289.2941 Evaluate side-chains 635 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 632 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 484 random chunks: chunk 409 optimal weight: 6.9990 chunk 335 optimal weight: 0.0770 chunk 115 optimal weight: 1.9990 chunk 364 optimal weight: 0.0870 chunk 301 optimal weight: 4.9990 chunk 465 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 355 optimal weight: 2.9990 chunk 193 optimal weight: 0.0970 chunk 288 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.3514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 3 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 204 HIS ** 4 699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 HIS ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 51 HIS L 166 HIS M 164 ASN N 32 GLN 2 516 GLN 2 548 ASN 2 606 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.224419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.208610 restraints weight = 118264.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.209944 restraints weight = 101201.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.210442 restraints weight = 85687.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.211064 restraints weight = 74303.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.211254 restraints weight = 69652.065| |-----------------------------------------------------------------------------| r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.7131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 39752 Z= 0.131 Angle : 0.751 16.271 53739 Z= 0.378 Chirality : 0.045 0.210 6083 Planarity : 0.005 0.081 6914 Dihedral : 10.014 175.501 5485 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.66 % Favored : 89.30 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.11), residues: 4775 helix: -1.52 (0.13), residues: 1482 sheet: -2.37 (0.22), residues: 457 loop : -2.85 (0.10), residues: 2836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 4 303 TYR 0.022 0.001 TYR 2 358 PHE 0.034 0.002 PHE 7 77 TRP 0.033 0.001 TRP L 47 HIS 0.010 0.001 HIS 2 668 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (39744) covalent geometry : angle 0.75054 / 0.38 (53737) SS BOND : bond 0.00232 / 0.12 ( 1) SS BOND : angle 5.12895 / 3.01 ( 2) hydrogen bonds : bond 0.03798 / 2.50 ( 889) hydrogen bonds : angle 5.83193 / 4.08 ( 2523) Misc. bond : bond 0.00063 / 0.03 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7613.46 seconds wall clock time: 132 minutes 21.13 seconds (7941.13 seconds total)