Starting phenix.real_space_refine on Tue Aug 26 18:12:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jc5_6535/08_2025/3jc5_6535.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jc5_6535/08_2025/3jc5_6535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jc5_6535/08_2025/3jc5_6535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jc5_6535/08_2025/3jc5_6535.map" model { file = "/net/cci-nas-00/data/ceres_data/3jc5_6535/08_2025/3jc5_6535.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jc5_6535/08_2025/3jc5_6535.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 175 5.16 5 C 25340 2.51 5 N 6943 2.21 5 O 7583 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40041 Number of models: 1 Model: "" Number of chains: 11 Chain: "2" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4600 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 544} Chain breaks: 4 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "3" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4613 Classifications: {'peptide': 588} Link IDs: {'CIS': 20, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 543} Chain breaks: 4 Chain: "4" Number of atoms: 4516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4516 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 19, 'PTRANS': 20, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "5" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5171 Classifications: {'peptide': 653} Link IDs: {'CIS': 14, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 614} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "6" Number of atoms: 5211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5211 Classifications: {'peptide': 671} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 34, 'PCIS': 2, 'PTRANS': 20, 'TRANS': 614} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 4, 'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 5, 'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "7" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5148 Classifications: {'peptide': 652} Link IDs: {'CIS': 25, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 597} Chain breaks: 4 Chain: "c" Number of atoms: 4470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4470 Classifications: {'peptide': 553} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 516} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1820 Classifications: {'peptide': 221} Link IDs: {'CIS': 12, 'PTRANS': 11, 'TRANS': 197} Chain breaks: 2 Chain: "B" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1513 Classifications: {'peptide': 181} Link IDs: {'CIS': 6, 'PTRANS': 9, 'TRANS': 165} Chain breaks: 1 Chain: "A" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1691 Classifications: {'peptide': 208} Link IDs: {'CIS': 13, 'PTRANS': 3, 'TRANS': 191} Chain: "C" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1288 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 145} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 9.71, per 1000 atoms: 0.24 Number of scatterers: 40041 At special positions: 0 Unit cell: (168.67, 215.13, 141.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 175 16.00 O 7583 8.00 N 6943 7.00 C 25340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 5 186 " - pdb=" SG CYS 5 211 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 474 " - pdb=" SG CYS 7 522 " 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 476.8 nanoseconds 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9626 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 37 sheets defined 45.0% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain '2' and resid 202 through 216 removed outlier: 3.895A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE 2 207 " --> pdb=" O VAL 2 203 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER 2 213 " --> pdb=" O ARG 2 209 " (cutoff:3.500A) Processing helix chain '2' and resid 225 through 237 Processing helix chain '2' and resid 245 through 253 Processing helix chain '2' and resid 253 through 261 removed outlier: 3.919A pdb=" N ALA 2 257 " --> pdb=" O LYS 2 253 " (cutoff:3.500A) Processing helix chain '2' and resid 263 through 283 removed outlier: 3.998A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 removed outlier: 3.523A pdb=" N ASN 2 313 " --> pdb=" O ARG 2 310 " (cutoff:3.500A) Processing helix chain '2' and resid 393 through 397 removed outlier: 3.601A pdb=" N VAL 2 397 " --> pdb=" O PRO 2 394 " (cutoff:3.500A) Processing helix chain '2' and resid 413 through 415 No H-bonds generated for 'chain '2' and resid 413 through 415' Processing helix chain '2' and resid 477 through 486 removed outlier: 4.347A pdb=" N LYS 2 486 " --> pdb=" O ARG 2 482 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 502 removed outlier: 4.195A pdb=" N ALA 2 502 " --> pdb=" O ILE 2 498 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 521 removed outlier: 3.816A pdb=" N LYS 2 512 " --> pdb=" O HIS 2 508 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL 2 515 " --> pdb=" O ILE 2 511 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 560 removed outlier: 4.461A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL 2 556 " --> pdb=" O ILE 2 552 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU 2 557 " --> pdb=" O LEU 2 553 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 Processing helix chain '2' and resid 609 through 612 Processing helix chain '2' and resid 613 through 627 removed outlier: 4.037A pdb=" N SER 2 619 " --> pdb=" O GLN 2 615 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 667 Processing helix chain '2' and resid 670 through 676 removed outlier: 3.771A pdb=" N ARG 2 676 " --> pdb=" O PRO 2 672 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 705 removed outlier: 3.560A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 4.181A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) Processing helix chain '2' and resid 784 through 799 removed outlier: 3.735A pdb=" N ARG 2 788 " --> pdb=" O ASP 2 784 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU 2 796 " --> pdb=" O ASP 2 792 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER 2 799 " --> pdb=" O ARG 2 795 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 4.048A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 849 removed outlier: 3.813A pdb=" N GLN 2 849 " --> pdb=" O PHE 2 845 " (cutoff:3.500A) Processing helix chain '2' and resid 852 through 858 removed outlier: 3.768A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) Processing helix chain '3' and resid 19 through 32 removed outlier: 3.594A pdb=" N GLU 3 30 " --> pdb=" O ARG 3 26 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 38 through 55 removed outlier: 3.645A pdb=" N ASN 3 49 " --> pdb=" O ILE 3 45 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 101 No H-bonds generated for 'chain '3' and resid 99 through 101' Processing helix chain '3' and resid 102 through 107 removed outlier: 4.145A pdb=" N PHE 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 removed outlier: 3.568A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE 3 114 " --> pdb=" O PHE 3 110 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 135 removed outlier: 3.553A pdb=" N SER 3 135 " --> pdb=" O ASP 3 131 " (cutoff:3.500A) Processing helix chain '3' and resid 261 through 265 removed outlier: 3.538A pdb=" N ALA 3 265 " --> pdb=" O PRO 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 279 through 283 Processing helix chain '3' and resid 344 through 354 removed outlier: 3.785A pdb=" N ARG 3 348 " --> pdb=" O ASP 3 344 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 removed outlier: 3.812A pdb=" N ILE 3 362 " --> pdb=" O ASP 3 358 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU 3 367 " --> pdb=" O LEU 3 363 " (cutoff:3.500A) Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 426 removed outlier: 3.687A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG 3 420 " --> pdb=" O SER 3 416 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE 3 421 " --> pdb=" O GLN 3 417 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 479 through 491 removed outlier: 3.878A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 543 removed outlier: 3.586A pdb=" N SER 3 541 " --> pdb=" O ASP 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 569 removed outlier: 3.572A pdb=" N ARG 3 559 " --> pdb=" O GLU 3 555 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER 3 560 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) Processing helix chain '3' and resid 655 through 666 removed outlier: 3.922A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA 3 663 " --> pdb=" O TYR 3 659 " (cutoff:3.500A) Processing helix chain '3' and resid 675 through 694 removed outlier: 3.527A pdb=" N ILE 3 679 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR 3 692 " --> pdb=" O ASN 3 688 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 3.796A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 189 through 196 Processing helix chain '4' and resid 226 through 237 removed outlier: 3.791A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 264 removed outlier: 3.767A pdb=" N TYR 4 258 " --> pdb=" O THR 4 254 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 285 removed outlier: 3.660A pdb=" N VAL 4 268 " --> pdb=" O TYR 4 264 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 294 through 299 removed outlier: 3.571A pdb=" N THR 4 298 " --> pdb=" O ASP 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 420 through 424 Processing helix chain '4' and resid 478 through 483 removed outlier: 3.729A pdb=" N GLU 4 482 " --> pdb=" O THR 4 478 " (cutoff:3.500A) Processing helix chain '4' and resid 483 through 488 Processing helix chain '4' and resid 502 through 513 removed outlier: 3.928A pdb=" N LEU 4 506 " --> pdb=" O THR 4 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU 4 511 " --> pdb=" O ALA 4 507 " (cutoff:3.500A) Processing helix chain '4' and resid 514 through 516 No H-bonds generated for 'chain '4' and resid 514 through 516' Processing helix chain '4' and resid 517 through 527 removed outlier: 3.919A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 removed outlier: 3.555A pdb=" N LYS 4 537 " --> pdb=" O LEU 4 533 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 3.868A pdb=" N LEU 4 578 " --> pdb=" O LYS 4 574 " (cutoff:3.500A) Processing helix chain '4' and resid 620 through 624 Processing helix chain '4' and resid 633 through 637 Processing helix chain '4' and resid 644 through 652 removed outlier: 4.029A pdb=" N GLU 4 650 " --> pdb=" O HIS 4 646 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 692 Processing helix chain '4' and resid 695 through 702 removed outlier: 3.800A pdb=" N PHE 4 702 " --> pdb=" O LEU 4 698 " (cutoff:3.500A) Processing helix chain '4' and resid 716 through 725 Processing helix chain '4' and resid 745 through 758 removed outlier: 3.558A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) Processing helix chain '4' and resid 766 through 779 removed outlier: 3.531A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 811 Processing helix chain '4' and resid 812 through 814 No H-bonds generated for 'chain '4' and resid 812 through 814' Processing helix chain '4' and resid 821 through 835 removed outlier: 3.617A pdb=" N ALA 4 825 " --> pdb=" O ASP 4 821 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 37 removed outlier: 3.518A pdb=" N SER 5 30 " --> pdb=" O GLU 5 26 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU 5 37 " --> pdb=" O ASN 5 33 " (cutoff:3.500A) Processing helix chain '5' and resid 44 through 56 removed outlier: 4.052A pdb=" N VAL 5 56 " --> pdb=" O ASN 5 52 " (cutoff:3.500A) Processing helix chain '5' and resid 64 through 72 Processing helix chain '5' and resid 72 through 80 removed outlier: 4.166A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 102 Proline residue: 5 88 - end of helix removed outlier: 3.622A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 147 through 151 Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 351 through 361 Processing helix chain '5' and resid 365 through 371 Processing helix chain '5' and resid 381 through 393 removed outlier: 4.102A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) Processing helix chain '5' and resid 421 through 433 removed outlier: 3.858A pdb=" N LYS 5 427 " --> pdb=" O SER 5 423 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 482 through 485 removed outlier: 3.860A pdb=" N MET 5 485 " --> pdb=" O PHE 5 482 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 482 through 485' Processing helix chain '5' and resid 487 through 500 removed outlier: 3.721A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU 5 498 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN 5 499 " --> pdb=" O GLU 5 495 " (cutoff:3.500A) Processing helix chain '5' and resid 529 through 534 Processing helix chain '5' and resid 544 through 550 Processing helix chain '5' and resid 561 through 577 removed outlier: 3.973A pdb=" N THR 5 577 " --> pdb=" O ILE 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 582 through 592 removed outlier: 4.096A pdb=" N GLN 5 586 " --> pdb=" O ALA 5 582 " (cutoff:3.500A) Processing helix chain '5' and resid 596 through 610 removed outlier: 3.663A pdb=" N LYS 5 600 " --> pdb=" O ILE 5 596 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS 5 610 " --> pdb=" O CYS 5 606 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 637 Processing helix chain '5' and resid 638 through 640 No H-bonds generated for 'chain '5' and resid 638 through 640' Processing helix chain '5' and resid 649 through 668 removed outlier: 3.572A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 693 removed outlier: 3.788A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG 5 682 " --> pdb=" O ASP 5 678 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER 5 693 " --> pdb=" O MET 5 689 " (cutoff:3.500A) Processing helix chain '5' and resid 714 through 719 Processing helix chain '5' and resid 728 through 739 removed outlier: 4.022A pdb=" N ASP 5 739 " --> pdb=" O ARG 5 735 " (cutoff:3.500A) Processing helix chain '5' and resid 744 through 759 Processing helix chain '6' and resid 106 through 121 removed outlier: 3.648A pdb=" N LYS 6 110 " --> pdb=" O VAL 6 106 " (cutoff:3.500A) Processing helix chain '6' and resid 135 through 144 Processing helix chain '6' and resid 155 through 161 removed outlier: 3.869A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 170 removed outlier: 4.038A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE 6 170 " --> pdb=" O LEU 6 166 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 176 Processing helix chain '6' and resid 177 through 193 removed outlier: 3.819A pdb=" N LYS 6 191 " --> pdb=" O ARG 6 187 " (cutoff:3.500A) Processing helix chain '6' and resid 511 through 522 removed outlier: 4.191A pdb=" N GLU 6 515 " --> pdb=" O ASP 6 511 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 Processing helix chain '6' and resid 541 through 552 removed outlier: 4.088A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN 6 550 " --> pdb=" O GLY 6 546 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET 6 551 " --> pdb=" O ILE 6 547 " (cutoff:3.500A) Processing helix chain '6' and resid 580 through 592 removed outlier: 4.046A pdb=" N PHE 6 584 " --> pdb=" O SER 6 580 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 644 Processing helix chain '6' and resid 646 through 658 removed outlier: 3.908A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 707 Processing helix chain '6' and resid 721 through 736 Processing helix chain '6' and resid 749 through 759 removed outlier: 3.933A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) Processing helix chain '6' and resid 769 through 783 removed outlier: 3.655A pdb=" N LEU 6 773 " --> pdb=" O ALA 6 769 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS 6 782 " --> pdb=" O LYS 6 778 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 796 through 815 removed outlier: 3.711A pdb=" N LEU 6 800 " --> pdb=" O THR 6 796 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE 6 804 " --> pdb=" O LEU 6 800 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG 6 805 " --> pdb=" O GLU 6 801 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 837 removed outlier: 3.558A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) Processing helix chain '6' and resid 908 through 927 removed outlier: 3.598A pdb=" N ARG 6 925 " --> pdb=" O ALA 6 921 " (cutoff:3.500A) Processing helix chain '6' and resid 932 through 945 removed outlier: 3.960A pdb=" N ILE 6 936 " --> pdb=" O THR 6 932 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL 6 937 " --> pdb=" O ALA 6 933 " (cutoff:3.500A) Processing helix chain '6' and resid 950 through 969 removed outlier: 3.515A pdb=" N TYR 6 954 " --> pdb=" O SER 6 950 " (cutoff:3.500A) Processing helix chain '7' and resid 13 through 25 removed outlier: 3.757A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 3.817A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 7 70 " --> pdb=" O MET 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 92 removed outlier: 3.530A pdb=" N GLN 7 89 " --> pdb=" O ILE 7 85 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN 7 90 " --> pdb=" O LEU 7 86 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 7 91 " --> pdb=" O GLN 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 102 through 110 removed outlier: 3.771A pdb=" N GLN 7 107 " --> pdb=" O VAL 7 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 115 Processing helix chain '7' and resid 119 through 125 removed outlier: 4.025A pdb=" N ASN 7 123 " --> pdb=" O ARG 7 119 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 158 removed outlier: 3.599A pdb=" N LEU 7 143 " --> pdb=" O LEU 7 139 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 220 Processing helix chain '7' and resid 338 through 340 No H-bonds generated for 'chain '7' and resid 338 through 340' Processing helix chain '7' and resid 397 through 407 removed outlier: 3.633A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER 7 407 " --> pdb=" O GLU 7 403 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 Processing helix chain '7' and resid 425 through 438 removed outlier: 4.095A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 467 through 477 Processing helix chain '7' and resid 489 through 494 Processing helix chain '7' and resid 531 through 540 Processing helix chain '7' and resid 541 through 543 No H-bonds generated for 'chain '7' and resid 541 through 543' Processing helix chain '7' and resid 587 through 592 removed outlier: 3.564A pdb=" N LEU 7 591 " --> pdb=" O PRO 7 587 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER 7 592 " --> pdb=" O ALA 7 588 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 587 through 592' Processing helix chain '7' and resid 605 through 622 removed outlier: 3.762A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 Processing helix chain '7' and resid 653 through 674 removed outlier: 3.507A pdb=" N GLU 7 674 " --> pdb=" O ASP 7 670 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.939A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS 7 701 " --> pdb=" O GLN 7 697 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 7 703 " --> pdb=" O LEU 7 699 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 724 removed outlier: 3.564A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) Processing helix chain '7' and resid 725 through 729 removed outlier: 3.654A pdb=" N TYR 7 728 " --> pdb=" O GLU 7 725 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN 7 729 " --> pdb=" O SER 7 726 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 725 through 729' Processing helix chain 'c' and resid 7 through 18 Processing helix chain 'c' and resid 35 through 52 removed outlier: 3.780A pdb=" N LEU c 39 " --> pdb=" O ASN c 35 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET c 44 " --> pdb=" O CYS c 40 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN c 52 " --> pdb=" O LEU c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 63 through 74 removed outlier: 4.203A pdb=" N ARG c 68 " --> pdb=" O TYR c 64 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG c 69 " --> pdb=" O SER c 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 97 removed outlier: 3.521A pdb=" N PHE c 95 " --> pdb=" O ASP c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 135 removed outlier: 3.930A pdb=" N ILE c 134 " --> pdb=" O ASN c 130 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE c 135 " --> pdb=" O LEU c 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 130 through 135' Processing helix chain 'c' and resid 152 through 157 removed outlier: 3.622A pdb=" N LYS c 156 " --> pdb=" O LEU c 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 219 through 240 removed outlier: 3.946A pdb=" N VAL c 236 " --> pdb=" O GLU c 232 " (cutoff:3.500A) Processing helix chain 'c' and resid 250 through 263 removed outlier: 3.610A pdb=" N GLN c 254 " --> pdb=" O SER c 250 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA c 261 " --> pdb=" O SER c 257 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE c 262 " --> pdb=" O LEU c 258 " (cutoff:3.500A) Processing helix chain 'c' and resid 266 through 278 Processing helix chain 'c' and resid 287 through 289 No H-bonds generated for 'chain 'c' and resid 287 through 289' Processing helix chain 'c' and resid 290 through 301 removed outlier: 4.643A pdb=" N LEU c 294 " --> pdb=" O ARG c 290 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU c 298 " --> pdb=" O LEU c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 340 Processing helix chain 'c' and resid 341 through 348 removed outlier: 3.983A pdb=" N ALA c 346 " --> pdb=" O ASN c 342 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS c 347 " --> pdb=" O TYR c 343 " (cutoff:3.500A) Processing helix chain 'c' and resid 352 through 367 removed outlier: 3.752A pdb=" N LYS c 357 " --> pdb=" O GLU c 353 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG c 358 " --> pdb=" O ASN c 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU c 359 " --> pdb=" O GLY c 355 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS c 360 " --> pdb=" O LYS c 356 " (cutoff:3.500A) Processing helix chain 'c' and resid 369 through 375 removed outlier: 3.573A pdb=" N GLU c 375 " --> pdb=" O SER c 371 " (cutoff:3.500A) Processing helix chain 'c' and resid 376 through 380 removed outlier: 3.670A pdb=" N MET c 380 " --> pdb=" O TRP c 377 " (cutoff:3.500A) Processing helix chain 'c' and resid 381 through 387 Processing helix chain 'c' and resid 390 through 396 Processing helix chain 'c' and resid 397 through 400 Processing helix chain 'c' and resid 421 through 434 removed outlier: 3.662A pdb=" N VAL c 425 " --> pdb=" O ALA c 421 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU c 433 " --> pdb=" O THR c 429 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL c 434 " --> pdb=" O ALA c 430 " (cutoff:3.500A) Processing helix chain 'c' and resid 463 through 483 removed outlier: 3.944A pdb=" N TRP c 478 " --> pdb=" O VAL c 474 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU c 479 " --> pdb=" O SER c 475 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA c 483 " --> pdb=" O LEU c 479 " (cutoff:3.500A) Processing helix chain 'c' and resid 491 through 515 removed outlier: 3.572A pdb=" N LEU c 498 " --> pdb=" O ARG c 494 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP c 501 " --> pdb=" O GLN c 497 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN c 508 " --> pdb=" O ARG c 504 " (cutoff:3.500A) Processing helix chain 'c' and resid 537 through 540 Processing helix chain 'c' and resid 541 through 557 removed outlier: 3.636A pdb=" N ALA c 557 " --> pdb=" O ILE c 553 " (cutoff:3.500A) Processing helix chain 'c' and resid 604 through 614 removed outlier: 3.588A pdb=" N ILE c 612 " --> pdb=" O ALA c 608 " (cutoff:3.500A) Processing helix chain 'c' and resid 633 through 646 removed outlier: 4.484A pdb=" N SER c 638 " --> pdb=" O ARG c 634 " (cutoff:3.500A) Proline residue: c 639 - end of helix Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 80 through 105 removed outlier: 4.027A pdb=" N ARG D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 164 removed outlier: 3.640A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 198 Processing helix chain 'D' and resid 279 through 288 removed outlier: 5.006A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.867A pdb=" N GLN B 17 " --> pdb=" O PRO B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.782A pdb=" N GLN B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 107 removed outlier: 4.029A pdb=" N ARG B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 107 " --> pdb=" O GLN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 4.219A pdb=" N PHE B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 133 Processing helix chain 'B' and resid 140 through 160 removed outlier: 3.653A pdb=" N ARG B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLN B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 199 removed outlier: 3.536A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 4.208A pdb=" N ASP B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 22 removed outlier: 4.021A pdb=" N ASN A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 61 removed outlier: 4.007A pdb=" N GLN A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 104 removed outlier: 4.089A pdb=" N GLN A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N MET A 100 " --> pdb=" O ILE A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.613A pdb=" N TYR A 130 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 201 removed outlier: 4.034A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.574A pdb=" N VAL C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.706A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 80 Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 104 through 116 removed outlier: 4.395A pdb=" N LYS C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N MET C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 removed outlier: 3.970A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL C 123 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 3.743A pdb=" N LEU C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 removed outlier: 3.550A pdb=" N PHE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing sheet with id=A, first strand: chain '2' and resid 331 through 333 removed outlier: 3.534A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) Processing sheet with id=B, first strand: chain '2' and resid 331 through 333 removed outlier: 3.534A pdb=" N PHE 2 331 " --> pdb=" O TYR 2 385 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR 2 385 " --> pdb=" O PHE 2 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG 2 383 " --> pdb=" O GLN 2 333 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) Processing sheet with id=C, first strand: chain '2' and resid 563 through 565 removed outlier: 6.189A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) Processing sheet with id=D, first strand: chain '2' and resid 629 through 631 Processing sheet with id=E, first strand: chain '3' and resid 179 through 180 removed outlier: 7.141A pdb=" N ASP 3 275 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) Processing sheet with id=F, first strand: chain '3' and resid 210 through 213 Processing sheet with id=G, first strand: chain '3' and resid 391 through 392 removed outlier: 4.016A pdb=" N LYS 3 391 " --> pdb=" O LEU 3 399 " (cutoff:3.500A) Processing sheet with id=H, first strand: chain '3' and resid 431 through 433 removed outlier: 7.103A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY 3 409 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=I, first strand: chain '3' and resid 494 through 497 Processing sheet with id=J, first strand: chain '4' and resid 332 through 335 removed outlier: 6.611A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS 4 398 " --> pdb=" O ARG 4 334 " (cutoff:3.500A) Processing sheet with id=K, first strand: chain '4' and resid 339 through 342 Processing sheet with id=L, first strand: chain '4' and resid 344 through 345 Processing sheet with id=M, first strand: chain '4' and resid 365 through 366 removed outlier: 6.902A pdb=" N ILE 4 365 " --> pdb=" O THR 6 420 " (cutoff:3.500A) No H-bonds generated for sheet with id=M Processing sheet with id=N, first strand: chain '4' and resid 434 through 436 removed outlier: 4.197A pdb=" N GLU 4 434 " --> pdb=" O LYS 4 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS 4 467 " --> pdb=" O GLU 4 434 " (cutoff:3.500A) Processing sheet with id=O, first strand: chain '4' and resid 439 through 442 Processing sheet with id=P, first strand: chain '4' and resid 590 through 591 removed outlier: 3.701A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=Q, first strand: chain '5' and resid 60 through 63 removed outlier: 6.246A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=Q Processing sheet with id=R, first strand: chain '5' and resid 298 through 301 removed outlier: 8.913A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL 5 292 " --> pdb=" O GLY 5 164 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN 5 334 " --> pdb=" O THR 5 293 " (cutoff:3.500A) Processing sheet with id=S, first strand: chain '5' and resid 190 through 193 removed outlier: 6.897A pdb=" N SER 5 247 " --> pdb=" O SER 5 180 " (cutoff:3.500A) removed outlier: 11.534A pdb=" N MET 5 182 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N HIS 5 245 " --> pdb=" O MET 5 182 " (cutoff:3.500A) Processing sheet with id=T, first strand: chain '5' and resid 436 through 440 removed outlier: 3.842A pdb=" N ASP 5 480 " --> pdb=" O THR 5 439 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL 5 477 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) Processing sheet with id=U, first strand: chain '6' and resid 150 through 154 removed outlier: 3.674A pdb=" N SER 6 266 " --> pdb=" O ILE 6 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE 6 153 " --> pdb=" O SER 6 266 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE 6 268 " --> pdb=" O ILE 6 153 " (cutoff:3.500A) Processing sheet with id=V, first strand: chain '6' and resid 273 through 274 Processing sheet with id=W, first strand: chain '6' and resid 454 through 456 removed outlier: 6.330A pdb=" N ASP 6 378 " --> pdb=" O PHE 6 454 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ALA 6 456 " --> pdb=" O ASP 6 378 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE 6 380 " --> pdb=" O ALA 6 456 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY 6 292 " --> pdb=" O CYS 6 395 " (cutoff:3.500A) Processing sheet with id=X, first strand: chain '6' and resid 404 through 405 Processing sheet with id=Y, first strand: chain '6' and resid 570 through 574 removed outlier: 3.579A pdb=" N ILE 6 571 " --> pdb=" O ILE 6 678 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) Processing sheet with id=Z, first strand: chain '6' and resid 660 through 664 Processing sheet with id=AA, first strand: chain '7' and resid 77 through 81 Processing sheet with id=AB, first strand: chain '7' and resid 252 through 253 removed outlier: 6.777A pdb=" N ASN 7 332 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain '7' and resid 252 through 253 removed outlier: 3.587A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) Processing sheet with id=AD, first strand: chain '7' and resid 269 through 270 removed outlier: 3.856A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain '7' and resid 481 through 483 removed outlier: 6.605A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN 7 455 " --> pdb=" O ILE 7 596 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE 7 598 " --> pdb=" O ASN 7 455 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) Processing sheet with id=AF, first strand: chain 'c' and resid 119 through 123 removed outlier: 6.946A pdb=" N LEU c 81 " --> pdb=" O TYR c 121 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N LEU c 123 " --> pdb=" O LEU c 81 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU c 83 " --> pdb=" O LEU c 123 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL c 28 " --> pdb=" O SER c 80 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE c 58 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN A 188 " --> pdb=" O ILE c 58 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 191 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AG, first strand: chain 'c' and resid 318 through 321 removed outlier: 5.506A pdb=" N THR c 412 " --> pdb=" O ILE c 419 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE c 419 " --> pdb=" O THR c 412 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY c 414 " --> pdb=" O GLY c 417 " (cutoff:3.500A) Processing sheet with id=AH, first strand: chain 'c' and resid 569 through 571 removed outlier: 3.993A pdb=" N LEU c 569 " --> pdb=" O ALA c 582 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA c 582 " --> pdb=" O LEU c 569 " (cutoff:3.500A) Processing sheet with id=AI, first strand: chain 'D' and resid 227 through 228 removed outlier: 4.021A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AJ, first strand: chain 'B' and resid 69 through 72 Processing sheet with id=AK, first strand: chain 'C' and resid 15 through 19 removed outlier: 3.607A pdb=" N LEU C 44 " --> pdb=" O CYS C 18 " (cutoff:3.500A) 1486 hydrogen bonds defined for protein. 4272 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: 9.21 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6782 1.30 - 1.44: 10114 1.44 - 1.57: 23482 1.57 - 1.71: 16 1.71 - 1.84: 286 Bond restraints: 40680 Sorted by residual: bond pdb=" N PRO 3 232 " pdb=" CD PRO 3 232 " ideal model delta sigma weight residual 1.473 1.700 -0.227 1.40e-02 5.10e+03 2.63e+02 bond pdb=" C ARG 5 720 " pdb=" N ARG 5 721 " ideal model delta sigma weight residual 1.332 1.173 0.160 1.40e-02 5.10e+03 1.30e+02 bond pdb=" C GLU 6 929 " pdb=" O GLU 6 929 " ideal model delta sigma weight residual 1.235 1.376 -0.141 1.26e-02 6.30e+03 1.25e+02 bond pdb=" C GLN 5 745 " pdb=" N LEU 5 746 " ideal model delta sigma weight residual 1.335 1.451 -0.116 1.36e-02 5.41e+03 7.25e+01 bond pdb=" C GLU 6 930 " pdb=" N LEU 6 931 " ideal model delta sigma weight residual 1.332 1.440 -0.108 1.40e-02 5.10e+03 5.93e+01 ... (remaining 40675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 54025 4.66 - 9.31: 849 9.31 - 13.97: 74 13.97 - 18.63: 11 18.63 - 23.28: 4 Bond angle restraints: 54963 Sorted by residual: angle pdb=" C THR 5 325 " pdb=" N PRO 5 326 " pdb=" CA PRO 5 326 " ideal model delta sigma weight residual 119.83 140.34 -20.51 1.08e+00 8.57e-01 3.61e+02 angle pdb=" N ARG 5 742 " pdb=" CA ARG 5 742 " pdb=" C ARG 5 742 " ideal model delta sigma weight residual 113.18 134.21 -21.03 1.33e+00 5.65e-01 2.50e+02 angle pdb=" C GLU 4 378 " pdb=" N PRO 4 379 " pdb=" CA PRO 4 379 " ideal model delta sigma weight residual 119.56 134.54 -14.98 1.02e+00 9.61e-01 2.16e+02 angle pdb=" N THR 3 550 " pdb=" CA THR 3 550 " pdb=" C THR 3 550 " ideal model delta sigma weight residual 109.24 86.57 22.67 1.63e+00 3.76e-01 1.93e+02 angle pdb=" C CYS 6 333 " pdb=" N PRO 6 334 " pdb=" CA PRO 6 334 " ideal model delta sigma weight residual 119.84 136.29 -16.45 1.25e+00 6.40e-01 1.73e+02 ... (remaining 54958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.97: 24329 26.97 - 53.95: 606 53.95 - 80.92: 63 80.92 - 107.89: 13 107.89 - 134.87: 2 Dihedral angle restraints: 25013 sinusoidal: 10229 harmonic: 14784 Sorted by residual: dihedral pdb=" CA ASN 4 377 " pdb=" C ASN 4 377 " pdb=" N GLU 4 378 " pdb=" CA GLU 4 378 " ideal model delta harmonic sigma weight residual -180.00 -45.13 -134.87 0 5.00e+00 4.00e-02 7.28e+02 dihedral pdb=" CA GLY 6 600 " pdb=" C GLY 6 600 " pdb=" N LYS 6 601 " pdb=" CA LYS 6 601 " ideal model delta harmonic sigma weight residual 180.00 45.82 134.18 0 5.00e+00 4.00e-02 7.20e+02 dihedral pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" N ASN A 105 " pdb=" CA ASN A 105 " ideal model delta harmonic sigma weight residual 180.00 122.46 57.54 0 5.00e+00 4.00e-02 1.32e+02 ... (remaining 25010 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 6326 0.203 - 0.406: 39 0.406 - 0.609: 2 0.609 - 0.812: 0 0.812 - 1.015: 1 Chirality restraints: 6368 Sorted by residual: chirality pdb=" CA ARG 5 742 " pdb=" N ARG 5 742 " pdb=" C ARG 5 742 " pdb=" CB ARG 5 742 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CA LEU 6 931 " pdb=" N LEU 6 931 " pdb=" C LEU 6 931 " pdb=" CB LEU 6 931 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" CA GLU 6 929 " pdb=" N GLU 6 929 " pdb=" C GLU 6 929 " pdb=" CB GLU 6 929 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.22e+00 ... (remaining 6365 not shown) Planarity restraints: 7045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR 6 954 " 0.056 2.00e-02 2.50e+03 5.56e-02 6.19e+01 pdb=" CG TYR 6 954 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR 6 954 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR 6 954 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR 6 954 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR 6 954 " -0.053 2.00e-02 2.50e+03 pdb=" CZ TYR 6 954 " -0.054 2.00e-02 2.50e+03 pdb=" OH TYR 6 954 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL 6 923 " 0.032 2.00e-02 2.50e+03 6.40e-02 4.10e+01 pdb=" C VAL 6 923 " -0.111 2.00e-02 2.50e+03 pdb=" O VAL 6 923 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP 6 924 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN 6 943 " 0.032 2.00e-02 2.50e+03 6.28e-02 3.95e+01 pdb=" CD GLN 6 943 " -0.109 2.00e-02 2.50e+03 pdb=" OE1 GLN 6 943 " 0.042 2.00e-02 2.50e+03 pdb=" NE2 GLN 6 943 " 0.035 2.00e-02 2.50e+03 ... (remaining 7042 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 23 1.44 - 2.30: 286 2.30 - 3.17: 39538 3.17 - 4.03: 98541 4.03 - 4.90: 177224 Warning: very small nonbonded interaction distances. Nonbonded interactions: 315612 Sorted by model distance: nonbonded pdb=" O ASN 2 658 " pdb=" CE1 HIS 5 741 " model vdw 0.572 3.260 nonbonded pdb=" CD LYS 4 636 " pdb=" CG GLU 7 539 " model vdw 0.692 3.840 nonbonded pdb=" CZ PHE 2 803 " pdb=" CE1 HIS 5 560 " model vdw 0.747 2.848 nonbonded pdb=" OE2 GLU 4 633 " pdb=" CB GLU 7 542 " model vdw 0.777 3.440 nonbonded pdb=" OG SER 4 638 " pdb=" OG SER 7 549 " model vdw 0.874 3.040 ... (remaining 315607 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: 1.590 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: 0.050 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.140 Process input model: 39.040 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 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 1.130 40693 Z= 1.123 Angle : 1.575 54.571 54967 Z= 1.015 Chirality : 0.062 1.015 6368 Planarity : 0.006 0.074 7045 Dihedral : 12.175 134.866 15381 Min Nonbonded Distance : 0.572 Molprobity Statistics. All-atom Clashscore : 46.27 Ramachandran Plot: Outliers : 1.70 % Allowed : 9.37 % Favored : 88.93 % Rotamer: Outliers : 0.63 % Allowed : 5.10 % Favored : 94.27 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.21 % Cis-general : 3.46 % Twisted Proline : 0.53 % Twisted General : 0.56 % 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 aren not related in a simple way. whole: -4.21 (0.09), residues: 4931 helix: -3.22 (0.08), residues: 1935 sheet: -2.19 (0.17), residues: 594 loop : -2.51 (0.11), residues: 2402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG 6 958 TYR 0.113 0.003 TYR 6 954 PHE 0.041 0.003 PHE 5 743 TRP 0.062 0.004 TRP 6 939 HIS 0.028 0.002 HIS 5 758 Details of bonding type rmsd covalent geometry : bond 0.00923 (40680) covalent geometry : angle 1.54394 (54963) SS BOND : bond 0.00853 ( 2) SS BOND : angle 36.79322 ( 4) hydrogen bonds : bond 0.18919 ( 1483) hydrogen bonds : angle 9.78772 ( 4272) Misc. bond : bond 0.58618 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 1360 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 221 GLU cc_start: 0.9015 (mp0) cc_final: 0.8643 (mp0) REVERT: 2 258 LEU cc_start: 0.9313 (tp) cc_final: 0.9089 (mm) REVERT: 2 265 GLU cc_start: 0.9347 (tp30) cc_final: 0.9124 (tp30) REVERT: 2 292 GLU cc_start: 0.9693 (tp30) cc_final: 0.9303 (tm-30) REVERT: 2 456 ILE cc_start: 0.9349 (mm) cc_final: 0.9003 (mm) REVERT: 2 537 ILE cc_start: 0.7481 (mp) cc_final: 0.6908 (mm) REVERT: 2 596 LEU cc_start: 0.8337 (mt) cc_final: 0.7870 (mm) REVERT: 2 612 MET cc_start: 0.6213 (mtp) cc_final: 0.5216 (ttp) REVERT: 2 620 ILE cc_start: 0.8894 (mt) cc_final: 0.8686 (mt) REVERT: 2 780 GLN cc_start: 0.5241 (tt0) cc_final: 0.4991 (mm-40) REVERT: 2 816 ILE cc_start: 0.9000 (mt) cc_final: 0.8706 (tp) REVERT: 3 100 LEU cc_start: 0.9307 (mt) cc_final: 0.9097 (mp) REVERT: 3 183 GLU cc_start: 0.9214 (pm20) cc_final: 0.9012 (mm-30) REVERT: 3 250 PHE cc_start: 0.8600 (m-80) cc_final: 0.8389 (m-10) REVERT: 3 260 GLU cc_start: 0.8284 (pm20) cc_final: 0.8034 (tm-30) REVERT: 3 278 LEU cc_start: 0.8858 (mt) cc_final: 0.8406 (mt) REVERT: 3 472 ILE cc_start: 0.7687 (mt) cc_final: 0.7471 (mp) REVERT: 3 683 TYR cc_start: 0.6152 (t80) cc_final: 0.5481 (t80) REVERT: 3 706 ILE cc_start: 0.7944 (pt) cc_final: 0.7612 (pt) REVERT: 4 262 LEU cc_start: 0.9263 (tp) cc_final: 0.8987 (mt) REVERT: 4 328 LEU cc_start: 0.8871 (mt) cc_final: 0.8591 (mt) REVERT: 4 329 LYS cc_start: 0.8354 (mtmt) cc_final: 0.7702 (tmtt) REVERT: 4 382 MET cc_start: 0.8344 (tpp) cc_final: 0.7699 (mmp) REVERT: 4 486 MET cc_start: -0.0670 (mtt) cc_final: -0.1078 (ttt) REVERT: 4 637 MET cc_start: -0.1155 (mmt) cc_final: -0.3225 (ttt) REVERT: 5 41 ASP cc_start: 0.9274 (m-30) cc_final: 0.8612 (t0) REVERT: 5 55 LEU cc_start: 0.9614 (mt) cc_final: 0.8573 (tp) REVERT: 5 68 LEU cc_start: 0.9716 (tt) cc_final: 0.9402 (tt) REVERT: 5 75 ILE cc_start: 0.9536 (pt) cc_final: 0.9236 (pt) REVERT: 5 76 TYR cc_start: 0.9065 (t80) cc_final: 0.8745 (t80) REVERT: 5 169 THR cc_start: 0.8447 (p) cc_final: 0.8195 (p) REVERT: 5 181 ILE cc_start: 0.8720 (mt) cc_final: 0.8023 (mm) REVERT: 5 242 ILE cc_start: 0.9395 (mt) cc_final: 0.9142 (tp) REVERT: 5 252 ASP cc_start: 0.8834 (t0) cc_final: 0.8427 (t0) REVERT: 5 275 THR cc_start: 0.8756 (m) cc_final: 0.8148 (p) REVERT: 5 281 TYR cc_start: 0.8683 (m-80) cc_final: 0.8327 (m-80) REVERT: 5 285 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8966 (mtpp) REVERT: 5 357 PHE cc_start: 0.8008 (m-10) cc_final: 0.7147 (m-80) REVERT: 5 391 LEU cc_start: 0.8804 (tt) cc_final: 0.8444 (tt) REVERT: 5 550 PHE cc_start: 0.6643 (m-10) cc_final: 0.6374 (m-10) REVERT: 5 583 MET cc_start: 0.0725 (OUTLIER) cc_final: -0.0443 (ptt) REVERT: 6 178 LEU cc_start: 0.9435 (mp) cc_final: 0.9132 (tp) REVERT: 6 270 LEU cc_start: 0.9340 (mt) cc_final: 0.8888 (tt) REVERT: 6 287 LEU cc_start: 0.8515 (mp) cc_final: 0.7845 (pt) REVERT: 6 359 VAL cc_start: 0.9114 (m) cc_final: 0.8648 (m) REVERT: 6 628 LEU cc_start: 0.8213 (tt) cc_final: 0.7884 (tp) REVERT: 7 14 TYR cc_start: 0.8422 (m-80) cc_final: 0.7124 (m-80) REVERT: 7 66 MET cc_start: 0.9072 (ttp) cc_final: 0.8782 (tpp) REVERT: 7 116 LEU cc_start: 0.9363 (tt) cc_final: 0.9004 (mt) REVERT: 7 202 LEU cc_start: 0.9606 (tt) cc_final: 0.9323 (tt) REVERT: 7 211 CYS cc_start: 0.7255 (p) cc_final: 0.6804 (t) REVERT: 7 235 LEU cc_start: 0.8338 (mt) cc_final: 0.7902 (mm) REVERT: 7 260 TYR cc_start: 0.6551 (p90) cc_final: 0.6335 (p90) REVERT: 7 457 CYS cc_start: 0.7345 (t) cc_final: 0.5484 (t) REVERT: 7 540 VAL cc_start: 0.7730 (t) cc_final: 0.7242 (m) REVERT: c 297 ASP cc_start: 0.9472 (m-30) cc_final: 0.9253 (p0) REVERT: c 361 LYS cc_start: 0.9479 (ttmt) cc_final: 0.9271 (tttm) REVERT: c 375 GLU cc_start: 0.9303 (tt0) cc_final: 0.8934 (pt0) REVERT: c 391 ILE cc_start: 0.9560 (mt) cc_final: 0.8864 (tp) REVERT: c 413 LEU cc_start: 0.7330 (tp) cc_final: 0.6888 (mt) REVERT: c 469 LEU cc_start: 0.9277 (tt) cc_final: 0.8861 (pp) REVERT: c 524 ILE cc_start: 0.6959 (mt) cc_final: 0.6397 (mt) REVERT: c 576 THR cc_start: 0.7707 (p) cc_final: 0.7468 (t) REVERT: c 607 MET cc_start: 0.9154 (mtp) cc_final: 0.8761 (mpp) REVERT: D 67 TRP cc_start: 0.9059 (t60) cc_final: 0.8710 (t60) REVERT: D 133 LEU cc_start: 0.9258 (tt) cc_final: 0.8896 (pp) REVERT: D 148 LEU cc_start: 0.9695 (mt) cc_final: 0.9473 (pp) REVERT: D 156 LEU cc_start: 0.9511 (mt) cc_final: 0.9309 (tp) REVERT: D 200 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8989 (mttt) REVERT: D 256 TYR cc_start: 0.7845 (p90) cc_final: 0.7282 (p90) REVERT: B 19 ILE cc_start: 0.9157 (mt) cc_final: 0.8820 (mp) REVERT: B 53 ILE cc_start: 0.8772 (mp) cc_final: 0.8499 (pt) REVERT: B 74 TRP cc_start: 0.9149 (p-90) cc_final: 0.7827 (p-90) REVERT: B 104 TYR cc_start: 0.9104 (t80) cc_final: 0.8757 (t80) REVERT: B 119 TRP cc_start: 0.8653 (p-90) cc_final: 0.8198 (p-90) REVERT: B 132 ASP cc_start: 0.9506 (p0) cc_final: 0.9202 (p0) REVERT: B 138 ILE cc_start: 0.9054 (pt) cc_final: 0.8852 (pt) REVERT: B 145 ILE cc_start: 0.9074 (pp) cc_final: 0.8781 (pp) REVERT: B 147 ASP cc_start: 0.9514 (t0) cc_final: 0.9185 (t0) REVERT: B 155 LYS cc_start: 0.9212 (ttmt) cc_final: 0.8773 (ttmt) REVERT: B 177 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8916 (mt-10) REVERT: B 186 THR cc_start: 0.9387 (p) cc_final: 0.9068 (t) REVERT: A 2 TYR cc_start: 0.6881 (t80) cc_final: 0.6246 (t80) REVERT: A 24 ASN cc_start: 0.8901 (t0) cc_final: 0.8471 (m-40) REVERT: A 176 THR cc_start: 0.8117 (m) cc_final: 0.7827 (p) REVERT: C 12 ASP cc_start: 0.9392 (m-30) cc_final: 0.9021 (m-30) REVERT: C 96 ASP cc_start: 0.9148 (t0) cc_final: 0.8900 (t0) REVERT: C 126 GLU cc_start: 0.9400 (tp30) cc_final: 0.9178 (mm-30) REVERT: C 134 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8722 (tm-30) outliers start: 28 outliers final: 8 residues processed: 1383 average time/residue: 0.2884 time to fit residues: 618.9770 Evaluate side-chains 752 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 743 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 432 ASN 2 439 ASN 2 809 HIS 2 856 GLN 3 29 GLN 3 210 HIS 3 349 ASN 3 351 ASN 3 374 HIS ** 3 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 ASN 4 184 ASN 4 400 GLN 4 579 GLN 4 646 HIS 4 757 HIS ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN 5 494 HIS 5 524 ASN 5 574 ASN 5 576 HIS 5 581 ASN 5 585 ASN 5 625 ASN 5 758 HIS 6 364 ASN 6 570 ASN 6 690 ASN 6 698 ASN 6 735 HIS ** 6 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 145 GLN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 229 GLN 7 311 GLN 7 384 HIS 7 538 HIS 7 544 GLN 7 585 ASN ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 26 GLN c 243 GLN c 249 ASN c 286 GLN ** c 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 382 HIS c 395 ASN ** c 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 550 ASN D 81 HIS D 162 ASN B 103 GLN A 28 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 188 GLN A 192 GLN C 138 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.086253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.063465 restraints weight = 227164.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.065542 restraints weight = 147292.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.066998 restraints weight = 107021.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.068071 restraints weight = 84052.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.068852 restraints weight = 69807.830| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 40693 Z= 0.218 Angle : 0.998 16.653 54967 Z= 0.520 Chirality : 0.052 0.623 6368 Planarity : 0.006 0.067 7045 Dihedral : 6.741 73.313 5476 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 1.10 % Allowed : 8.19 % Favored : 90.71 % Rotamer: Outliers : 0.56 % Allowed : 4.43 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.53 % Twisted General : 0.25 % 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 aren not related in a simple way. whole: -2.76 (0.11), residues: 4931 helix: -1.37 (0.10), residues: 1981 sheet: -1.85 (0.18), residues: 632 loop : -2.17 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG 2 795 TYR 0.037 0.002 TYR 4 519 PHE 0.026 0.002 PHE 2 803 TRP 0.031 0.002 TRP c 478 HIS 0.024 0.002 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00462 (40680) covalent geometry : angle 0.99802 (54963) SS BOND : bond 0.00153 ( 2) SS BOND : angle 2.27957 ( 4) hydrogen bonds : bond 0.05347 ( 1483) hydrogen bonds : angle 6.51304 ( 4272) Misc. bond : bond 0.00458 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 927 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 2 258 LEU cc_start: 0.9501 (tp) cc_final: 0.9286 (mm) REVERT: 2 266 GLU cc_start: 0.8272 (pm20) cc_final: 0.7865 (pm20) REVERT: 2 267 MET cc_start: 0.8912 (ppp) cc_final: 0.8442 (ppp) REVERT: 2 269 LYS cc_start: 0.9230 (mtmm) cc_final: 0.8927 (mtmm) REVERT: 2 274 VAL cc_start: 0.9254 (t) cc_final: 0.8924 (t) REVERT: 2 419 LYS cc_start: 0.9100 (mppt) cc_final: 0.8894 (mmtm) REVERT: 2 537 ILE cc_start: 0.8280 (mp) cc_final: 0.7988 (mm) REVERT: 2 612 MET cc_start: 0.7971 (mtp) cc_final: 0.6997 (ttp) REVERT: 2 629 ILE cc_start: 0.7837 (tp) cc_final: 0.7594 (tp) REVERT: 2 780 GLN cc_start: 0.5766 (tt0) cc_final: 0.5091 (mm-40) REVERT: 2 816 ILE cc_start: 0.9704 (mt) cc_final: 0.9351 (pt) REVERT: 3 178 LYS cc_start: 0.9138 (mptt) cc_final: 0.8937 (mptt) REVERT: 3 205 LYS cc_start: 0.9331 (mppt) cc_final: 0.8695 (tptt) REVERT: 3 250 PHE cc_start: 0.8656 (m-80) cc_final: 0.8411 (m-10) REVERT: 3 252 ASP cc_start: 0.8337 (t0) cc_final: 0.8019 (t0) REVERT: 3 261 MET cc_start: 0.7939 (mmm) cc_final: 0.7194 (mmm) REVERT: 3 278 LEU cc_start: 0.9486 (mt) cc_final: 0.9281 (mt) REVERT: 3 281 ASP cc_start: 0.8846 (p0) cc_final: 0.8642 (p0) REVERT: 3 375 ASP cc_start: 0.9417 (m-30) cc_final: 0.9094 (t0) REVERT: 3 530 HIS cc_start: 0.8691 (p-80) cc_final: 0.8178 (t70) REVERT: 3 665 GLU cc_start: 0.5497 (OUTLIER) cc_final: 0.5132 (pp20) REVERT: 3 683 TYR cc_start: 0.8264 (t80) cc_final: 0.7914 (t80) REVERT: 4 322 ILE cc_start: 0.9354 (pt) cc_final: 0.8786 (mp) REVERT: 4 382 MET cc_start: 0.8650 (tpp) cc_final: 0.8315 (mmp) REVERT: 4 391 PHE cc_start: 0.9097 (m-80) cc_final: 0.8664 (m-80) REVERT: 4 486 MET cc_start: -0.0140 (mtt) cc_final: -0.0454 (ttt) REVERT: 4 562 ILE cc_start: 0.8095 (pt) cc_final: 0.7148 (pt) REVERT: 4 637 MET cc_start: -0.4158 (mmt) cc_final: -0.5160 (ttm) REVERT: 5 32 LYS cc_start: 0.9568 (mttt) cc_final: 0.9106 (mmtm) REVERT: 5 55 LEU cc_start: 0.9228 (mt) cc_final: 0.8980 (tp) REVERT: 5 58 ASN cc_start: 0.9242 (t0) cc_final: 0.9013 (t0) REVERT: 5 76 TYR cc_start: 0.9117 (t80) cc_final: 0.8873 (t80) REVERT: 5 148 LEU cc_start: 0.9405 (tt) cc_final: 0.9048 (tt) REVERT: 5 166 ILE cc_start: 0.9762 (mt) cc_final: 0.9268 (tp) REVERT: 5 181 ILE cc_start: 0.8948 (mt) cc_final: 0.8475 (mm) REVERT: 5 276 MET cc_start: 0.9061 (mtm) cc_final: 0.8746 (mtm) REVERT: 5 285 LYS cc_start: 0.9326 (ttmm) cc_final: 0.9022 (mtpt) REVERT: 5 355 GLU cc_start: 0.9677 (tm-30) cc_final: 0.9394 (tp30) REVERT: 5 357 PHE cc_start: 0.7719 (m-10) cc_final: 0.7414 (m-80) REVERT: 5 497 MET cc_start: 0.9383 (ptm) cc_final: 0.8833 (ppp) REVERT: 5 500 GLN cc_start: 0.8150 (tp40) cc_final: 0.7670 (tm-30) REVERT: 5 514 ASN cc_start: 0.9323 (m-40) cc_final: 0.8841 (t0) REVERT: 5 551 ASP cc_start: 0.6882 (m-30) cc_final: 0.6609 (m-30) REVERT: 5 583 MET cc_start: 0.0850 (mmp) cc_final: -0.0613 (ptt) REVERT: 5 605 TYR cc_start: 0.8934 (t80) cc_final: 0.8653 (t80) REVERT: 5 689 MET cc_start: 0.9181 (mmp) cc_final: 0.8773 (mmm) REVERT: 6 160 MET cc_start: 0.9027 (ptt) cc_final: 0.8557 (ptp) REVERT: 6 168 MET cc_start: 0.9158 (mmp) cc_final: 0.8808 (mmp) REVERT: 6 270 LEU cc_start: 0.9247 (mt) cc_final: 0.8935 (tt) REVERT: 6 287 LEU cc_start: 0.8875 (mp) cc_final: 0.8484 (pt) REVERT: 6 378 ASP cc_start: 0.9141 (m-30) cc_final: 0.8782 (m-30) REVERT: 6 395 CYS cc_start: 0.8592 (m) cc_final: 0.8328 (m) REVERT: 6 452 ILE cc_start: 0.9432 (mt) cc_final: 0.9180 (mt) REVERT: 6 551 MET cc_start: 0.9298 (mtp) cc_final: 0.8999 (mpp) REVERT: 6 583 GLN cc_start: 0.9583 (mp10) cc_final: 0.9354 (mp10) REVERT: 6 608 LEU cc_start: 0.8405 (pt) cc_final: 0.8184 (pp) REVERT: 6 644 MET cc_start: 0.6502 (mtm) cc_final: 0.6294 (mtt) REVERT: 6 699 LEU cc_start: 0.8491 (pt) cc_final: 0.8164 (pt) REVERT: 6 940 TYR cc_start: 0.8298 (t80) cc_final: 0.8082 (t80) REVERT: 7 14 TYR cc_start: 0.8605 (m-80) cc_final: 0.7082 (m-80) REVERT: 7 29 LYS cc_start: 0.8242 (tptt) cc_final: 0.7807 (tmtt) REVERT: 7 116 LEU cc_start: 0.9460 (tt) cc_final: 0.9102 (mt) REVERT: 7 235 LEU cc_start: 0.8952 (mt) cc_final: 0.8700 (mm) REVERT: 7 247 ARG cc_start: 0.8757 (tmt-80) cc_final: 0.8353 (tpt90) REVERT: 7 307 PHE cc_start: 0.8321 (m-80) cc_final: 0.7780 (m-10) REVERT: 7 600 MET cc_start: 0.6698 (ptp) cc_final: 0.6391 (ptt) REVERT: c 43 LYS cc_start: 0.9396 (tptt) cc_final: 0.9165 (tptm) REVERT: c 44 MET cc_start: 0.8858 (ptt) cc_final: 0.8604 (ptt) REVERT: c 45 LEU cc_start: 0.9666 (tp) cc_final: 0.9317 (tp) REVERT: c 49 PHE cc_start: 0.9282 (m-10) cc_final: 0.8679 (m-80) REVERT: c 339 TYR cc_start: 0.9300 (t80) cc_final: 0.9054 (t80) REVERT: c 375 GLU cc_start: 0.9066 (tt0) cc_final: 0.8686 (tm-30) REVERT: c 377 TRP cc_start: 0.9072 (t60) cc_final: 0.8753 (t60) REVERT: c 391 ILE cc_start: 0.9315 (mt) cc_final: 0.9090 (mm) REVERT: c 469 LEU cc_start: 0.9360 (tt) cc_final: 0.8977 (pp) REVERT: c 524 ILE cc_start: 0.6792 (mt) cc_final: 0.6528 (mt) REVERT: c 543 LEU cc_start: 0.9419 (pt) cc_final: 0.9179 (pt) REVERT: c 558 GLU cc_start: 0.7835 (mp0) cc_final: 0.7252 (tp30) REVERT: c 576 THR cc_start: 0.8109 (p) cc_final: 0.7892 (t) REVERT: c 607 MET cc_start: 0.9143 (mtp) cc_final: 0.8765 (mpp) REVERT: D 58 GLN cc_start: 0.9335 (mm-40) cc_final: 0.9071 (mt0) REVERT: D 62 ASP cc_start: 0.9311 (m-30) cc_final: 0.9010 (m-30) REVERT: D 64 MET cc_start: 0.9147 (mmp) cc_final: 0.8621 (mmm) REVERT: D 72 CYS cc_start: 0.9198 (m) cc_final: 0.8943 (m) REVERT: D 93 MET cc_start: 0.8945 (mtm) cc_final: 0.8667 (ptp) REVERT: D 148 LEU cc_start: 0.9716 (mt) cc_final: 0.9071 (pp) REVERT: D 152 ASP cc_start: 0.8977 (m-30) cc_final: 0.8475 (m-30) REVERT: D 200 LYS cc_start: 0.9397 (mmmt) cc_final: 0.9080 (mtmm) REVERT: D 202 MET cc_start: 0.8748 (tpp) cc_final: 0.8421 (tpp) REVERT: D 227 PHE cc_start: 0.8433 (m-80) cc_final: 0.7986 (m-80) REVERT: B 9 GLN cc_start: 0.9559 (mm110) cc_final: 0.9318 (mm110) REVERT: B 74 TRP cc_start: 0.8971 (p-90) cc_final: 0.8645 (p-90) REVERT: B 81 GLN cc_start: 0.9425 (tm-30) cc_final: 0.9138 (tm-30) REVERT: B 99 ASP cc_start: 0.9314 (m-30) cc_final: 0.9099 (m-30) REVERT: B 110 ASP cc_start: 0.9122 (p0) cc_final: 0.8517 (t0) REVERT: B 119 TRP cc_start: 0.8977 (p-90) cc_final: 0.8517 (p-90) REVERT: B 131 LYS cc_start: 0.9214 (ptpp) cc_final: 0.8935 (ptpp) REVERT: B 132 ASP cc_start: 0.9302 (p0) cc_final: 0.9086 (p0) REVERT: B 142 ARG cc_start: 0.8081 (ptp-110) cc_final: 0.7390 (tpp80) REVERT: B 150 GLU cc_start: 0.8849 (mp0) cc_final: 0.8629 (mp0) REVERT: B 177 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8765 (mt-10) REVERT: B 195 ILE cc_start: 0.9499 (pt) cc_final: 0.9188 (pt) REVERT: A 1 MET cc_start: 0.6306 (ppp) cc_final: 0.6011 (ppp) REVERT: A 38 ARG cc_start: 0.9530 (ttm110) cc_final: 0.9111 (tpp-160) REVERT: A 73 PHE cc_start: 0.9093 (m-80) cc_final: 0.8870 (m-80) REVERT: A 98 ASP cc_start: 0.8872 (m-30) cc_final: 0.8604 (m-30) REVERT: C 8 ASP cc_start: 0.9643 (t0) cc_final: 0.9418 (t0) REVERT: C 10 LEU cc_start: 0.9460 (tp) cc_final: 0.9190 (tp) REVERT: C 12 ASP cc_start: 0.9146 (m-30) cc_final: 0.8837 (m-30) REVERT: C 20 PHE cc_start: 0.9269 (m-80) cc_final: 0.8120 (m-80) REVERT: C 24 ILE cc_start: 0.8844 (mp) cc_final: 0.8578 (mm) REVERT: C 44 LEU cc_start: 0.9103 (tp) cc_final: 0.8827 (mm) REVERT: C 48 LEU cc_start: 0.9646 (tp) cc_final: 0.9409 (tp) REVERT: C 126 GLU cc_start: 0.9293 (tp30) cc_final: 0.9060 (mm-30) REVERT: C 176 ILE cc_start: 0.9111 (pt) cc_final: 0.8842 (pt) REVERT: C 185 LYS cc_start: 0.9381 (mtpt) cc_final: 0.9119 (mtpp) REVERT: C 191 MET cc_start: 0.9429 (tpt) cc_final: 0.8985 (tpp) outliers start: 25 outliers final: 3 residues processed: 948 average time/residue: 0.2200 time to fit residues: 338.2392 Evaluate side-chains 666 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 662 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 39 optimal weight: 0.0970 chunk 368 optimal weight: 40.0000 chunk 4 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 chunk 233 optimal weight: 20.0000 chunk 243 optimal weight: 10.0000 chunk 448 optimal weight: 0.0980 chunk 442 optimal weight: 20.0000 chunk 432 optimal weight: 10.0000 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 391 GLN ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 GLN 3 374 HIS 3 376 HIS 3 417 GLN ** 3 503 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 532 ASN ** 3 569 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 673 GLN 4 543 GLN ** 5 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 245 HIS 5 500 GLN 6 362 GLN 6 364 ASN 6 943 GLN 7 87 GLN 7 538 HIS ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 395 ASN c 503 GLN D 110 ASN D 162 ASN D 186 HIS ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.085397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.062619 restraints weight = 228659.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.064629 restraints weight = 149401.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.066085 restraints weight = 109212.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.067105 restraints weight = 86095.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.067842 restraints weight = 71970.011| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 40693 Z= 0.186 Angle : 0.900 19.257 54967 Z= 0.467 Chirality : 0.049 0.349 6368 Planarity : 0.005 0.060 7045 Dihedral : 6.277 56.169 5476 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.93 % Allowed : 8.68 % Favored : 90.39 % Rotamer: Outliers : 0.36 % Allowed : 4.94 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 aren not related in a simple way. whole: -2.16 (0.11), residues: 4931 helix: -0.64 (0.11), residues: 2001 sheet: -1.82 (0.19), residues: 606 loop : -2.00 (0.12), residues: 2324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG 6 918 TYR 0.025 0.002 TYR 4 519 PHE 0.028 0.002 PHE C 80 TRP 0.022 0.002 TRP 3 111 HIS 0.020 0.002 HIS 5 741 Details of bonding type rmsd covalent geometry : bond 0.00396 (40680) covalent geometry : angle 0.89997 (54963) SS BOND : bond 0.00300 ( 2) SS BOND : angle 1.32736 ( 4) hydrogen bonds : bond 0.04474 ( 1483) hydrogen bonds : angle 5.91642 ( 4272) Misc. bond : bond 0.00300 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 814 time to evaluate : 1.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.9499 (tp) cc_final: 0.9266 (mm) REVERT: 2 266 GLU cc_start: 0.8358 (pm20) cc_final: 0.7993 (pm20) REVERT: 2 267 MET cc_start: 0.8797 (ppp) cc_final: 0.8229 (ppp) REVERT: 2 277 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8392 (tm-30) REVERT: 2 293 ILE cc_start: 0.9440 (mp) cc_final: 0.9132 (tt) REVERT: 2 334 LEU cc_start: 0.9756 (tp) cc_final: 0.9537 (pt) REVERT: 2 419 LYS cc_start: 0.9086 (mppt) cc_final: 0.8865 (mmtm) REVERT: 2 501 MET cc_start: 0.8757 (tmm) cc_final: 0.8232 (ttp) REVERT: 2 612 MET cc_start: 0.8462 (mtp) cc_final: 0.7726 (ttp) REVERT: 2 620 ILE cc_start: 0.8617 (mt) cc_final: 0.8361 (mt) REVERT: 2 816 ILE cc_start: 0.9678 (mt) cc_final: 0.8871 (tp) REVERT: 3 205 LYS cc_start: 0.9285 (mppt) cc_final: 0.8657 (tptt) REVERT: 3 260 GLU cc_start: 0.7779 (pm20) cc_final: 0.6756 (pm20) REVERT: 3 264 MET cc_start: 0.6799 (ppp) cc_final: 0.6597 (ppp) REVERT: 3 278 LEU cc_start: 0.9531 (mt) cc_final: 0.9236 (mt) REVERT: 3 281 ASP cc_start: 0.8933 (p0) cc_final: 0.8538 (p0) REVERT: 3 282 LEU cc_start: 0.9436 (mt) cc_final: 0.9146 (mt) REVERT: 3 375 ASP cc_start: 0.9489 (m-30) cc_final: 0.9114 (t0) REVERT: 3 421 PHE cc_start: 0.8335 (t80) cc_final: 0.8095 (t80) REVERT: 3 430 ILE cc_start: 0.8232 (mp) cc_final: 0.7857 (pt) REVERT: 3 683 TYR cc_start: 0.8153 (t80) cc_final: 0.7871 (t80) REVERT: 4 293 LEU cc_start: 0.8212 (tp) cc_final: 0.7777 (pt) REVERT: 4 391 PHE cc_start: 0.8975 (m-80) cc_final: 0.8611 (m-80) REVERT: 4 486 MET cc_start: 0.0571 (mtt) cc_final: 0.0319 (ttt) REVERT: 4 585 THR cc_start: 0.6747 (m) cc_final: 0.6287 (t) REVERT: 4 637 MET cc_start: -0.4204 (mmt) cc_final: -0.4828 (ttm) REVERT: 4 801 MET cc_start: 0.1022 (tpt) cc_final: 0.0739 (tpt) REVERT: 5 32 LYS cc_start: 0.9551 (mttt) cc_final: 0.9264 (mtpp) REVERT: 5 58 ASN cc_start: 0.9230 (t0) cc_final: 0.8980 (t0) REVERT: 5 66 GLU cc_start: 0.8885 (mp0) cc_final: 0.8480 (mp0) REVERT: 5 99 LYS cc_start: 0.9590 (mmtt) cc_final: 0.8922 (mmmt) REVERT: 5 166 ILE cc_start: 0.9766 (mt) cc_final: 0.9307 (tp) REVERT: 5 181 ILE cc_start: 0.8905 (mt) cc_final: 0.8576 (mp) REVERT: 5 276 MET cc_start: 0.9099 (mtm) cc_final: 0.8512 (mtm) REVERT: 5 285 LYS cc_start: 0.9347 (ttmm) cc_final: 0.8981 (mtpt) REVERT: 5 497 MET cc_start: 0.9281 (ptm) cc_final: 0.8866 (ppp) REVERT: 5 500 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7669 (tm-30) REVERT: 5 550 PHE cc_start: 0.9088 (m-10) cc_final: 0.8780 (m-10) REVERT: 5 583 MET cc_start: 0.0323 (mmp) cc_final: -0.1118 (ptt) REVERT: 5 689 MET cc_start: 0.9240 (mmp) cc_final: 0.8856 (mmm) REVERT: 6 160 MET cc_start: 0.9066 (ptt) cc_final: 0.8680 (ptp) REVERT: 6 262 VAL cc_start: 0.9001 (m) cc_final: 0.8759 (t) REVERT: 6 270 LEU cc_start: 0.9238 (mt) cc_final: 0.8911 (tt) REVERT: 6 287 LEU cc_start: 0.8813 (mp) cc_final: 0.8286 (pt) REVERT: 6 454 PHE cc_start: 0.8761 (t80) cc_final: 0.8348 (t80) REVERT: 6 551 MET cc_start: 0.9287 (mtp) cc_final: 0.8964 (mpp) REVERT: 6 644 MET cc_start: 0.6455 (mtm) cc_final: 0.5353 (mtt) REVERT: 6 688 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7816 (mpt180) REVERT: 6 736 MET cc_start: 0.2699 (ptp) cc_final: 0.2372 (ptp) REVERT: 6 915 MET cc_start: 0.7901 (tmm) cc_final: 0.7566 (tmm) REVERT: 6 940 TYR cc_start: 0.8209 (t80) cc_final: 0.7762 (t80) REVERT: 7 14 TYR cc_start: 0.8489 (m-80) cc_final: 0.7295 (m-80) REVERT: 7 29 LYS cc_start: 0.8107 (tptt) cc_final: 0.7704 (tmtt) REVERT: 7 116 LEU cc_start: 0.9461 (tt) cc_final: 0.9155 (mt) REVERT: 7 237 GLN cc_start: 0.7628 (mt0) cc_final: 0.7206 (mt0) REVERT: 7 239 ILE cc_start: 0.9600 (mm) cc_final: 0.9390 (mm) REVERT: 7 307 PHE cc_start: 0.8180 (m-80) cc_final: 0.7640 (m-10) REVERT: 7 402 MET cc_start: 0.9387 (mmp) cc_final: 0.9146 (mmp) REVERT: 7 513 LEU cc_start: 0.9332 (mt) cc_final: 0.9122 (tp) REVERT: c 40 CYS cc_start: 0.9149 (m) cc_final: 0.8884 (p) REVERT: c 45 LEU cc_start: 0.9658 (tp) cc_final: 0.9188 (tp) REVERT: c 49 PHE cc_start: 0.9340 (m-10) cc_final: 0.8603 (m-80) REVERT: c 280 LEU cc_start: 0.9414 (pp) cc_final: 0.8714 (tt) REVERT: c 339 TYR cc_start: 0.9349 (t80) cc_final: 0.9006 (t80) REVERT: c 403 ASP cc_start: 0.8607 (t0) cc_final: 0.8363 (t70) REVERT: c 524 ILE cc_start: 0.7030 (mt) cc_final: 0.6690 (mt) REVERT: c 547 ARG cc_start: 0.9520 (mtp85) cc_final: 0.9288 (ptm160) REVERT: c 554 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8171 (mm-30) REVERT: c 558 GLU cc_start: 0.7634 (mp0) cc_final: 0.7308 (tp30) REVERT: c 576 THR cc_start: 0.8123 (p) cc_final: 0.7914 (t) REVERT: D 58 GLN cc_start: 0.9294 (mm-40) cc_final: 0.9071 (mt0) REVERT: D 62 ASP cc_start: 0.9312 (m-30) cc_final: 0.9003 (m-30) REVERT: D 64 MET cc_start: 0.9147 (mmp) cc_final: 0.8626 (mmm) REVERT: D 89 ASN cc_start: 0.9409 (m110) cc_final: 0.9159 (m110) REVERT: D 134 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9108 (mm-30) REVERT: D 148 LEU cc_start: 0.9750 (mt) cc_final: 0.9214 (pp) REVERT: D 152 ASP cc_start: 0.9023 (m-30) cc_final: 0.8100 (m-30) REVERT: D 156 LEU cc_start: 0.9435 (mt) cc_final: 0.8959 (tp) REVERT: D 200 LYS cc_start: 0.9413 (mmmt) cc_final: 0.9200 (mtmm) REVERT: D 202 MET cc_start: 0.8871 (tpp) cc_final: 0.8537 (tpp) REVERT: D 218 MET cc_start: 0.8435 (mpp) cc_final: 0.7055 (mpp) REVERT: D 227 PHE cc_start: 0.8214 (m-80) cc_final: 0.7594 (m-80) REVERT: D 277 MET cc_start: 0.8730 (mmp) cc_final: 0.7785 (mmm) REVERT: B 9 GLN cc_start: 0.9540 (mm110) cc_final: 0.9303 (mm110) REVERT: B 81 GLN cc_start: 0.9484 (tm-30) cc_final: 0.9272 (tm-30) REVERT: B 99 ASP cc_start: 0.9349 (m-30) cc_final: 0.9128 (m-30) REVERT: B 110 ASP cc_start: 0.9062 (p0) cc_final: 0.8186 (t0) REVERT: B 119 TRP cc_start: 0.9025 (p-90) cc_final: 0.8550 (p-90) REVERT: B 131 LYS cc_start: 0.9218 (ptpp) cc_final: 0.8831 (ptpp) REVERT: B 138 ILE cc_start: 0.8778 (pt) cc_final: 0.8563 (pt) REVERT: B 177 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8698 (mt-10) REVERT: A 73 PHE cc_start: 0.9083 (m-80) cc_final: 0.8870 (m-80) REVERT: A 98 ASP cc_start: 0.9035 (m-30) cc_final: 0.8191 (m-30) REVERT: C 12 ASP cc_start: 0.9077 (m-30) cc_final: 0.8831 (m-30) REVERT: C 20 PHE cc_start: 0.9141 (m-80) cc_final: 0.8317 (m-80) REVERT: C 24 ILE cc_start: 0.8843 (mp) cc_final: 0.8563 (mm) REVERT: C 48 LEU cc_start: 0.9569 (tp) cc_final: 0.9354 (tp) REVERT: C 96 ASP cc_start: 0.8898 (t0) cc_final: 0.8467 (t0) REVERT: C 126 GLU cc_start: 0.9242 (tp30) cc_final: 0.9031 (mm-30) REVERT: C 138 HIS cc_start: 0.9303 (m-70) cc_final: 0.8868 (m170) REVERT: C 191 MET cc_start: 0.9369 (tpt) cc_final: 0.8880 (tpp) outliers start: 16 outliers final: 2 residues processed: 828 average time/residue: 0.2281 time to fit residues: 310.6992 Evaluate side-chains 601 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 598 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 23 optimal weight: 20.0000 chunk 299 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 205 optimal weight: 0.0870 chunk 245 optimal weight: 5.9990 chunk 127 optimal weight: 30.0000 chunk 338 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 121 optimal weight: 0.2980 chunk 440 optimal weight: 0.9980 overall best weight: 2.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 768 HIS 2 779 HIS 3 374 HIS 3 398 HIS 3 493 GLN 3 503 HIS 3 569 HIS ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN ** 5 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 145 GLN ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN B 22 ASN B 179 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.085711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.063059 restraints weight = 224712.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065056 restraints weight = 148225.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066477 restraints weight = 108813.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.067496 restraints weight = 86121.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.068172 restraints weight = 72008.795| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40693 Z= 0.170 Angle : 0.870 15.348 54967 Z= 0.450 Chirality : 0.049 0.332 6368 Planarity : 0.005 0.113 7045 Dihedral : 6.004 44.111 5476 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.89 % Allowed : 8.70 % Favored : 90.41 % Rotamer: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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 aren not related in a simple way. whole: -1.86 (0.11), residues: 4931 helix: -0.31 (0.11), residues: 2009 sheet: -1.66 (0.20), residues: 599 loop : -1.93 (0.12), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 15 TYR 0.026 0.002 TYR 2 434 PHE 0.025 0.002 PHE 6 641 TRP 0.056 0.002 TRP 6 939 HIS 0.011 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00356 (40680) covalent geometry : angle 0.87028 (54963) SS BOND : bond 0.00184 ( 2) SS BOND : angle 1.64430 ( 4) hydrogen bonds : bond 0.04055 ( 1483) hydrogen bonds : angle 5.62824 ( 4272) Misc. bond : bond 0.00370 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 794 time to evaluate : 1.548 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.9533 (tp) cc_final: 0.9287 (mm) REVERT: 2 266 GLU cc_start: 0.8358 (pm20) cc_final: 0.8094 (pm20) REVERT: 2 267 MET cc_start: 0.8787 (ppp) cc_final: 0.8266 (ppp) REVERT: 2 274 VAL cc_start: 0.9245 (t) cc_final: 0.9005 (t) REVERT: 2 277 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8466 (tm-30) REVERT: 2 415 VAL cc_start: 0.9400 (t) cc_final: 0.8722 (t) REVERT: 2 501 MET cc_start: 0.8579 (tmm) cc_final: 0.7957 (ttm) REVERT: 2 551 GLN cc_start: 0.9340 (mt0) cc_final: 0.9067 (mp10) REVERT: 2 606 ILE cc_start: 0.9056 (mt) cc_final: 0.8809 (mm) REVERT: 2 612 MET cc_start: 0.8101 (mtp) cc_final: 0.7534 (ttp) REVERT: 2 620 ILE cc_start: 0.8501 (mt) cc_final: 0.8134 (mt) REVERT: 2 816 ILE cc_start: 0.9591 (mt) cc_final: 0.9384 (tt) REVERT: 3 178 LYS cc_start: 0.9292 (mptt) cc_final: 0.9070 (mptt) REVERT: 3 260 GLU cc_start: 0.7796 (pm20) cc_final: 0.6974 (pm20) REVERT: 3 278 LEU cc_start: 0.9574 (mt) cc_final: 0.9350 (mt) REVERT: 3 281 ASP cc_start: 0.8871 (p0) cc_final: 0.8617 (p0) REVERT: 3 282 LEU cc_start: 0.9508 (mt) cc_final: 0.9276 (mt) REVERT: 3 375 ASP cc_start: 0.9518 (m-30) cc_final: 0.9145 (t0) REVERT: 3 430 ILE cc_start: 0.8249 (mp) cc_final: 0.7909 (pt) REVERT: 3 683 TYR cc_start: 0.8084 (t80) cc_final: 0.7823 (t80) REVERT: 4 293 LEU cc_start: 0.8223 (tp) cc_final: 0.7849 (pt) REVERT: 4 382 MET cc_start: 0.8597 (mmp) cc_final: 0.6592 (tpp) REVERT: 4 391 PHE cc_start: 0.8909 (m-80) cc_final: 0.8657 (m-80) REVERT: 4 486 MET cc_start: 0.0674 (mtt) cc_final: 0.0445 (ttt) REVERT: 4 585 THR cc_start: 0.6750 (m) cc_final: 0.6223 (t) REVERT: 4 637 MET cc_start: -0.4300 (mmt) cc_final: -0.4732 (ttt) REVERT: 4 801 MET cc_start: 0.1355 (tpt) cc_final: 0.0829 (tpt) REVERT: 5 66 GLU cc_start: 0.8818 (mp0) cc_final: 0.8199 (mp0) REVERT: 5 166 ILE cc_start: 0.9730 (mt) cc_final: 0.9226 (tp) REVERT: 5 169 THR cc_start: 0.8119 (p) cc_final: 0.7604 (p) REVERT: 5 181 ILE cc_start: 0.8830 (mt) cc_final: 0.8319 (mm) REVERT: 5 182 MET cc_start: 0.8423 (tpt) cc_final: 0.8156 (tpp) REVERT: 5 254 GLN cc_start: 0.9363 (tp40) cc_final: 0.8212 (tm-30) REVERT: 5 276 MET cc_start: 0.8895 (mtm) cc_final: 0.8392 (mtm) REVERT: 5 285 LYS cc_start: 0.9229 (ttmm) cc_final: 0.8928 (mtpt) REVERT: 5 298 TYR cc_start: 0.8258 (t80) cc_final: 0.8046 (t80) REVERT: 5 393 MET cc_start: 0.8463 (ttt) cc_final: 0.8172 (ttt) REVERT: 5 497 MET cc_start: 0.9196 (ptm) cc_final: 0.8679 (ppp) REVERT: 5 550 PHE cc_start: 0.9104 (m-10) cc_final: 0.8844 (m-10) REVERT: 5 552 MET cc_start: 0.9044 (tpt) cc_final: 0.8577 (tmm) REVERT: 5 573 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6718 (mp) REVERT: 5 574 ASN cc_start: 0.9474 (m110) cc_final: 0.8983 (t0) REVERT: 5 583 MET cc_start: 0.0566 (mmp) cc_final: -0.0883 (ptt) REVERT: 5 689 MET cc_start: 0.9254 (mmp) cc_final: 0.8839 (mmm) REVERT: 6 160 MET cc_start: 0.9105 (ptt) cc_final: 0.8524 (ptp) REVERT: 6 270 LEU cc_start: 0.9247 (mt) cc_final: 0.8881 (tt) REVERT: 6 287 LEU cc_start: 0.8784 (mp) cc_final: 0.7999 (pt) REVERT: 6 393 ASP cc_start: 0.9173 (t0) cc_final: 0.8784 (p0) REVERT: 6 395 CYS cc_start: 0.8713 (m) cc_final: 0.7923 (m) REVERT: 6 454 PHE cc_start: 0.8754 (t80) cc_final: 0.8193 (t80) REVERT: 6 519 MET cc_start: 0.7347 (tpp) cc_final: 0.6785 (mmp) REVERT: 6 583 GLN cc_start: 0.9573 (mp10) cc_final: 0.9287 (mp10) REVERT: 6 644 MET cc_start: 0.5309 (mtm) cc_final: 0.5068 (mtt) REVERT: 6 688 ARG cc_start: 0.8075 (mtt-85) cc_final: 0.7850 (mpt180) REVERT: 6 736 MET cc_start: 0.3099 (ptp) cc_final: 0.2746 (ptp) REVERT: 7 14 TYR cc_start: 0.8514 (m-80) cc_final: 0.7400 (m-10) REVERT: 7 29 LYS cc_start: 0.8087 (tptt) cc_final: 0.7536 (tmtt) REVERT: 7 237 GLN cc_start: 0.7766 (mt0) cc_final: 0.7410 (mt0) REVERT: 7 239 ILE cc_start: 0.9609 (mm) cc_final: 0.9392 (mm) REVERT: 7 247 ARG cc_start: 0.8069 (tpp80) cc_final: 0.7357 (ttp-170) REVERT: 7 307 PHE cc_start: 0.8132 (m-80) cc_final: 0.7513 (m-10) REVERT: 7 459 MET cc_start: 0.8897 (mpp) cc_final: 0.8613 (mmm) REVERT: 7 529 MET cc_start: 0.5110 (ptt) cc_final: 0.4761 (ptt) REVERT: 7 620 HIS cc_start: 0.7740 (p-80) cc_final: 0.7524 (p-80) REVERT: c 40 CYS cc_start: 0.9248 (m) cc_final: 0.8848 (m) REVERT: c 45 LEU cc_start: 0.9701 (tp) cc_final: 0.9245 (tp) REVERT: c 49 PHE cc_start: 0.9306 (m-10) cc_final: 0.8560 (m-80) REVERT: c 122 VAL cc_start: 0.9376 (p) cc_final: 0.8924 (m) REVERT: c 280 LEU cc_start: 0.9515 (pp) cc_final: 0.8762 (tt) REVERT: c 339 TYR cc_start: 0.9395 (t80) cc_final: 0.8982 (t80) REVERT: c 380 MET cc_start: 0.8476 (mtm) cc_final: 0.8238 (mtm) REVERT: c 387 GLU cc_start: 0.7809 (pp20) cc_final: 0.7578 (pp20) REVERT: c 388 LEU cc_start: 0.8714 (mt) cc_final: 0.8492 (mt) REVERT: c 524 ILE cc_start: 0.7027 (mt) cc_final: 0.6691 (mt) REVERT: c 547 ARG cc_start: 0.9508 (mtp85) cc_final: 0.9208 (ptm160) REVERT: c 554 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8293 (mm-30) REVERT: c 558 GLU cc_start: 0.7603 (mp0) cc_final: 0.7364 (tp30) REVERT: c 576 THR cc_start: 0.8131 (p) cc_final: 0.7922 (t) REVERT: D 58 GLN cc_start: 0.9296 (mm-40) cc_final: 0.9078 (mt0) REVERT: D 62 ASP cc_start: 0.9297 (m-30) cc_final: 0.8989 (m-30) REVERT: D 64 MET cc_start: 0.9133 (mmp) cc_final: 0.8629 (mmm) REVERT: D 129 MET cc_start: 0.9468 (mmp) cc_final: 0.9202 (mmm) REVERT: D 134 GLU cc_start: 0.9454 (mm-30) cc_final: 0.8884 (mm-30) REVERT: D 148 LEU cc_start: 0.9668 (mt) cc_final: 0.9365 (mt) REVERT: D 156 LEU cc_start: 0.9464 (mt) cc_final: 0.8958 (tp) REVERT: D 200 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9234 (mtmm) REVERT: D 202 MET cc_start: 0.8913 (tpp) cc_final: 0.8552 (tpp) REVERT: D 218 MET cc_start: 0.8511 (mpp) cc_final: 0.7209 (mpp) REVERT: D 277 MET cc_start: 0.8611 (mmp) cc_final: 0.7858 (mmm) REVERT: B 99 ASP cc_start: 0.9105 (m-30) cc_final: 0.8856 (m-30) REVERT: B 110 ASP cc_start: 0.9057 (p0) cc_final: 0.8165 (t0) REVERT: B 119 TRP cc_start: 0.9045 (p-90) cc_final: 0.8470 (p-90) REVERT: B 131 LYS cc_start: 0.9162 (ptpp) cc_final: 0.8863 (ptpp) REVERT: B 138 ILE cc_start: 0.8814 (pt) cc_final: 0.8583 (pt) REVERT: B 150 GLU cc_start: 0.9131 (mp0) cc_final: 0.8926 (mp0) REVERT: B 160 LEU cc_start: 0.9670 (tp) cc_final: 0.9456 (tp) REVERT: B 177 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8747 (mt-10) REVERT: A 12 GLU cc_start: 0.9331 (pt0) cc_final: 0.9111 (pt0) REVERT: A 34 GLU cc_start: 0.8874 (mp0) cc_final: 0.8260 (mp0) REVERT: A 38 ARG cc_start: 0.9551 (ttm110) cc_final: 0.9154 (tpp-160) REVERT: A 73 PHE cc_start: 0.9105 (m-80) cc_final: 0.8898 (m-80) REVERT: A 79 MET cc_start: 0.9066 (mmm) cc_final: 0.8834 (mmm) REVERT: A 198 ARG cc_start: 0.7650 (ptp-170) cc_final: 0.7306 (ptp-170) REVERT: C 8 ASP cc_start: 0.9573 (t0) cc_final: 0.9342 (t0) REVERT: C 12 ASP cc_start: 0.9099 (m-30) cc_final: 0.8787 (m-30) REVERT: C 20 PHE cc_start: 0.9292 (m-80) cc_final: 0.8868 (m-10) REVERT: C 24 ILE cc_start: 0.8872 (mp) cc_final: 0.8620 (mm) REVERT: C 48 LEU cc_start: 0.9565 (tp) cc_final: 0.9256 (tp) REVERT: C 126 GLU cc_start: 0.9322 (tp30) cc_final: 0.9010 (mm-30) REVERT: C 138 HIS cc_start: 0.9376 (m-70) cc_final: 0.8938 (m-70) REVERT: C 182 GLU cc_start: 0.9257 (mp0) cc_final: 0.8715 (mp0) REVERT: C 185 LYS cc_start: 0.9392 (mtpt) cc_final: 0.9032 (mtmm) REVERT: C 191 MET cc_start: 0.9344 (tpt) cc_final: 0.8671 (tpp) outliers start: 5 outliers final: 1 residues processed: 799 average time/residue: 0.2170 time to fit residues: 284.5987 Evaluate side-chains 595 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 593 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 23 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 333 optimal weight: 10.0000 chunk 246 optimal weight: 0.0970 chunk 236 optimal weight: 20.0000 chunk 307 optimal weight: 5.9990 chunk 308 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 416 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS 3 210 HIS 3 374 HIS 3 398 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 673 GLN ** 3 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 543 GLN 5 155 HIS ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 585 ASN ** 7 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 GLN ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 186 HIS A 28 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.081964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.059805 restraints weight = 234574.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.061713 restraints weight = 153843.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.063070 restraints weight = 112771.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.064061 restraints weight = 89519.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.064757 restraints weight = 74982.603| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.208 40693 Z= 0.204 Angle : 0.878 16.384 54967 Z= 0.455 Chirality : 0.048 0.352 6368 Planarity : 0.005 0.119 7045 Dihedral : 6.330 164.045 5476 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.31 % Favored : 89.82 % Rotamer: Outliers : 0.07 % Allowed : 3.84 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.71 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 aren not related in a simple way. whole: -1.80 (0.11), residues: 4931 helix: -0.19 (0.11), residues: 2025 sheet: -1.72 (0.19), residues: 605 loop : -1.96 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 3 657 TYR 0.028 0.002 TYR 2 434 PHE 0.056 0.002 PHE D 227 TRP 0.031 0.002 TRP 6 939 HIS 0.010 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00433 (40680) covalent geometry : angle 0.87777 (54963) SS BOND : bond 0.00091 ( 2) SS BOND : angle 1.32458 ( 4) hydrogen bonds : bond 0.03979 ( 1483) hydrogen bonds : angle 5.58247 ( 4272) Misc. bond : bond 0.00846 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 735 time to evaluate : 1.464 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 258 LEU cc_start: 0.9537 (tp) cc_final: 0.9322 (mm) REVERT: 2 266 GLU cc_start: 0.8282 (pm20) cc_final: 0.8029 (pm20) REVERT: 2 267 MET cc_start: 0.8769 (ppp) cc_final: 0.8374 (ppp) REVERT: 2 274 VAL cc_start: 0.9315 (t) cc_final: 0.9077 (t) REVERT: 2 277 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8610 (tm-30) REVERT: 2 331 PHE cc_start: 0.9052 (m-80) cc_final: 0.8728 (m-80) REVERT: 2 501 MET cc_start: 0.8543 (tmm) cc_final: 0.7920 (ttm) REVERT: 2 629 ILE cc_start: 0.7760 (tp) cc_final: 0.7507 (mm) REVERT: 2 677 PHE cc_start: 0.8916 (m-10) cc_final: 0.8533 (m-80) REVERT: 2 816 ILE cc_start: 0.9638 (mt) cc_final: 0.9418 (tt) REVERT: 3 178 LYS cc_start: 0.9192 (mptt) cc_final: 0.8967 (mppt) REVERT: 3 260 GLU cc_start: 0.7771 (pm20) cc_final: 0.7016 (pm20) REVERT: 3 261 MET cc_start: 0.7692 (mmm) cc_final: 0.7181 (mmm) REVERT: 3 278 LEU cc_start: 0.9629 (mt) cc_final: 0.9381 (mt) REVERT: 3 281 ASP cc_start: 0.8933 (p0) cc_final: 0.8564 (p0) REVERT: 3 282 LEU cc_start: 0.9579 (mt) cc_final: 0.9374 (mt) REVERT: 3 474 GLU cc_start: 0.9313 (mp0) cc_final: 0.9108 (mp0) REVERT: 4 293 LEU cc_start: 0.8339 (tp) cc_final: 0.8005 (pt) REVERT: 4 382 MET cc_start: 0.8710 (mmp) cc_final: 0.8455 (mmp) REVERT: 4 391 PHE cc_start: 0.8920 (m-80) cc_final: 0.8502 (m-80) REVERT: 4 457 TYR cc_start: 0.9470 (m-10) cc_final: 0.9238 (m-80) REVERT: 4 582 HIS cc_start: 0.8472 (t70) cc_final: 0.8258 (t70) REVERT: 4 585 THR cc_start: 0.6587 (m) cc_final: 0.6134 (t) REVERT: 4 637 MET cc_start: -0.4197 (mmt) cc_final: -0.4599 (ttt) REVERT: 4 801 MET cc_start: 0.1473 (tpt) cc_final: 0.0689 (tpt) REVERT: 5 48 ASP cc_start: 0.9206 (m-30) cc_final: 0.8846 (p0) REVERT: 5 58 ASN cc_start: 0.9311 (t0) cc_final: 0.9105 (t0) REVERT: 5 66 GLU cc_start: 0.8682 (mp0) cc_final: 0.8334 (mp0) REVERT: 5 99 LYS cc_start: 0.9478 (mmtt) cc_final: 0.8884 (mmmt) REVERT: 5 166 ILE cc_start: 0.9792 (mt) cc_final: 0.9326 (tp) REVERT: 5 181 ILE cc_start: 0.8815 (mt) cc_final: 0.8525 (mp) REVERT: 5 276 MET cc_start: 0.8979 (mtm) cc_final: 0.8349 (mtm) REVERT: 5 285 LYS cc_start: 0.9287 (ttmm) cc_final: 0.8928 (mtpp) REVERT: 5 357 PHE cc_start: 0.7944 (m-10) cc_final: 0.7728 (m-80) REVERT: 5 393 MET cc_start: 0.8529 (ttt) cc_final: 0.8263 (ttm) REVERT: 5 497 MET cc_start: 0.9255 (ptm) cc_final: 0.9004 (ppp) REVERT: 5 500 GLN cc_start: 0.8782 (mm-40) cc_final: 0.8434 (mm110) REVERT: 5 550 PHE cc_start: 0.9218 (m-10) cc_final: 0.8994 (m-10) REVERT: 5 552 MET cc_start: 0.9067 (tpt) cc_final: 0.8631 (tpp) REVERT: 5 574 ASN cc_start: 0.9383 (m110) cc_final: 0.8736 (t0) REVERT: 5 583 MET cc_start: 0.0585 (mmp) cc_final: -0.0906 (ptt) REVERT: 5 599 MET cc_start: 0.9504 (ptp) cc_final: 0.9034 (ptp) REVERT: 5 684 PHE cc_start: 0.8921 (t80) cc_final: 0.8705 (t80) REVERT: 5 689 MET cc_start: 0.9278 (mmp) cc_final: 0.8884 (mmm) REVERT: 6 160 MET cc_start: 0.9181 (ptt) cc_final: 0.8582 (ptp) REVERT: 6 270 LEU cc_start: 0.9252 (mt) cc_final: 0.8956 (tp) REVERT: 6 287 LEU cc_start: 0.8782 (mp) cc_final: 0.8094 (pt) REVERT: 6 393 ASP cc_start: 0.9262 (t0) cc_final: 0.8834 (p0) REVERT: 6 395 CYS cc_start: 0.8786 (m) cc_final: 0.7082 (m) REVERT: 6 519 MET cc_start: 0.7260 (tpp) cc_final: 0.6786 (mmp) REVERT: 6 652 ILE cc_start: 0.9275 (tp) cc_final: 0.8994 (tp) REVERT: 6 688 ARG cc_start: 0.8056 (mtt-85) cc_final: 0.7781 (mpt180) REVERT: 6 736 MET cc_start: 0.3082 (ptp) cc_final: 0.2739 (ptp) REVERT: 7 14 TYR cc_start: 0.8604 (m-80) cc_final: 0.7600 (m-10) REVERT: 7 29 LYS cc_start: 0.8227 (tptt) cc_final: 0.7940 (mmmt) REVERT: 7 307 PHE cc_start: 0.8347 (m-80) cc_final: 0.7690 (m-10) REVERT: 7 313 CYS cc_start: 0.9321 (p) cc_final: 0.9113 (p) REVERT: 7 600 MET cc_start: 0.6194 (ptt) cc_final: 0.5947 (ptp) REVERT: c 45 LEU cc_start: 0.9709 (tp) cc_final: 0.9356 (tp) REVERT: c 49 PHE cc_start: 0.9361 (m-10) cc_final: 0.8604 (m-80) REVERT: c 50 LYS cc_start: 0.9716 (ttmt) cc_final: 0.9443 (ttmt) REVERT: c 280 LEU cc_start: 0.9556 (pp) cc_final: 0.8868 (tt) REVERT: c 339 TYR cc_start: 0.9451 (t80) cc_final: 0.8900 (t80) REVERT: c 361 LYS cc_start: 0.9146 (ttmt) cc_final: 0.8564 (tptp) REVERT: c 375 GLU cc_start: 0.9007 (tt0) cc_final: 0.8746 (tt0) REVERT: c 387 GLU cc_start: 0.8060 (pp20) cc_final: 0.7816 (pp20) REVERT: c 388 LEU cc_start: 0.8974 (mt) cc_final: 0.8655 (mt) REVERT: c 403 ASP cc_start: 0.8837 (t70) cc_final: 0.8578 (t70) REVERT: c 524 ILE cc_start: 0.7255 (mt) cc_final: 0.6901 (mt) REVERT: c 547 ARG cc_start: 0.9545 (mtp85) cc_final: 0.9094 (ptp-110) REVERT: c 554 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8458 (mm-30) REVERT: c 576 THR cc_start: 0.8020 (p) cc_final: 0.7804 (t) REVERT: D 58 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9105 (mt0) REVERT: D 62 ASP cc_start: 0.9342 (m-30) cc_final: 0.9020 (m-30) REVERT: D 64 MET cc_start: 0.9161 (mmp) cc_final: 0.8665 (mmm) REVERT: D 134 GLU cc_start: 0.9417 (mm-30) cc_final: 0.8969 (mm-30) REVERT: D 148 LEU cc_start: 0.9752 (mt) cc_final: 0.9480 (mt) REVERT: D 152 ASP cc_start: 0.8675 (m-30) cc_final: 0.8280 (m-30) REVERT: D 156 LEU cc_start: 0.9477 (mt) cc_final: 0.8906 (tp) REVERT: D 202 MET cc_start: 0.8987 (tpp) cc_final: 0.8616 (tpp) REVERT: D 218 MET cc_start: 0.8683 (mpp) cc_final: 0.7402 (mpp) REVERT: D 251 PHE cc_start: 0.8500 (m-80) cc_final: 0.8262 (m-80) REVERT: D 277 MET cc_start: 0.9018 (mmp) cc_final: 0.8651 (mmp) REVERT: B 74 TRP cc_start: 0.8993 (p-90) cc_final: 0.8682 (p-90) REVERT: B 95 THR cc_start: 0.8031 (t) cc_final: 0.7654 (m) REVERT: B 99 ASP cc_start: 0.9159 (m-30) cc_final: 0.8942 (m-30) REVERT: B 119 TRP cc_start: 0.9171 (p-90) cc_final: 0.8380 (p-90) REVERT: B 138 ILE cc_start: 0.8870 (pt) cc_final: 0.8649 (pt) REVERT: B 160 LEU cc_start: 0.9669 (tp) cc_final: 0.9407 (tt) REVERT: B 175 LEU cc_start: 0.9752 (tp) cc_final: 0.9437 (mt) REVERT: B 177 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8687 (mt-10) REVERT: A 34 GLU cc_start: 0.8801 (mp0) cc_final: 0.8522 (mp0) REVERT: A 85 CYS cc_start: 0.9428 (t) cc_final: 0.9217 (m) REVERT: C 8 ASP cc_start: 0.9579 (t0) cc_final: 0.9347 (t0) REVERT: C 12 ASP cc_start: 0.9169 (m-30) cc_final: 0.8828 (m-30) REVERT: C 20 PHE cc_start: 0.9481 (m-80) cc_final: 0.8500 (m-10) REVERT: C 24 ILE cc_start: 0.8978 (mp) cc_final: 0.8751 (mm) REVERT: C 48 LEU cc_start: 0.9553 (tp) cc_final: 0.9342 (tp) REVERT: C 126 GLU cc_start: 0.9312 (tp30) cc_final: 0.9096 (mm-30) REVERT: C 138 HIS cc_start: 0.9420 (m-70) cc_final: 0.9052 (m-70) REVERT: C 191 MET cc_start: 0.9340 (tpt) cc_final: 0.8665 (tpt) outliers start: 4 outliers final: 1 residues processed: 738 average time/residue: 0.2253 time to fit residues: 275.2535 Evaluate side-chains 560 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 559 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 145 optimal weight: 0.3980 chunk 144 optimal weight: 8.9990 chunk 137 optimal weight: 0.0370 chunk 167 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 308 optimal weight: 9.9990 chunk 407 optimal weight: 1.9990 chunk 436 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 344 optimal weight: 20.0000 overall best weight: 2.0864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 398 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 646 HIS 6 659 GLN ** 7 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 13 ASN D 162 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 179 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.083279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.061068 restraints weight = 235774.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.063086 restraints weight = 152029.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064520 restraints weight = 110057.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.065533 restraints weight = 86336.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.066281 restraints weight = 72026.254| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 40693 Z= 0.164 Angle : 0.855 17.697 54967 Z= 0.441 Chirality : 0.048 0.390 6368 Planarity : 0.006 0.298 7045 Dihedral : 6.090 141.722 5476 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.83 % Allowed : 8.70 % Favored : 90.47 % Rotamer: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.75 % 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 aren not related in a simple way. whole: -1.69 (0.12), residues: 4931 helix: -0.04 (0.11), residues: 2028 sheet: -1.72 (0.20), residues: 595 loop : -1.93 (0.13), residues: 2308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 3 657 TYR 0.027 0.001 TYR 2 434 PHE 0.046 0.002 PHE 3 28 TRP 0.033 0.002 TRP 6 939 HIS 0.009 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00342 (40680) covalent geometry : angle 0.85524 (54963) SS BOND : bond 0.00306 ( 2) SS BOND : angle 1.20132 ( 4) hydrogen bonds : bond 0.03785 ( 1483) hydrogen bonds : angle 5.41210 ( 4272) Misc. bond : bond 0.00302 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 737 time to evaluate : 0.974 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 242 LEU cc_start: 0.9486 (tt) cc_final: 0.9285 (tt) REVERT: 2 258 LEU cc_start: 0.9540 (tp) cc_final: 0.9322 (mm) REVERT: 2 266 GLU cc_start: 0.8127 (pm20) cc_final: 0.7818 (pm20) REVERT: 2 267 MET cc_start: 0.8788 (ppp) cc_final: 0.8420 (ppp) REVERT: 2 274 VAL cc_start: 0.9345 (t) cc_final: 0.9065 (t) REVERT: 2 331 PHE cc_start: 0.9029 (m-80) cc_final: 0.8727 (m-80) REVERT: 2 501 MET cc_start: 0.8474 (tmm) cc_final: 0.7882 (ttm) REVERT: 2 551 GLN cc_start: 0.9343 (mt0) cc_final: 0.9100 (mp10) REVERT: 2 612 MET cc_start: 0.9054 (ptt) cc_final: 0.8318 (ttp) REVERT: 2 651 ASN cc_start: 0.8876 (m110) cc_final: 0.8214 (p0) REVERT: 2 677 PHE cc_start: 0.8903 (m-10) cc_final: 0.8530 (m-80) REVERT: 2 816 ILE cc_start: 0.9626 (mt) cc_final: 0.8980 (tt) REVERT: 3 136 MET cc_start: 0.8202 (mmp) cc_final: 0.7811 (mmm) REVERT: 3 178 LYS cc_start: 0.9219 (mptt) cc_final: 0.8977 (mptt) REVERT: 3 260 GLU cc_start: 0.7613 (pm20) cc_final: 0.7373 (pm20) REVERT: 3 278 LEU cc_start: 0.9596 (mt) cc_final: 0.9378 (mt) REVERT: 3 281 ASP cc_start: 0.8788 (p0) cc_final: 0.8529 (p0) REVERT: 3 282 LEU cc_start: 0.9548 (mt) cc_final: 0.9325 (mt) REVERT: 3 474 GLU cc_start: 0.9330 (mp0) cc_final: 0.9104 (mp0) REVERT: 4 293 LEU cc_start: 0.8270 (tp) cc_final: 0.8039 (pt) REVERT: 4 391 PHE cc_start: 0.8730 (m-80) cc_final: 0.8448 (m-80) REVERT: 4 457 TYR cc_start: 0.9459 (m-10) cc_final: 0.9252 (m-80) REVERT: 4 582 HIS cc_start: 0.8457 (t70) cc_final: 0.8232 (t70) REVERT: 4 585 THR cc_start: 0.6467 (m) cc_final: 0.6005 (t) REVERT: 4 637 MET cc_start: -0.3896 (mmt) cc_final: -0.4434 (ttt) REVERT: 4 801 MET cc_start: 0.1522 (tpt) cc_final: 0.0670 (tpt) REVERT: 5 48 ASP cc_start: 0.9201 (m-30) cc_final: 0.8815 (p0) REVERT: 5 58 ASN cc_start: 0.9294 (t0) cc_final: 0.9066 (t0) REVERT: 5 66 GLU cc_start: 0.8594 (mp0) cc_final: 0.8232 (mp0) REVERT: 5 99 LYS cc_start: 0.9438 (mmtt) cc_final: 0.8879 (mmmt) REVERT: 5 166 ILE cc_start: 0.9689 (mt) cc_final: 0.8965 (tp) REVERT: 5 181 ILE cc_start: 0.8771 (mt) cc_final: 0.8496 (mp) REVERT: 5 182 MET cc_start: 0.8296 (tpt) cc_final: 0.7947 (tpp) REVERT: 5 276 MET cc_start: 0.8817 (mtm) cc_final: 0.8232 (mtm) REVERT: 5 285 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8919 (mtpt) REVERT: 5 497 MET cc_start: 0.9258 (ptm) cc_final: 0.9047 (ppp) REVERT: 5 500 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8397 (mm110) REVERT: 5 552 MET cc_start: 0.9137 (tpt) cc_final: 0.8791 (tpp) REVERT: 5 583 MET cc_start: 0.0668 (mmp) cc_final: -0.0819 (ptt) REVERT: 5 599 MET cc_start: 0.9395 (ptp) cc_final: 0.8880 (ptp) REVERT: 5 684 PHE cc_start: 0.8905 (t80) cc_final: 0.8696 (t80) REVERT: 5 689 MET cc_start: 0.9278 (mmp) cc_final: 0.8871 (mmm) REVERT: 6 160 MET cc_start: 0.9164 (ptt) cc_final: 0.8580 (ptp) REVERT: 6 270 LEU cc_start: 0.9211 (mt) cc_final: 0.8845 (tt) REVERT: 6 287 LEU cc_start: 0.8530 (mp) cc_final: 0.7858 (pt) REVERT: 6 393 ASP cc_start: 0.9249 (t0) cc_final: 0.8817 (p0) REVERT: 6 395 CYS cc_start: 0.8845 (m) cc_final: 0.7177 (m) REVERT: 6 401 GLU cc_start: 0.8825 (tt0) cc_final: 0.8347 (tt0) REVERT: 6 519 MET cc_start: 0.7350 (tpp) cc_final: 0.6906 (mmp) REVERT: 6 644 MET cc_start: 0.4405 (mtt) cc_final: 0.4074 (mtt) REVERT: 6 652 ILE cc_start: 0.9272 (tp) cc_final: 0.9044 (tp) REVERT: 6 688 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7767 (mpt180) REVERT: 6 736 MET cc_start: 0.3264 (ptp) cc_final: 0.2862 (ptp) REVERT: 6 779 GLU cc_start: 0.9283 (pt0) cc_final: 0.8754 (tm-30) REVERT: 7 14 TYR cc_start: 0.8629 (m-80) cc_final: 0.7728 (m-80) REVERT: 7 29 LYS cc_start: 0.8121 (tptt) cc_final: 0.7821 (mmmt) REVERT: 7 235 LEU cc_start: 0.9283 (mm) cc_final: 0.9054 (mm) REVERT: 7 250 ASP cc_start: 0.9470 (p0) cc_final: 0.8906 (t70) REVERT: 7 307 PHE cc_start: 0.8295 (m-80) cc_final: 0.7582 (m-10) REVERT: 7 313 CYS cc_start: 0.9325 (p) cc_final: 0.9113 (m) REVERT: 7 314 LYS cc_start: 0.9572 (mmpt) cc_final: 0.8993 (mmtp) REVERT: 7 600 MET cc_start: 0.6258 (ptt) cc_final: 0.5975 (ptp) REVERT: c 45 LEU cc_start: 0.9649 (tp) cc_final: 0.9291 (tp) REVERT: c 49 PHE cc_start: 0.9329 (m-10) cc_final: 0.8552 (m-80) REVERT: c 50 LYS cc_start: 0.9704 (ttmt) cc_final: 0.9410 (ttmm) REVERT: c 280 LEU cc_start: 0.9546 (pp) cc_final: 0.8854 (tt) REVERT: c 339 TYR cc_start: 0.9499 (t80) cc_final: 0.8878 (t80) REVERT: c 375 GLU cc_start: 0.9015 (tt0) cc_final: 0.8774 (tt0) REVERT: c 387 GLU cc_start: 0.8017 (pp20) cc_final: 0.7774 (pp20) REVERT: c 388 LEU cc_start: 0.8917 (mt) cc_final: 0.8590 (mt) REVERT: c 403 ASP cc_start: 0.8780 (t70) cc_final: 0.8510 (t70) REVERT: c 426 GLU cc_start: 0.9426 (mp0) cc_final: 0.9188 (mp0) REVERT: c 469 LEU cc_start: 0.9320 (tt) cc_final: 0.8891 (pp) REVERT: c 524 ILE cc_start: 0.7252 (mt) cc_final: 0.6897 (mt) REVERT: c 547 ARG cc_start: 0.9521 (mtp85) cc_final: 0.9083 (ptp-110) REVERT: c 554 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8389 (mm-30) REVERT: D 58 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9102 (mt0) REVERT: D 62 ASP cc_start: 0.9334 (m-30) cc_final: 0.9011 (m-30) REVERT: D 64 MET cc_start: 0.9125 (mmp) cc_final: 0.8606 (mmm) REVERT: D 131 THR cc_start: 0.9693 (p) cc_final: 0.9489 (p) REVERT: D 134 GLU cc_start: 0.9434 (mm-30) cc_final: 0.8975 (mm-30) REVERT: D 148 LEU cc_start: 0.9649 (mt) cc_final: 0.9111 (pp) REVERT: D 152 ASP cc_start: 0.8530 (m-30) cc_final: 0.8291 (m-30) REVERT: D 156 LEU cc_start: 0.9471 (mt) cc_final: 0.8983 (tp) REVERT: D 175 LEU cc_start: 0.9186 (mp) cc_final: 0.8588 (tp) REVERT: D 202 MET cc_start: 0.8880 (tpp) cc_final: 0.8610 (tpp) REVERT: D 218 MET cc_start: 0.8637 (mpp) cc_final: 0.7656 (mpp) REVERT: D 227 PHE cc_start: 0.8435 (m-80) cc_final: 0.7602 (m-10) REVERT: D 251 PHE cc_start: 0.8450 (m-80) cc_final: 0.8183 (m-80) REVERT: D 277 MET cc_start: 0.8926 (mmp) cc_final: 0.8123 (mmp) REVERT: B 7 LEU cc_start: 0.8710 (mp) cc_final: 0.8411 (mp) REVERT: B 95 THR cc_start: 0.8043 (t) cc_final: 0.7675 (m) REVERT: B 99 ASP cc_start: 0.9156 (m-30) cc_final: 0.8924 (m-30) REVERT: B 119 TRP cc_start: 0.9141 (p-90) cc_final: 0.8253 (p-90) REVERT: B 138 ILE cc_start: 0.8889 (pt) cc_final: 0.8657 (pt) REVERT: B 160 LEU cc_start: 0.9646 (tp) cc_final: 0.9387 (tt) REVERT: B 175 LEU cc_start: 0.9761 (tp) cc_final: 0.9454 (mt) REVERT: B 177 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8703 (mt-10) REVERT: A 38 ARG cc_start: 0.9548 (ttm110) cc_final: 0.9146 (tpp-160) REVERT: A 49 LYS cc_start: 0.9324 (mptt) cc_final: 0.9054 (ptpt) REVERT: C 8 ASP cc_start: 0.9548 (t0) cc_final: 0.9269 (t0) REVERT: C 12 ASP cc_start: 0.9120 (m-30) cc_final: 0.8781 (m-30) REVERT: C 20 PHE cc_start: 0.9352 (m-80) cc_final: 0.8487 (m-10) REVERT: C 48 LEU cc_start: 0.9514 (tp) cc_final: 0.9272 (tp) REVERT: C 109 ILE cc_start: 0.9636 (pt) cc_final: 0.9210 (tp) REVERT: C 126 GLU cc_start: 0.9298 (tp30) cc_final: 0.9062 (mm-30) REVERT: C 138 HIS cc_start: 0.9426 (m-70) cc_final: 0.8792 (m-70) REVERT: C 182 GLU cc_start: 0.9325 (mp0) cc_final: 0.9030 (mp0) REVERT: C 185 LYS cc_start: 0.9446 (mtpt) cc_final: 0.9170 (mtmm) REVERT: C 191 MET cc_start: 0.9298 (tpt) cc_final: 0.8657 (tpp) outliers start: 2 outliers final: 1 residues processed: 739 average time/residue: 0.2070 time to fit residues: 253.0477 Evaluate side-chains 563 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 562 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 144 optimal weight: 30.0000 chunk 333 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 399 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 218 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 331 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 201 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS 3 398 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 76 ASN 7 209 GLN ** 7 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 493 ASN ** c 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN B 172 ASN B 179 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.080303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.058436 restraints weight = 241756.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.060383 restraints weight = 155281.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.061751 restraints weight = 112580.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.062708 restraints weight = 88632.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.063408 restraints weight = 74153.177| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 40693 Z= 0.204 Angle : 0.867 18.674 54967 Z= 0.450 Chirality : 0.048 0.436 6368 Planarity : 0.005 0.233 7045 Dihedral : 6.143 151.423 5476 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.13 % Favored : 90.04 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.73 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -1.72 (0.12), residues: 4931 helix: -0.04 (0.11), residues: 2017 sheet: -1.83 (0.20), residues: 594 loop : -1.94 (0.12), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 6 918 TYR 0.017 0.002 TYR D 256 PHE 0.029 0.002 PHE C 115 TRP 0.069 0.002 TRP 6 939 HIS 0.009 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00430 (40680) covalent geometry : angle 0.86694 (54963) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.16734 ( 4) hydrogen bonds : bond 0.03786 ( 1483) hydrogen bonds : angle 5.50206 ( 4272) Misc. bond : bond 0.00494 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 680 time to evaluate : 1.274 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 242 LEU cc_start: 0.9500 (tt) cc_final: 0.9299 (tt) REVERT: 2 266 GLU cc_start: 0.8385 (pm20) cc_final: 0.8012 (pm20) REVERT: 2 267 MET cc_start: 0.8893 (ppp) cc_final: 0.8509 (ppp) REVERT: 2 277 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8705 (tm-30) REVERT: 2 314 LEU cc_start: 0.9421 (pp) cc_final: 0.9169 (pp) REVERT: 2 331 PHE cc_start: 0.9014 (m-80) cc_final: 0.8631 (m-80) REVERT: 2 416 ASP cc_start: 0.8903 (t70) cc_final: 0.8662 (t0) REVERT: 2 501 MET cc_start: 0.8498 (tmm) cc_final: 0.7833 (ttm) REVERT: 2 551 GLN cc_start: 0.9372 (mt0) cc_final: 0.9119 (mp10) REVERT: 2 612 MET cc_start: 0.9175 (ptt) cc_final: 0.8154 (ttp) REVERT: 2 616 ASP cc_start: 0.9154 (t0) cc_final: 0.8862 (t70) REVERT: 2 620 ILE cc_start: 0.8692 (mt) cc_final: 0.8215 (mt) REVERT: 2 651 ASN cc_start: 0.8835 (m110) cc_final: 0.7968 (p0) REVERT: 2 677 PHE cc_start: 0.8901 (m-10) cc_final: 0.8469 (m-80) REVERT: 3 136 MET cc_start: 0.8184 (mmp) cc_final: 0.7776 (mmm) REVERT: 3 176 LEU cc_start: 0.9092 (tt) cc_final: 0.8710 (tp) REVERT: 3 178 LYS cc_start: 0.9192 (mptt) cc_final: 0.8958 (mppt) REVERT: 3 278 LEU cc_start: 0.9634 (mt) cc_final: 0.9419 (mt) REVERT: 3 281 ASP cc_start: 0.8918 (p0) cc_final: 0.8590 (p0) REVERT: 3 474 GLU cc_start: 0.9377 (mp0) cc_final: 0.9037 (mp0) REVERT: 4 382 MET cc_start: 0.8855 (mmt) cc_final: 0.8283 (mmp) REVERT: 4 391 PHE cc_start: 0.8761 (m-80) cc_final: 0.8471 (m-80) REVERT: 4 457 TYR cc_start: 0.9498 (m-10) cc_final: 0.9207 (m-80) REVERT: 4 582 HIS cc_start: 0.8555 (t70) cc_final: 0.8343 (t70) REVERT: 4 585 THR cc_start: 0.6464 (m) cc_final: 0.6006 (t) REVERT: 4 801 MET cc_start: 0.1337 (tpt) cc_final: 0.0674 (tpt) REVERT: 5 48 ASP cc_start: 0.9213 (m-30) cc_final: 0.8849 (p0) REVERT: 5 58 ASN cc_start: 0.9333 (t0) cc_final: 0.9074 (t0) REVERT: 5 66 GLU cc_start: 0.8530 (mp0) cc_final: 0.8240 (mp0) REVERT: 5 166 ILE cc_start: 0.9664 (mt) cc_final: 0.9056 (tp) REVERT: 5 181 ILE cc_start: 0.8783 (mt) cc_final: 0.8486 (mp) REVERT: 5 182 MET cc_start: 0.8413 (tpt) cc_final: 0.8155 (tpp) REVERT: 5 276 MET cc_start: 0.8835 (mtm) cc_final: 0.8297 (mtm) REVERT: 5 285 LYS cc_start: 0.9261 (ttmm) cc_final: 0.8894 (mtpp) REVERT: 5 393 MET cc_start: 0.8493 (ttt) cc_final: 0.7856 (ttt) REVERT: 5 412 VAL cc_start: 0.8848 (t) cc_final: 0.7126 (t) REVERT: 5 500 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8475 (mm110) REVERT: 5 551 ASP cc_start: 0.7442 (m-30) cc_final: 0.7100 (m-30) REVERT: 5 552 MET cc_start: 0.9091 (tpt) cc_final: 0.8562 (tmm) REVERT: 5 574 ASN cc_start: 0.9257 (m110) cc_final: 0.8666 (t0) REVERT: 5 583 MET cc_start: 0.0546 (mmp) cc_final: -0.0948 (ptt) REVERT: 5 599 MET cc_start: 0.9456 (ptp) cc_final: 0.8932 (ptp) REVERT: 5 689 MET cc_start: 0.9333 (mmp) cc_final: 0.8918 (mmm) REVERT: 6 160 MET cc_start: 0.9258 (ptt) cc_final: 0.8701 (ptp) REVERT: 6 270 LEU cc_start: 0.9223 (mt) cc_final: 0.9012 (tp) REVERT: 6 395 CYS cc_start: 0.8841 (m) cc_final: 0.8483 (m) REVERT: 6 644 MET cc_start: 0.4694 (mtt) cc_final: 0.4395 (mtt) REVERT: 6 652 ILE cc_start: 0.9256 (tp) cc_final: 0.9005 (tp) REVERT: 6 736 MET cc_start: 0.3225 (ptp) cc_final: 0.2854 (ptp) REVERT: 7 14 TYR cc_start: 0.8463 (m-80) cc_final: 0.7388 (m-10) REVERT: 7 29 LYS cc_start: 0.8226 (tptt) cc_final: 0.7911 (mmmt) REVERT: 7 210 ASN cc_start: 0.8896 (m-40) cc_final: 0.8327 (p0) REVERT: 7 250 ASP cc_start: 0.9539 (p0) cc_final: 0.8887 (t70) REVERT: 7 600 MET cc_start: 0.6163 (ptt) cc_final: 0.5962 (ptp) REVERT: c 45 LEU cc_start: 0.9658 (tp) cc_final: 0.9325 (tp) REVERT: c 49 PHE cc_start: 0.9407 (m-10) cc_final: 0.8671 (m-80) REVERT: c 50 LYS cc_start: 0.9688 (ttmt) cc_final: 0.9420 (ttmt) REVERT: c 280 LEU cc_start: 0.9557 (pp) cc_final: 0.8811 (tt) REVERT: c 339 TYR cc_start: 0.9545 (t80) cc_final: 0.8605 (t80) REVERT: c 524 ILE cc_start: 0.7302 (mt) cc_final: 0.7016 (mt) REVERT: c 547 ARG cc_start: 0.9551 (mtp85) cc_final: 0.9027 (ptp-110) REVERT: c 554 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8578 (mm-30) REVERT: D 58 GLN cc_start: 0.9413 (mm-40) cc_final: 0.9066 (tp40) REVERT: D 62 ASP cc_start: 0.9361 (m-30) cc_final: 0.8927 (m-30) REVERT: D 64 MET cc_start: 0.9146 (mmp) cc_final: 0.8657 (mmm) REVERT: D 131 THR cc_start: 0.9698 (p) cc_final: 0.9397 (p) REVERT: D 134 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9005 (mm-30) REVERT: D 156 LEU cc_start: 0.9464 (mt) cc_final: 0.9185 (tp) REVERT: D 175 LEU cc_start: 0.9262 (mp) cc_final: 0.8646 (tp) REVERT: D 202 MET cc_start: 0.8984 (tpp) cc_final: 0.8677 (tpp) REVERT: D 218 MET cc_start: 0.8755 (mpp) cc_final: 0.7798 (mpp) REVERT: D 227 PHE cc_start: 0.8664 (m-80) cc_final: 0.7843 (m-10) REVERT: D 251 PHE cc_start: 0.8515 (m-80) cc_final: 0.8170 (m-80) REVERT: D 277 MET cc_start: 0.8995 (mmp) cc_final: 0.8155 (mmp) REVERT: B 99 ASP cc_start: 0.9207 (m-30) cc_final: 0.8939 (m-30) REVERT: B 119 TRP cc_start: 0.9239 (p-90) cc_final: 0.8345 (p-90) REVERT: B 138 ILE cc_start: 0.8949 (pt) cc_final: 0.8665 (pt) REVERT: B 160 LEU cc_start: 0.9636 (tp) cc_final: 0.9410 (tp) REVERT: B 175 LEU cc_start: 0.9773 (tp) cc_final: 0.9419 (mt) REVERT: B 177 GLU cc_start: 0.9134 (mt-10) cc_final: 0.8641 (mt-10) REVERT: A 43 GLU cc_start: 0.9318 (tm-30) cc_final: 0.8972 (tm-30) REVERT: A 49 LYS cc_start: 0.9326 (mptt) cc_final: 0.9010 (ptpt) REVERT: A 73 PHE cc_start: 0.9147 (m-80) cc_final: 0.8930 (m-80) REVERT: A 175 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8999 (tp-100) REVERT: C 8 ASP cc_start: 0.9544 (t0) cc_final: 0.9308 (t0) REVERT: C 12 ASP cc_start: 0.9178 (m-30) cc_final: 0.8829 (m-30) REVERT: C 20 PHE cc_start: 0.9364 (m-80) cc_final: 0.8714 (m-10) REVERT: C 109 ILE cc_start: 0.9671 (pt) cc_final: 0.9258 (tp) REVERT: C 126 GLU cc_start: 0.9340 (tp30) cc_final: 0.9106 (mm-30) REVERT: C 191 MET cc_start: 0.9305 (tpt) cc_final: 0.8625 (tpt) outliers start: 1 outliers final: 1 residues processed: 681 average time/residue: 0.2119 time to fit residues: 239.2535 Evaluate side-chains 520 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 519 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 23 optimal weight: 3.9990 chunk 345 optimal weight: 0.0470 chunk 237 optimal weight: 30.0000 chunk 137 optimal weight: 0.6980 chunk 469 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 chunk 474 optimal weight: 9.9990 chunk 448 optimal weight: 5.9990 chunk 399 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 overall best weight: 2.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 398 HIS 3 661 GLN ** 3 688 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 269 ASN c 493 ASN D 162 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 179 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.082273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.060558 restraints weight = 240211.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.062486 restraints weight = 156523.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.063821 restraints weight = 114333.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.064822 restraints weight = 90583.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.065511 restraints weight = 75827.419| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40693 Z= 0.162 Angle : 0.860 18.027 54967 Z= 0.442 Chirality : 0.048 0.431 6368 Planarity : 0.005 0.058 7045 Dihedral : 6.151 174.600 5476 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.75 % Allowed : 8.70 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.75 % 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 aren not related in a simple way. whole: -1.65 (0.12), residues: 4931 helix: 0.01 (0.11), residues: 2017 sheet: -1.64 (0.20), residues: 585 loop : -1.95 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 7 721 TYR 0.029 0.001 TYR 2 434 PHE 0.035 0.002 PHE 5 684 TRP 0.054 0.002 TRP 6 939 HIS 0.009 0.001 HIS 7 620 Details of bonding type rmsd covalent geometry : bond 0.00336 (40680) covalent geometry : angle 0.85982 (54963) SS BOND : bond 0.00391 ( 2) SS BOND : angle 2.23297 ( 4) hydrogen bonds : bond 0.03682 ( 1483) hydrogen bonds : angle 5.37551 ( 4272) Misc. bond : bond 0.00599 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 707 time to evaluate : 1.316 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 242 LEU cc_start: 0.9492 (tt) cc_final: 0.9291 (tt) REVERT: 2 266 GLU cc_start: 0.8158 (pm20) cc_final: 0.7784 (pm20) REVERT: 2 267 MET cc_start: 0.8841 (ppp) cc_final: 0.8461 (ppp) REVERT: 2 274 VAL cc_start: 0.9321 (t) cc_final: 0.9107 (t) REVERT: 2 277 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8695 (tm-30) REVERT: 2 314 LEU cc_start: 0.9374 (pp) cc_final: 0.9108 (pp) REVERT: 2 331 PHE cc_start: 0.9026 (m-80) cc_final: 0.8665 (m-80) REVERT: 2 416 ASP cc_start: 0.8790 (t70) cc_final: 0.8549 (t0) REVERT: 2 501 MET cc_start: 0.8394 (tmm) cc_final: 0.8054 (tpp) REVERT: 2 551 GLN cc_start: 0.9350 (mt0) cc_final: 0.9113 (mp10) REVERT: 2 612 MET cc_start: 0.9192 (ptt) cc_final: 0.7983 (ttp) REVERT: 2 616 ASP cc_start: 0.9154 (t0) cc_final: 0.8755 (t70) REVERT: 2 620 ILE cc_start: 0.8611 (mt) cc_final: 0.8079 (mt) REVERT: 2 677 PHE cc_start: 0.8857 (m-10) cc_final: 0.8453 (m-80) REVERT: 2 783 MET cc_start: 0.3595 (mmt) cc_final: 0.3298 (mmt) REVERT: 3 136 MET cc_start: 0.7943 (mmp) cc_final: 0.7602 (mmm) REVERT: 3 176 LEU cc_start: 0.9059 (tt) cc_final: 0.8679 (tt) REVERT: 3 178 LYS cc_start: 0.9236 (mptt) cc_final: 0.8970 (mppt) REVERT: 3 278 LEU cc_start: 0.9615 (mt) cc_final: 0.9392 (mt) REVERT: 3 281 ASP cc_start: 0.8828 (p0) cc_final: 0.8586 (p0) REVERT: 3 282 LEU cc_start: 0.9568 (mt) cc_final: 0.9339 (mt) REVERT: 3 474 GLU cc_start: 0.9379 (mp0) cc_final: 0.9058 (mp0) REVERT: 4 382 MET cc_start: 0.8779 (mmt) cc_final: 0.8262 (mmp) REVERT: 4 391 PHE cc_start: 0.8683 (m-80) cc_final: 0.7655 (m-80) REVERT: 4 457 TYR cc_start: 0.9464 (m-10) cc_final: 0.9166 (m-80) REVERT: 4 801 MET cc_start: 0.1233 (tpt) cc_final: 0.0775 (tpt) REVERT: 5 48 ASP cc_start: 0.9170 (m-30) cc_final: 0.8788 (p0) REVERT: 5 55 LEU cc_start: 0.9619 (mm) cc_final: 0.9010 (tp) REVERT: 5 58 ASN cc_start: 0.9271 (t0) cc_final: 0.8926 (t0) REVERT: 5 66 GLU cc_start: 0.8744 (mp0) cc_final: 0.8441 (mp0) REVERT: 5 166 ILE cc_start: 0.9630 (mt) cc_final: 0.9007 (tp) REVERT: 5 181 ILE cc_start: 0.8659 (mt) cc_final: 0.8362 (mp) REVERT: 5 182 MET cc_start: 0.8349 (tpt) cc_final: 0.8074 (tpp) REVERT: 5 250 PHE cc_start: 0.9316 (m-10) cc_final: 0.9063 (m-10) REVERT: 5 276 MET cc_start: 0.8741 (mtm) cc_final: 0.8236 (mtm) REVERT: 5 285 LYS cc_start: 0.9111 (ttmm) cc_final: 0.8885 (mtpt) REVERT: 5 393 MET cc_start: 0.8439 (ttt) cc_final: 0.8075 (ttt) REVERT: 5 500 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8356 (mm110) REVERT: 5 520 LEU cc_start: 0.9102 (mm) cc_final: 0.8864 (mm) REVERT: 5 552 MET cc_start: 0.9121 (tpt) cc_final: 0.8742 (tpp) REVERT: 5 574 ASN cc_start: 0.9186 (m110) cc_final: 0.8535 (t0) REVERT: 5 583 MET cc_start: 0.0255 (mmp) cc_final: -0.1212 (ptt) REVERT: 5 599 MET cc_start: 0.9442 (ptp) cc_final: 0.8912 (ptp) REVERT: 5 689 MET cc_start: 0.9334 (mmp) cc_final: 0.8912 (mmm) REVERT: 6 160 MET cc_start: 0.9251 (ptt) cc_final: 0.8673 (ptp) REVERT: 6 270 LEU cc_start: 0.9179 (mt) cc_final: 0.8808 (tt) REVERT: 6 393 ASP cc_start: 0.9259 (t0) cc_final: 0.8828 (p0) REVERT: 6 395 CYS cc_start: 0.8852 (m) cc_final: 0.7239 (m) REVERT: 6 519 MET cc_start: 0.6972 (tpp) cc_final: 0.6577 (mmm) REVERT: 6 644 MET cc_start: 0.4402 (mtt) cc_final: 0.4019 (mtt) REVERT: 6 652 ILE cc_start: 0.9278 (tp) cc_final: 0.9052 (tp) REVERT: 6 736 MET cc_start: 0.3296 (ptp) cc_final: 0.2911 (ptp) REVERT: 6 779 GLU cc_start: 0.9246 (pt0) cc_final: 0.8733 (tm-30) REVERT: 7 14 TYR cc_start: 0.8447 (m-80) cc_final: 0.7252 (m-10) REVERT: 7 29 LYS cc_start: 0.8176 (tptt) cc_final: 0.7840 (mmmt) REVERT: 7 210 ASN cc_start: 0.8857 (m-40) cc_final: 0.8326 (p0) REVERT: 7 250 ASP cc_start: 0.9470 (p0) cc_final: 0.8881 (t0) REVERT: c 45 LEU cc_start: 0.9630 (tp) cc_final: 0.9306 (tp) REVERT: c 49 PHE cc_start: 0.9360 (m-10) cc_final: 0.8631 (m-80) REVERT: c 50 LYS cc_start: 0.9687 (ttmt) cc_final: 0.9417 (ttmt) REVERT: c 82 LEU cc_start: 0.9628 (tp) cc_final: 0.9390 (mm) REVERT: c 280 LEU cc_start: 0.9509 (pp) cc_final: 0.8804 (tt) REVERT: c 339 TYR cc_start: 0.9548 (t80) cc_final: 0.8781 (t80) REVERT: c 382 HIS cc_start: 0.8083 (t-170) cc_final: 0.7716 (t-170) REVERT: c 386 ARG cc_start: 0.8046 (mtm180) cc_final: 0.7530 (mtm180) REVERT: c 426 GLU cc_start: 0.9514 (mp0) cc_final: 0.9241 (mp0) REVERT: c 469 LEU cc_start: 0.9289 (tt) cc_final: 0.8847 (pp) REVERT: c 524 ILE cc_start: 0.7226 (mt) cc_final: 0.6866 (mt) REVERT: c 547 ARG cc_start: 0.9491 (mtp85) cc_final: 0.8983 (ptp-110) REVERT: c 554 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8576 (mm-30) REVERT: D 58 GLN cc_start: 0.9375 (mm-40) cc_final: 0.9114 (mt0) REVERT: D 62 ASP cc_start: 0.9304 (m-30) cc_final: 0.8973 (m-30) REVERT: D 64 MET cc_start: 0.9059 (mmp) cc_final: 0.8592 (mmm) REVERT: D 131 THR cc_start: 0.9691 (p) cc_final: 0.9379 (p) REVERT: D 134 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9004 (mm-30) REVERT: D 148 LEU cc_start: 0.9705 (mt) cc_final: 0.9461 (mt) REVERT: D 152 ASP cc_start: 0.8667 (m-30) cc_final: 0.8440 (m-30) REVERT: D 156 LEU cc_start: 0.9454 (mt) cc_final: 0.9149 (tp) REVERT: D 174 LEU cc_start: 0.8855 (mp) cc_final: 0.8527 (mp) REVERT: D 175 LEU cc_start: 0.9292 (mp) cc_final: 0.8664 (tp) REVERT: D 202 MET cc_start: 0.8975 (tpp) cc_final: 0.8658 (tpp) REVERT: D 218 MET cc_start: 0.8607 (mpp) cc_final: 0.8226 (mpp) REVERT: D 227 PHE cc_start: 0.8624 (m-80) cc_final: 0.7935 (m-10) REVERT: D 251 PHE cc_start: 0.8426 (m-80) cc_final: 0.8094 (m-80) REVERT: D 277 MET cc_start: 0.8879 (mmp) cc_final: 0.8137 (mmp) REVERT: B 99 ASP cc_start: 0.9170 (m-30) cc_final: 0.8882 (m-30) REVERT: B 119 TRP cc_start: 0.9242 (p-90) cc_final: 0.8771 (p-90) REVERT: B 138 ILE cc_start: 0.8930 (pt) cc_final: 0.8662 (pt) REVERT: B 175 LEU cc_start: 0.9771 (tp) cc_final: 0.9432 (mt) REVERT: B 177 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8451 (mt-10) REVERT: B 184 PHE cc_start: 0.8805 (t80) cc_final: 0.8542 (t80) REVERT: A 43 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8877 (tm-30) REVERT: A 49 LYS cc_start: 0.9333 (mptt) cc_final: 0.9126 (ptpt) REVERT: A 73 PHE cc_start: 0.9134 (m-80) cc_final: 0.8839 (m-80) REVERT: A 175 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8963 (tp-100) REVERT: C 8 ASP cc_start: 0.9509 (t0) cc_final: 0.9209 (t0) REVERT: C 12 ASP cc_start: 0.9079 (m-30) cc_final: 0.8749 (m-30) REVERT: C 20 PHE cc_start: 0.9310 (m-80) cc_final: 0.8549 (m-10) REVERT: C 109 ILE cc_start: 0.9626 (pt) cc_final: 0.9255 (tp) REVERT: C 126 GLU cc_start: 0.9282 (tp30) cc_final: 0.9079 (mm-30) REVERT: C 136 ASN cc_start: 0.9502 (t0) cc_final: 0.9187 (t0) REVERT: C 138 HIS cc_start: 0.9416 (m-70) cc_final: 0.8754 (m90) REVERT: C 191 MET cc_start: 0.9199 (tpt) cc_final: 0.8582 (tpp) outliers start: 1 outliers final: 1 residues processed: 708 average time/residue: 0.2204 time to fit residues: 259.9651 Evaluate side-chains 537 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 536 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 75 optimal weight: 6.9990 chunk 478 optimal weight: 0.5980 chunk 266 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 498 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 288 optimal weight: 0.0020 chunk 285 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 398 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 ASN ** 7 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 269 ASN D 162 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.081862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060340 restraints weight = 243727.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.062355 restraints weight = 155740.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.063767 restraints weight = 112008.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.064765 restraints weight = 87349.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.065496 restraints weight = 72394.146| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 40693 Z= 0.161 Angle : 0.861 18.591 54967 Z= 0.443 Chirality : 0.048 0.437 6368 Planarity : 0.005 0.067 7045 Dihedral : 6.082 176.053 5476 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.79 % Allowed : 9.02 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.75 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.62 (0.12), residues: 4931 helix: -0.02 (0.11), residues: 2027 sheet: -1.60 (0.20), residues: 587 loop : -1.88 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG 6 350 TYR 0.028 0.001 TYR 2 434 PHE 0.034 0.002 PHE 5 357 TRP 0.049 0.002 TRP 6 939 HIS 0.008 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00337 (40680) covalent geometry : angle 0.86096 (54963) SS BOND : bond 0.00139 ( 2) SS BOND : angle 2.03191 ( 4) hydrogen bonds : bond 0.03699 ( 1483) hydrogen bonds : angle 5.35175 ( 4272) Misc. bond : bond 0.00296 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 683 time to evaluate : 1.616 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 266 GLU cc_start: 0.8155 (pm20) cc_final: 0.7816 (pm20) REVERT: 2 267 MET cc_start: 0.8844 (ppp) cc_final: 0.8448 (ppp) REVERT: 2 274 VAL cc_start: 0.9331 (t) cc_final: 0.9089 (t) REVERT: 2 314 LEU cc_start: 0.9381 (pp) cc_final: 0.9084 (pp) REVERT: 2 331 PHE cc_start: 0.9008 (m-80) cc_final: 0.8645 (m-80) REVERT: 2 416 ASP cc_start: 0.8817 (t70) cc_final: 0.8590 (t0) REVERT: 2 501 MET cc_start: 0.8828 (tmm) cc_final: 0.8532 (ttp) REVERT: 2 551 GLN cc_start: 0.9335 (mt0) cc_final: 0.9113 (mp10) REVERT: 2 576 LEU cc_start: 0.5296 (mt) cc_final: 0.5027 (mt) REVERT: 2 612 MET cc_start: 0.9197 (ptt) cc_final: 0.8074 (ttp) REVERT: 2 616 ASP cc_start: 0.9241 (t0) cc_final: 0.8866 (t70) REVERT: 2 620 ILE cc_start: 0.8738 (mt) cc_final: 0.8233 (mt) REVERT: 2 677 PHE cc_start: 0.8855 (m-10) cc_final: 0.8451 (m-80) REVERT: 2 783 MET cc_start: 0.2717 (mmt) cc_final: 0.2406 (mmt) REVERT: 3 136 MET cc_start: 0.7773 (mmp) cc_final: 0.7455 (mmm) REVERT: 3 176 LEU cc_start: 0.9016 (tt) cc_final: 0.8560 (tt) REVERT: 3 178 LYS cc_start: 0.9248 (mptt) cc_final: 0.9041 (mptt) REVERT: 3 257 THR cc_start: 0.9240 (p) cc_final: 0.8901 (t) REVERT: 3 278 LEU cc_start: 0.9607 (mt) cc_final: 0.9399 (mt) REVERT: 3 281 ASP cc_start: 0.8960 (p0) cc_final: 0.8661 (p0) REVERT: 3 282 LEU cc_start: 0.9576 (mt) cc_final: 0.9364 (mt) REVERT: 3 306 MET cc_start: 0.7667 (pmm) cc_final: 0.7046 (pmm) REVERT: 3 430 ILE cc_start: 0.7782 (mm) cc_final: 0.7137 (pt) REVERT: 3 474 GLU cc_start: 0.9368 (mp0) cc_final: 0.9031 (mp0) REVERT: 4 293 LEU cc_start: 0.8327 (tp) cc_final: 0.7978 (pt) REVERT: 4 382 MET cc_start: 0.8826 (mmt) cc_final: 0.8388 (mmp) REVERT: 4 457 TYR cc_start: 0.9452 (m-10) cc_final: 0.9205 (m-80) REVERT: 4 582 HIS cc_start: 0.8510 (t70) cc_final: 0.8291 (t70) REVERT: 4 585 THR cc_start: 0.6287 (m) cc_final: 0.5834 (t) REVERT: 4 801 MET cc_start: 0.1218 (tpt) cc_final: 0.0535 (tpt) REVERT: 5 48 ASP cc_start: 0.9134 (m-30) cc_final: 0.8716 (p0) REVERT: 5 58 ASN cc_start: 0.9229 (t0) cc_final: 0.8939 (t0) REVERT: 5 66 GLU cc_start: 0.8551 (mp0) cc_final: 0.8320 (mp0) REVERT: 5 181 ILE cc_start: 0.8706 (mt) cc_final: 0.8406 (mp) REVERT: 5 182 MET cc_start: 0.8375 (tpt) cc_final: 0.8085 (tpp) REVERT: 5 250 PHE cc_start: 0.9285 (m-10) cc_final: 0.9050 (m-10) REVERT: 5 276 MET cc_start: 0.8743 (mtm) cc_final: 0.8309 (mtm) REVERT: 5 285 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8872 (mtpt) REVERT: 5 393 MET cc_start: 0.8502 (ttt) cc_final: 0.8039 (ttt) REVERT: 5 552 MET cc_start: 0.9133 (tpt) cc_final: 0.8699 (tpp) REVERT: 5 574 ASN cc_start: 0.9133 (m110) cc_final: 0.8480 (t0) REVERT: 5 583 MET cc_start: 0.0042 (mmp) cc_final: -0.1468 (ptt) REVERT: 5 599 MET cc_start: 0.9453 (ptp) cc_final: 0.8908 (ptp) REVERT: 5 689 MET cc_start: 0.9339 (mmp) cc_final: 0.8911 (mmm) REVERT: 6 160 MET cc_start: 0.9267 (ptt) cc_final: 0.8680 (ptp) REVERT: 6 270 LEU cc_start: 0.9157 (mt) cc_final: 0.8778 (tt) REVERT: 6 393 ASP cc_start: 0.9288 (t0) cc_final: 0.8866 (p0) REVERT: 6 395 CYS cc_start: 0.8858 (m) cc_final: 0.7190 (m) REVERT: 6 451 LYS cc_start: 0.9436 (tttm) cc_final: 0.9127 (tptt) REVERT: 6 519 MET cc_start: 0.6940 (tpp) cc_final: 0.6600 (mmm) REVERT: 6 652 ILE cc_start: 0.9304 (tp) cc_final: 0.9068 (tp) REVERT: 6 699 LEU cc_start: 0.8016 (pt) cc_final: 0.7587 (pt) REVERT: 6 706 MET cc_start: 0.8348 (ppp) cc_final: 0.8077 (mmp) REVERT: 6 736 MET cc_start: 0.3502 (ptp) cc_final: 0.3108 (ptp) REVERT: 6 779 GLU cc_start: 0.9250 (pt0) cc_final: 0.8789 (tm-30) REVERT: 7 14 TYR cc_start: 0.8375 (m-80) cc_final: 0.7269 (m-80) REVERT: 7 29 LYS cc_start: 0.8165 (tptt) cc_final: 0.7829 (mmmt) REVERT: 7 210 ASN cc_start: 0.8872 (m-40) cc_final: 0.8338 (p0) REVERT: 7 250 ASP cc_start: 0.9443 (p0) cc_final: 0.8837 (t0) REVERT: 7 307 PHE cc_start: 0.8396 (m-80) cc_final: 0.7565 (m-10) REVERT: c 45 LEU cc_start: 0.9622 (tp) cc_final: 0.9130 (tp) REVERT: c 49 PHE cc_start: 0.9373 (m-10) cc_final: 0.8526 (m-80) REVERT: c 50 LYS cc_start: 0.9685 (ttmt) cc_final: 0.9407 (ttmt) REVERT: c 82 LEU cc_start: 0.9624 (tp) cc_final: 0.9273 (tp) REVERT: c 280 LEU cc_start: 0.9543 (pp) cc_final: 0.8862 (tt) REVERT: c 297 ASP cc_start: 0.9079 (t0) cc_final: 0.8650 (p0) REVERT: c 339 TYR cc_start: 0.9516 (t80) cc_final: 0.8449 (t80) REVERT: c 382 HIS cc_start: 0.7994 (t-170) cc_final: 0.7468 (t-170) REVERT: c 386 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7609 (mtm180) REVERT: c 469 LEU cc_start: 0.9264 (tt) cc_final: 0.8873 (pp) REVERT: c 524 ILE cc_start: 0.7176 (mt) cc_final: 0.6831 (mt) REVERT: c 547 ARG cc_start: 0.9502 (mtp85) cc_final: 0.8987 (ptp-110) REVERT: D 58 GLN cc_start: 0.9393 (mm-40) cc_final: 0.9115 (mt0) REVERT: D 62 ASP cc_start: 0.9324 (m-30) cc_final: 0.8991 (m-30) REVERT: D 64 MET cc_start: 0.9101 (mmp) cc_final: 0.8643 (mmm) REVERT: D 131 THR cc_start: 0.9689 (p) cc_final: 0.9454 (p) REVERT: D 134 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9039 (mm-30) REVERT: D 148 LEU cc_start: 0.9719 (mt) cc_final: 0.9484 (mt) REVERT: D 152 ASP cc_start: 0.8705 (m-30) cc_final: 0.8461 (m-30) REVERT: D 156 LEU cc_start: 0.9432 (mt) cc_final: 0.8944 (tp) REVERT: D 174 LEU cc_start: 0.8862 (mp) cc_final: 0.8548 (mp) REVERT: D 175 LEU cc_start: 0.9269 (mp) cc_final: 0.8608 (tp) REVERT: D 202 MET cc_start: 0.8911 (tpp) cc_final: 0.8599 (tpp) REVERT: D 218 MET cc_start: 0.8761 (mpp) cc_final: 0.7892 (mpp) REVERT: D 227 PHE cc_start: 0.8646 (m-80) cc_final: 0.7956 (m-10) REVERT: D 251 PHE cc_start: 0.8432 (m-80) cc_final: 0.8079 (m-80) REVERT: D 277 MET cc_start: 0.8834 (mmp) cc_final: 0.8101 (mmp) REVERT: B 99 ASP cc_start: 0.9191 (m-30) cc_final: 0.8882 (m-30) REVERT: B 119 TRP cc_start: 0.9237 (p-90) cc_final: 0.8772 (p-90) REVERT: B 138 ILE cc_start: 0.8968 (pt) cc_final: 0.8708 (pt) REVERT: B 175 LEU cc_start: 0.9753 (tp) cc_final: 0.9408 (mt) REVERT: B 177 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8377 (mt-10) REVERT: B 184 PHE cc_start: 0.8748 (t80) cc_final: 0.8472 (t80) REVERT: A 38 ARG cc_start: 0.9624 (ttm110) cc_final: 0.9036 (mtm110) REVERT: A 43 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8861 (tm-30) REVERT: A 49 LYS cc_start: 0.9330 (mptt) cc_final: 0.9049 (ptpt) REVERT: A 73 PHE cc_start: 0.9122 (m-80) cc_final: 0.8880 (m-80) REVERT: C 8 ASP cc_start: 0.9467 (t0) cc_final: 0.9162 (t0) REVERT: C 12 ASP cc_start: 0.9068 (m-30) cc_final: 0.8736 (m-30) REVERT: C 20 PHE cc_start: 0.9337 (m-80) cc_final: 0.8537 (m-10) REVERT: C 109 ILE cc_start: 0.9616 (pt) cc_final: 0.9253 (tp) REVERT: C 136 ASN cc_start: 0.9474 (t0) cc_final: 0.9221 (t0) REVERT: C 138 HIS cc_start: 0.9407 (m-70) cc_final: 0.8772 (m90) REVERT: C 191 MET cc_start: 0.9175 (tpt) cc_final: 0.8584 (tpp) outliers start: 1 outliers final: 1 residues processed: 684 average time/residue: 0.2319 time to fit residues: 264.9007 Evaluate side-chains 530 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 529 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 156 optimal weight: 7.9990 chunk 352 optimal weight: 20.0000 chunk 472 optimal weight: 8.9990 chunk 100 optimal weight: 30.0000 chunk 168 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 543 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 107 GLN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 622 HIS c 493 ASN D 162 ASN A 7 ASN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN A 122 ASN C 138 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.078940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.057699 restraints weight = 244982.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.059531 restraints weight = 159938.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.060831 restraints weight = 116860.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061735 restraints weight = 92403.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.062410 restraints weight = 77576.942| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.7319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40693 Z= 0.225 Angle : 0.899 18.056 54967 Z= 0.467 Chirality : 0.049 0.418 6368 Planarity : 0.005 0.062 7045 Dihedral : 6.245 172.901 5476 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.57 % Favored : 89.60 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.75 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.72 (0.12), residues: 4931 helix: -0.07 (0.11), residues: 2009 sheet: -1.76 (0.20), residues: 594 loop : -1.92 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG 4 642 TYR 0.029 0.002 TYR 2 434 PHE 0.041 0.002 PHE 5 684 TRP 0.065 0.003 TRP c 481 HIS 0.009 0.002 HIS 6 735 Details of bonding type rmsd covalent geometry : bond 0.00471 (40680) covalent geometry : angle 0.89873 (54963) SS BOND : bond 0.00062 ( 2) SS BOND : angle 2.01567 ( 4) hydrogen bonds : bond 0.03958 ( 1483) hydrogen bonds : angle 5.56339 ( 4272) Misc. bond : bond 0.00301 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9862 Ramachandran restraints generated. 4931 Oldfield, 0 Emsley, 4931 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 631 time to evaluate : 1.733 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 Corrupt residue: chain: 5 residue: PRO 326 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 266 GLU cc_start: 0.8511 (pm20) cc_final: 0.8212 (pm20) REVERT: 2 267 MET cc_start: 0.8890 (ppp) cc_final: 0.8419 (ppp) REVERT: 2 274 VAL cc_start: 0.9361 (t) cc_final: 0.9139 (t) REVERT: 2 331 PHE cc_start: 0.8969 (m-80) cc_final: 0.8724 (m-10) REVERT: 2 415 VAL cc_start: 0.9432 (t) cc_final: 0.8952 (t) REVERT: 2 416 ASP cc_start: 0.8897 (t70) cc_final: 0.8665 (p0) REVERT: 2 501 MET cc_start: 0.8889 (tmm) cc_final: 0.8648 (ttm) REVERT: 2 519 LEU cc_start: 0.9485 (pp) cc_final: 0.9243 (pp) REVERT: 2 551 GLN cc_start: 0.9356 (mt0) cc_final: 0.9137 (mp10) REVERT: 2 576 LEU cc_start: 0.5637 (mt) cc_final: 0.5361 (mt) REVERT: 2 612 MET cc_start: 0.9286 (ptt) cc_final: 0.8274 (ttp) REVERT: 2 616 ASP cc_start: 0.9261 (t0) cc_final: 0.8877 (t70) REVERT: 2 620 ILE cc_start: 0.8766 (mt) cc_final: 0.8242 (mt) REVERT: 2 677 PHE cc_start: 0.8914 (m-10) cc_final: 0.8489 (m-80) REVERT: 2 783 MET cc_start: 0.2886 (mmt) cc_final: 0.2637 (mmt) REVERT: 3 136 MET cc_start: 0.8021 (mmp) cc_final: 0.7658 (mmm) REVERT: 3 178 LYS cc_start: 0.9205 (mptt) cc_final: 0.8941 (mppt) REVERT: 3 281 ASP cc_start: 0.8826 (p0) cc_final: 0.8579 (p0) REVERT: 3 282 LEU cc_start: 0.9606 (mt) cc_final: 0.9291 (mt) REVERT: 3 306 MET cc_start: 0.7871 (pmm) cc_final: 0.7265 (pmm) REVERT: 3 474 GLU cc_start: 0.9379 (mp0) cc_final: 0.9074 (mp0) REVERT: 3 478 MET cc_start: 0.8669 (tpp) cc_final: 0.8432 (tpt) REVERT: 3 483 ARG cc_start: 0.8633 (ttt180) cc_final: 0.8428 (ttt180) REVERT: 4 293 LEU cc_start: 0.8378 (tp) cc_final: 0.8068 (pt) REVERT: 4 382 MET cc_start: 0.8884 (mmt) cc_final: 0.8661 (mmp) REVERT: 4 457 TYR cc_start: 0.9390 (m-10) cc_final: 0.9150 (m-80) REVERT: 4 582 HIS cc_start: 0.8579 (t70) cc_final: 0.8339 (t70) REVERT: 4 585 THR cc_start: 0.6675 (m) cc_final: 0.6186 (t) REVERT: 4 637 MET cc_start: -0.5686 (ttt) cc_final: -0.5914 (tmm) REVERT: 4 801 MET cc_start: 0.1749 (tpt) cc_final: 0.0896 (tpt) REVERT: 5 48 ASP cc_start: 0.9133 (m-30) cc_final: 0.8822 (p0) REVERT: 5 58 ASN cc_start: 0.9335 (t0) cc_final: 0.9021 (t0) REVERT: 5 99 LYS cc_start: 0.9440 (mmtt) cc_final: 0.9006 (mmmt) REVERT: 5 181 ILE cc_start: 0.8836 (mt) cc_final: 0.8564 (mp) REVERT: 5 182 MET cc_start: 0.8384 (tpt) cc_final: 0.8164 (tpp) REVERT: 5 276 MET cc_start: 0.8891 (mtm) cc_final: 0.8430 (mtm) REVERT: 5 285 LYS cc_start: 0.9250 (ttmm) cc_final: 0.8895 (mtpp) REVERT: 5 393 MET cc_start: 0.8576 (ttt) cc_final: 0.8187 (ttt) REVERT: 5 415 LEU cc_start: 0.9435 (pt) cc_final: 0.8782 (tp) REVERT: 5 450 THR cc_start: 0.9115 (p) cc_final: 0.8384 (p) REVERT: 5 478 CYS cc_start: 0.9475 (m) cc_final: 0.9218 (m) REVERT: 5 500 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8380 (mm-40) REVERT: 5 551 ASP cc_start: 0.7549 (m-30) cc_final: 0.7346 (m-30) REVERT: 5 552 MET cc_start: 0.9009 (tpt) cc_final: 0.8645 (tpp) REVERT: 5 574 ASN cc_start: 0.9141 (m110) cc_final: 0.8453 (t0) REVERT: 5 583 MET cc_start: -0.0103 (mmp) cc_final: -0.1672 (ptt) REVERT: 5 599 MET cc_start: 0.9478 (ptp) cc_final: 0.8950 (ptp) REVERT: 5 689 MET cc_start: 0.9346 (mmp) cc_final: 0.8904 (mmm) REVERT: 6 160 MET cc_start: 0.9337 (ptt) cc_final: 0.8796 (ptp) REVERT: 6 270 LEU cc_start: 0.9223 (mt) cc_final: 0.8862 (tt) REVERT: 6 451 LYS cc_start: 0.9477 (tttm) cc_final: 0.9156 (tptt) REVERT: 6 519 MET cc_start: 0.7035 (tpp) cc_final: 0.6676 (mmm) REVERT: 6 779 GLU cc_start: 0.9262 (pt0) cc_final: 0.8766 (tm-30) REVERT: 6 830 LEU cc_start: 0.9744 (tt) cc_final: 0.9421 (mt) REVERT: 7 14 TYR cc_start: 0.8332 (m-80) cc_final: 0.7862 (m-10) REVERT: 7 29 LYS cc_start: 0.8252 (tptt) cc_final: 0.7879 (mmmt) REVERT: 7 250 ASP cc_start: 0.9518 (p0) cc_final: 0.8822 (t70) REVERT: c 45 LEU cc_start: 0.9640 (tp) cc_final: 0.9209 (tp) REVERT: c 49 PHE cc_start: 0.9439 (m-10) cc_final: 0.8706 (m-80) REVERT: c 50 LYS cc_start: 0.9690 (ttmt) cc_final: 0.9393 (ttmm) REVERT: c 280 LEU cc_start: 0.9509 (pp) cc_final: 0.8761 (tt) REVERT: c 339 TYR cc_start: 0.9549 (t80) cc_final: 0.8791 (t80) REVERT: c 382 HIS cc_start: 0.8085 (t-170) cc_final: 0.7834 (t-170) REVERT: c 426 GLU cc_start: 0.9616 (mp0) cc_final: 0.9322 (mp0) REVERT: D 58 GLN cc_start: 0.9409 (mm-40) cc_final: 0.9133 (mt0) REVERT: D 62 ASP cc_start: 0.9301 (m-30) cc_final: 0.8981 (m-30) REVERT: D 64 MET cc_start: 0.9097 (mmp) cc_final: 0.8664 (mmm) REVERT: D 131 THR cc_start: 0.9688 (p) cc_final: 0.9409 (p) REVERT: D 134 GLU cc_start: 0.9407 (mm-30) cc_final: 0.8972 (mm-30) REVERT: D 148 LEU cc_start: 0.9742 (mt) cc_final: 0.9456 (mt) REVERT: D 152 ASP cc_start: 0.8765 (m-30) cc_final: 0.8560 (m-30) REVERT: D 175 LEU cc_start: 0.9341 (mp) cc_final: 0.8707 (tp) REVERT: D 202 MET cc_start: 0.9038 (tpp) cc_final: 0.8721 (tpp) REVERT: D 218 MET cc_start: 0.8761 (mpp) cc_final: 0.7891 (mpp) REVERT: D 227 PHE cc_start: 0.8782 (m-80) cc_final: 0.7882 (m-10) REVERT: D 277 MET cc_start: 0.8998 (mmp) cc_final: 0.8021 (mmp) REVERT: B 74 TRP cc_start: 0.9053 (p-90) cc_final: 0.8799 (p-90) REVERT: B 99 ASP cc_start: 0.9211 (m-30) cc_final: 0.8962 (m-30) REVERT: B 119 TRP cc_start: 0.9261 (p-90) cc_final: 0.8283 (p-90) REVERT: B 138 ILE cc_start: 0.9032 (pt) cc_final: 0.8827 (pt) REVERT: B 175 LEU cc_start: 0.9766 (tp) cc_final: 0.9465 (mt) REVERT: B 177 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8586 (mt-10) REVERT: A 43 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8952 (tm-30) REVERT: A 73 PHE cc_start: 0.9099 (m-80) cc_final: 0.8869 (m-80) REVERT: A 100 MET cc_start: 0.9238 (ppp) cc_final: 0.9023 (ppp) REVERT: C 8 ASP cc_start: 0.9510 (t0) cc_final: 0.9175 (t0) REVERT: C 12 ASP cc_start: 0.9084 (m-30) cc_final: 0.8766 (m-30) REVERT: C 20 PHE cc_start: 0.9338 (m-80) cc_final: 0.8746 (m-10) REVERT: C 109 ILE cc_start: 0.9643 (pt) cc_final: 0.9243 (tp) REVERT: C 191 MET cc_start: 0.9251 (tpt) cc_final: 0.8602 (tpp) outliers start: 1 outliers final: 1 residues processed: 632 average time/residue: 0.2187 time to fit residues: 230.5853 Evaluate side-chains 489 residues out of total 4511 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 488 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 499 random chunks: chunk 160 optimal weight: 0.0020 chunk 311 optimal weight: 10.0000 chunk 220 optimal weight: 20.0000 chunk 491 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 483 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 268 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 665 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 809 HIS 3 661 GLN ** 3 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 540 HIS 7 107 GLN ** 7 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 518 ASN ** c 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 493 ASN c 575 ASN D 162 ASN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.079265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057797 restraints weight = 246196.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.059721 restraints weight = 157335.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.061049 restraints weight = 113620.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.061980 restraints weight = 89236.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.062674 restraints weight = 74671.058| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40693 Z= 0.182 Angle : 0.879 19.561 54967 Z= 0.452 Chirality : 0.049 0.434 6368 Planarity : 0.005 0.101 7045 Dihedral : 6.179 167.654 5476 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.83 % Allowed : 9.11 % Favored : 90.06 % Rotamer: Outliers : 0.02 % Allowed : 0.36 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.74 % Cis-general : 3.75 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 aren not related in a simple way. whole: -1.67 (0.12), residues: 4931 helix: -0.06 (0.11), residues: 2009 sheet: -1.68 (0.20), residues: 576 loop : -1.89 (0.13), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 6 918 TYR 0.044 0.002 TYR 2 769 PHE 0.037 0.002 PHE 5 357 TRP 0.051 0.002 TRP c 481 HIS 0.008 0.001 HIS 2 405 Details of bonding type rmsd covalent geometry : bond 0.00384 (40680) covalent geometry : angle 0.87863 (54963) SS BOND : bond 0.00176 ( 2) SS BOND : angle 1.98211 ( 4) hydrogen bonds : bond 0.03772 ( 1483) hydrogen bonds : angle 5.49231 ( 4272) Misc. bond : bond 0.00551 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8790.51 seconds wall clock time: 152 minutes 7.41 seconds (9127.41 seconds total)