Starting phenix.real_space_refine on Tue Sep 15 15:23:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u8t_8519/09_2026/5u8t_8519_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u8t_8519/09_2026/5u8t_8519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u8t_8519/09_2026/5u8t_8519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u8t_8519/09_2026/5u8t_8519.map" model { file = "/net/cci-nas-00/data/ceres_data/5u8t_8519/09_2026/5u8t_8519_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u8t_8519/09_2026/5u8t_8519_neut.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 23 5.49 5 S 179 5.16 5 C 25736 2.51 5 N 7061 2.21 5 O 7789 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40788 Number of models: 1 Model: "" Number of chains: 15 Chain: "2" Number of atoms: 4591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4591 Classifications: {'peptide': 583} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 16, '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: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4624 Classifications: {'peptide': 589} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 543} Chain breaks: 4 Chain: "4" Number of atoms: 5318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 5318 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 23, 'PTRANS': 22, 'TRANS': 626} Chain breaks: 5 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: 4740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4740 Classifications: {'peptide': 602} Link IDs: {'CIS': 18, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 559} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 3 Chain: "6" Number of atoms: 5142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5142 Classifications: {'peptide': 661} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 33, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 606} Chain breaks: 5 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: 5201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5201 Classifications: {'peptide': 660} Link IDs: {'CIS': 25, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 604} Chain breaks: 3 Chain: "A" Number of atoms: 1696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1696 Classifications: {'peptide': 208} Link IDs: {'CIS': 13, 'PTRANS': 3, 'TRANS': 191} 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: "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 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: "E" Number of atoms: 4482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4482 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: "F" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 280 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.89, per 1000 atoms: 0.19 Number of scatterers: 40788 At special positions: 0 Unit cell: (183.3, 182, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 179 16.00 P 23 15.00 O 7789 8.00 N 7061 7.00 C 25736 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.8 seconds 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9716 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 46 sheets defined 43.3% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain '2' and resid 202 through 216 removed outlier: 3.924A pdb=" N THR 2 206 " --> pdb=" O ASN 2 202 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS 2 212 " --> pdb=" O ALA 2 208 " (cutoff:3.500A) removed outlier: 4.024A 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 removed outlier: 4.112A pdb=" N LEU 2 249 " --> pdb=" O ASN 2 245 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA 2 250 " --> pdb=" O TYR 2 246 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) Processing helix chain '2' and resid 257 through 261 Processing helix chain '2' and resid 263 through 283 removed outlier: 3.785A pdb=" N MET 2 267 " --> pdb=" O CYS 2 263 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE 2 270 " --> pdb=" O GLU 2 266 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU 2 277 " --> pdb=" O LEU 2 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS 2 282 " --> pdb=" O ALA 2 278 " (cutoff:3.500A) Processing helix chain '2' and resid 310 through 314 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 438 through 442 Processing helix chain '2' and resid 477 through 489 removed outlier: 3.801A pdb=" N LYS 2 486 " --> pdb=" O ARG 2 482 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 removed outlier: 3.516A pdb=" N ILE 2 498 " --> pdb=" O ILE 2 494 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER 2 499 " --> pdb=" O ASP 2 495 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET 2 501 " --> pdb=" O ILE 2 497 " (cutoff:3.500A) Processing helix chain '2' and resid 508 through 520 removed outlier: 3.634A pdb=" N LYS 2 512 " --> pdb=" O HIS 2 508 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR 2 513 " --> pdb=" O ARG 2 509 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA 2 514 " --> pdb=" O ASP 2 510 " (cutoff:3.500A) Processing helix chain '2' and resid 548 through 554 removed outlier: 3.546A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) Processing helix chain '2' and resid 554 through 560 removed outlier: 4.281A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 594 through 599 removed outlier: 3.864A pdb=" N LEU 2 598 " --> pdb=" O GLY 2 594 " (cutoff:3.500A) Processing helix chain '2' and resid 608 through 612 removed outlier: 3.534A pdb=" N MET 2 612 " --> pdb=" O PHE 2 609 " (cutoff:3.500A) Processing helix chain '2' and resid 619 through 627 removed outlier: 3.861A pdb=" N MET 2 624 " --> pdb=" O ILE 2 620 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU 2 625 " --> pdb=" O HIS 2 621 " (cutoff:3.500A) Processing helix chain '2' and resid 662 through 666 Processing helix chain '2' and resid 670 through 675 Processing helix chain '2' and resid 688 through 703 removed outlier: 4.164A pdb=" N ASP 2 692 " --> pdb=" O ASP 2 688 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU 2 693 " --> pdb=" O GLU 2 689 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 772 Processing helix chain '2' and resid 779 through 784 removed outlier: 3.641A pdb=" N MET 2 783 " --> pdb=" O HIS 2 779 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP 2 784 " --> pdb=" O GLN 2 780 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 779 through 784' Processing helix chain '2' and resid 784 through 795 Processing helix chain '2' and resid 806 through 825 removed outlier: 3.851A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG 2 815 " --> pdb=" O GLU 2 811 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER 2 819 " --> pdb=" O ARG 2 815 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE 2 820 " --> pdb=" O ILE 2 816 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 removed outlier: 3.729A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA 2 837 " --> pdb=" O ASP 2 833 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP 2 843 " --> pdb=" O LYS 2 839 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP 2 847 " --> pdb=" O ASP 2 843 " (cutoff:3.500A) Processing helix chain '2' and resid 852 through 861 removed outlier: 3.647A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG 2 858 " --> pdb=" O ARG 2 854 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER 2 860 " --> pdb=" O GLN 2 856 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE 2 861 " --> pdb=" O LEU 2 857 " (cutoff:3.500A) Processing helix chain '2' and resid 862 through 864 No H-bonds generated for 'chain '2' and resid 862 through 864' Processing helix chain '3' and resid 19 through 32 removed outlier: 3.783A pdb=" N GLU 3 30 " --> pdb=" O ARG 3 26 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE 3 31 " --> pdb=" O ARG 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 38 through 53 removed outlier: 4.485A pdb=" N SER 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) Processing helix chain '3' and resid 99 through 106 removed outlier: 3.967A pdb=" N ARG 3 104 " --> pdb=" O ASP 3 101 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 117 removed outlier: 4.595A pdb=" N GLY 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU 3 115 " --> pdb=" O TRP 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 117 through 136 Proline residue: 3 123 - end of helix Processing helix chain '3' and resid 281 through 283 No H-bonds generated for 'chain '3' and resid 281 through 283' Processing helix chain '3' and resid 344 through 355 removed outlier: 3.602A pdb=" N ASN 3 349 " --> pdb=" O PHE 3 345 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 366 Processing helix chain '3' and resid 374 through 387 removed outlier: 4.136A pdb=" N GLY 3 387 " --> pdb=" O LEU 3 383 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 425 removed outlier: 3.635A pdb=" N VAL 3 422 " --> pdb=" O LEU 3 418 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN 3 424 " --> pdb=" O ARG 3 420 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR 3 425 " --> pdb=" O PHE 3 421 " (cutoff:3.500A) Processing helix chain '3' and resid 460 through 465 Processing helix chain '3' and resid 481 through 491 removed outlier: 4.444A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 542 removed outlier: 3.701A pdb=" N SER 3 541 " --> pdb=" O ASP 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 554 through 570 removed outlier: 3.980A pdb=" N SER 3 560 " --> pdb=" O ILE 3 556 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS 3 564 " --> pdb=" O SER 3 560 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL 3 565 " --> pdb=" O ILE 3 561 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS 3 569 " --> pdb=" O VAL 3 565 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG 3 570 " --> pdb=" O LEU 3 566 " (cutoff:3.500A) Processing helix chain '3' and resid 652 through 666 removed outlier: 3.807A pdb=" N TYR 3 662 " --> pdb=" O LYS 3 658 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 688 removed outlier: 3.993A pdb=" N ILE 3 676 " --> pdb=" O THR 3 672 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL 3 680 " --> pdb=" O ILE 3 676 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N LYS 3 681 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 717 removed outlier: 3.673A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU 3 705 " --> pdb=" O THR 3 701 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 removed outlier: 3.635A pdb=" N ARG 3 734 " --> pdb=" O ALA 3 730 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE 3 735 " --> pdb=" O ASN 3 731 " (cutoff:3.500A) Processing helix chain '4' and resid 189 through 194 Processing helix chain '4' and resid 226 through 237 removed outlier: 3.855A pdb=" N LEU 4 230 " --> pdb=" O TYR 4 226 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG 4 234 " --> pdb=" O LEU 4 230 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU 4 235 " --> pdb=" O ASN 4 231 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU 4 236 " --> pdb=" O GLU 4 232 " (cutoff:3.500A) Processing helix chain '4' and resid 256 through 264 removed outlier: 3.533A pdb=" N LEU 4 262 " --> pdb=" O TYR 4 258 " (cutoff:3.500A) Processing helix chain '4' and resid 264 through 283 removed outlier: 3.781A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP 4 278 " --> pdb=" O GLN 4 274 " (cutoff:3.500A) Processing helix chain '4' and resid 283 through 288 removed outlier: 4.035A pdb=" N ASN 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) Processing helix chain '4' and resid 294 through 299 Processing helix chain '4' and resid 420 through 424 Processing helix chain '4' and resid 506 through 515 Processing helix chain '4' and resid 517 through 527 removed outlier: 4.142A pdb=" N ALA 4 523 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 545 removed outlier: 3.536A pdb=" N LYS 4 537 " --> pdb=" O LEU 4 533 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU 4 544 " --> pdb=" O ILE 4 540 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 removed outlier: 3.733A pdb=" N ILE 4 577 " --> pdb=" O SER 4 573 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LYS 4 583 " --> pdb=" O GLN 4 579 " (cutoff:3.500A) Processing helix chain '4' and resid 608 through 612 removed outlier: 3.946A pdb=" N THR 4 611 " --> pdb=" O ASP 4 608 " (cutoff:3.500A) Processing helix chain '4' and resid 619 through 625 removed outlier: 3.541A pdb=" N LEU 4 623 " --> pdb=" O GLY 4 619 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER 4 624 " --> pdb=" O ALA 4 620 " (cutoff:3.500A) Processing helix chain '4' and resid 644 through 649 Processing helix chain '4' and resid 687 through 692 removed outlier: 3.949A pdb=" N ASN 4 691 " --> pdb=" O PRO 4 687 " (cutoff:3.500A) Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 713 through 725 removed outlier: 5.225A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) Processing helix chain '4' and resid 745 through 757 removed outlier: 3.769A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS 4 755 " --> pdb=" O ILE 4 751 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLU 4 756 " --> pdb=" O SER 4 752 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N HIS 4 757 " --> pdb=" O TYR 4 753 " (cutoff:3.500A) Processing helix chain '4' and resid 765 through 779 removed outlier: 4.405A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG 4 772 " --> pdb=" O THR 4 768 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR 4 774 " --> pdb=" O LEU 4 770 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL 4 775 " --> pdb=" O VAL 4 771 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLY 4 776 " --> pdb=" O ARG 4 772 " (cutoff:3.500A) Processing helix chain '4' and resid 798 through 804 removed outlier: 3.799A pdb=" N ILE 4 802 " --> pdb=" O LEU 4 798 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG 4 803 " --> pdb=" O GLU 4 799 " (cutoff:3.500A) Processing helix chain '4' and resid 805 through 810 Processing helix chain '4' and resid 811 through 814 removed outlier: 3.601A pdb=" N LYS 4 814 " --> pdb=" O MET 4 811 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 811 through 814' Processing helix chain '4' and resid 821 through 834 removed outlier: 3.967A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) Processing helix chain '4' and resid 857 through 876 Processing helix chain '4' and resid 882 through 889 Processing helix chain '4' and resid 899 through 907 Processing helix chain '4' and resid 907 through 912 Processing helix chain '5' and resid 22 through 38 Processing helix chain '5' and resid 44 through 55 removed outlier: 3.593A pdb=" N ARG 5 51 " --> pdb=" O ARG 5 47 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 72 Processing helix chain '5' and resid 72 through 80 removed outlier: 4.085A pdb=" N TYR 5 76 " --> pdb=" O ASN 5 72 " (cutoff:3.500A) Processing helix chain '5' and resid 82 through 85 Processing helix chain '5' and resid 86 through 100 removed outlier: 3.508A pdb=" N ILE 5 94 " --> pdb=" O PHE 5 90 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS 5 99 " --> pdb=" O THR 5 95 " (cutoff:3.500A) Processing helix chain '5' and resid 279 through 283 Processing helix chain '5' and resid 351 through 363 removed outlier: 3.846A pdb=" N GLU 5 355 " --> pdb=" O GLU 5 351 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 375 removed outlier: 4.085A pdb=" N ALA 5 375 " --> pdb=" O THR 5 371 " (cutoff:3.500A) Processing helix chain '5' and resid 381 through 393 removed outlier: 4.243A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N CYS 5 390 " --> pdb=" O LYS 5 386 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU 5 391 " --> pdb=" O ALA 5 387 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU 5 392 " --> pdb=" O ILE 5 388 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET 5 393 " --> pdb=" O VAL 5 389 " (cutoff:3.500A) Processing helix chain '5' and resid 421 through 433 removed outlier: 4.267A pdb=" N LYS 5 431 " --> pdb=" O LYS 5 427 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 486 through 497 removed outlier: 3.892A pdb=" N VAL 5 491 " --> pdb=" O ASP 5 487 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA 5 492 " --> pdb=" O GLU 5 488 " (cutoff:3.500A) Processing helix chain '5' and resid 527 through 532 removed outlier: 3.979A pdb=" N ASP 5 531 " --> pdb=" O GLY 5 528 " (cutoff:3.500A) Processing helix chain '5' and resid 544 through 550 removed outlier: 3.918A pdb=" N SER 5 548 " --> pdb=" O THR 5 544 " (cutoff:3.500A) Processing helix chain '5' and resid 563 through 577 removed outlier: 3.581A pdb=" N SER 5 567 " --> pdb=" O GLU 5 563 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE 5 568 " --> pdb=" O ARG 5 564 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE 5 573 " --> pdb=" O ALA 5 569 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN 5 574 " --> pdb=" O ASN 5 570 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR 5 577 " --> pdb=" O ILE 5 573 " (cutoff:3.500A) Processing helix chain '5' and resid 579 through 584 removed outlier: 3.824A pdb=" N GLN 5 584 " --> pdb=" O ALA 5 580 " (cutoff:3.500A) Processing helix chain '5' and resid 586 through 592 Processing helix chain '5' and resid 596 through 608 removed outlier: 3.769A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU 5 608 " --> pdb=" O THR 5 604 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 636 removed outlier: 3.996A pdb=" N ALA 5 619 " --> pdb=" O SER 5 615 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) Processing helix chain '5' and resid 637 through 640 Processing helix chain '5' and resid 649 through 668 removed outlier: 3.924A pdb=" N LEU 5 653 " --> pdb=" O THR 5 649 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU 5 654 " --> pdb=" O ILE 5 650 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 692 removed outlier: 4.039A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA 5 686 " --> pdb=" O ARG 5 682 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER 5 687 " --> pdb=" O LEU 5 683 " (cutoff:3.500A) Processing helix chain '6' and resid 106 through 121 Processing helix chain '6' and resid 135 through 142 Processing helix chain '6' and resid 155 through 163 removed outlier: 3.802A pdb=" N MET 6 160 " --> pdb=" O GLN 6 156 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU 6 162 " --> pdb=" O LEU 6 158 " (cutoff:3.500A) Processing helix chain '6' and resid 164 through 173 removed outlier: 3.543A pdb=" N ALA 6 169 " --> pdb=" O ALA 6 165 " (cutoff:3.500A) Processing helix chain '6' and resid 173 through 190 Proline residue: 6 179 - end of helix removed outlier: 3.588A pdb=" N LYS 6 183 " --> pdb=" O PRO 6 179 " (cutoff:3.500A) Processing helix chain '6' and resid 280 through 284 Processing helix chain '6' and resid 512 through 522 removed outlier: 3.804A pdb=" N GLU 6 518 " --> pdb=" O ASN 6 514 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP 6 522 " --> pdb=" O GLU 6 518 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 532 removed outlier: 3.580A pdb=" N VAL 6 530 " --> pdb=" O TYR 6 526 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 552 removed outlier: 3.752A pdb=" N LYS 6 545 " --> pdb=" O GLU 6 541 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY 6 546 " --> pdb=" O ALA 6 542 " (cutoff:3.500A) Processing helix chain '6' and resid 581 through 590 removed outlier: 3.792A 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 653 through 658 Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 707 Processing helix chain '6' and resid 720 through 727 Processing helix chain '6' and resid 729 through 736 Processing helix chain '6' and resid 747 through 759 Processing helix chain '6' and resid 767 through 769 No H-bonds generated for 'chain '6' and resid 767 through 769' Processing helix chain '6' and resid 770 through 785 removed outlier: 4.160A pdb=" N ASP 6 783 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 815 removed outlier: 3.823A pdb=" N GLU 6 801 " --> pdb=" O VAL 6 797 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER 6 807 " --> pdb=" O MET 6 803 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA 6 809 " --> pdb=" O ARG 6 805 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG 6 812 " --> pdb=" O GLU 6 808 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 837 removed outlier: 4.152A pdb=" N SER 6 834 " --> pdb=" O LEU 6 830 " (cutoff:3.500A) Processing helix chain '6' and resid 911 through 924 removed outlier: 3.869A pdb=" N VAL 6 917 " --> pdb=" O MET 6 913 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE 6 920 " --> pdb=" O ILE 6 916 " (cutoff:3.500A) Processing helix chain '6' and resid 934 through 939 removed outlier: 3.606A pdb=" N TRP 6 939 " --> pdb=" O ASP 6 935 " (cutoff:3.500A) Processing helix chain '6' and resid 939 through 948 removed outlier: 3.610A pdb=" N GLN 6 943 " --> pdb=" O TRP 6 939 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU 6 945 " --> pdb=" O LEU 6 941 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN 6 946 " --> pdb=" O LEU 6 942 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP 6 947 " --> pdb=" O GLN 6 943 " (cutoff:3.500A) Processing helix chain '6' and resid 951 through 956 Processing helix chain '6' and resid 958 through 964 Processing helix chain '7' and resid 13 through 25 removed outlier: 4.270A pdb=" N LEU 7 17 " --> pdb=" O ASP 7 13 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN 7 19 " --> pdb=" O ASN 7 15 " (cutoff:3.500A) Processing helix chain '7' and resid 61 through 72 removed outlier: 4.329A pdb=" N ALA 7 65 " --> pdb=" O PRO 7 61 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET 7 66 " --> pdb=" O LYS 7 62 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU 7 67 " --> pdb=" O TYR 7 63 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN 7 68 " --> pdb=" O MET 7 64 " (cutoff:3.500A) Processing helix chain '7' and resid 82 through 92 Processing helix chain '7' and resid 102 through 108 Processing helix chain '7' and resid 111 through 115 Processing helix chain '7' and resid 120 through 125 removed outlier: 3.935A pdb=" N ASN 7 124 " --> pdb=" O ALA 7 120 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 158 removed outlier: 3.861A pdb=" N ARG 7 157 " --> pdb=" O MET 7 153 " (cutoff:3.500A) Processing helix chain '7' and resid 216 through 220 removed outlier: 3.574A pdb=" N ALA 7 219 " --> pdb=" O ARG 7 216 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 235 removed outlier: 3.567A pdb=" N LEU 7 235 " --> pdb=" O GLY 7 232 " (cutoff:3.500A) Processing helix chain '7' and resid 336 through 340 removed outlier: 4.275A pdb=" N LEU 7 339 " --> pdb=" O ASN 7 336 " (cutoff:3.500A) Processing helix chain '7' and resid 396 through 408 removed outlier: 3.801A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY 7 408 " --> pdb=" O LEU 7 404 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 417 Processing helix chain '7' and resid 425 through 438 removed outlier: 3.805A pdb=" N ALA 7 431 " --> pdb=" O ASP 7 427 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL 7 437 " --> pdb=" O LEU 7 433 " (cutoff:3.500A) Processing helix chain '7' and resid 465 through 477 removed outlier: 3.823A pdb=" N LEU 7 469 " --> pdb=" O ALA 7 465 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS 7 475 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) Processing helix chain '7' and resid 533 through 541 Processing helix chain '7' and resid 607 through 617 removed outlier: 3.639A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) Processing helix chain '7' and resid 617 through 622 removed outlier: 4.059A pdb=" N MET 7 621 " --> pdb=" O THR 7 617 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 removed outlier: 3.538A pdb=" N TYR 7 641 " --> pdb=" O LYS 7 637 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS 7 646 " --> pdb=" O ILE 7 642 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 671 removed outlier: 3.575A pdb=" N ALA 7 663 " --> pdb=" O TYR 7 659 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR 7 664 " --> pdb=" O VAL 7 660 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG 7 666 " --> pdb=" O GLN 7 662 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER 7 671 " --> pdb=" O LEU 7 667 " (cutoff:3.500A) Processing helix chain '7' and resid 685 through 704 removed outlier: 3.718A pdb=" N LEU 7 689 " --> pdb=" O THR 7 685 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS 7 701 " --> pdb=" O GLN 7 697 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU 7 702 " --> pdb=" O ALA 7 698 " (cutoff:3.500A) Processing helix chain '7' and resid 709 through 724 removed outlier: 4.391A pdb=" N ALA 7 716 " --> pdb=" O ASP 7 712 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU 7 719 " --> pdb=" O GLU 7 715 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG 7 721 " --> pdb=" O LEU 7 717 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL 7 722 " --> pdb=" O ARG 7 718 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 22 removed outlier: 3.685A pdb=" N LYS A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 22 " --> pdb=" O GLN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 58 removed outlier: 3.802A pdb=" N ILE A 37 " --> pdb=" O HIS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 104 removed outlier: 3.819A pdb=" N PHE A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 76 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LEU A 77 " --> pdb=" O PHE A 73 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 124 through 145 removed outlier: 3.658A pdb=" N ASP A 140 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 removed outlier: 3.709A pdb=" N GLU A 197 " --> pdb=" O GLN A 193 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 removed outlier: 3.741A pdb=" N PHE B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 Processing helix chain 'B' and resid 94 through 107 removed outlier: 3.631A pdb=" N ARG B 100 " --> pdb=" O LYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 removed outlier: 3.679A 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 Processing helix chain 'B' and resid 174 through 199 removed outlier: 3.870A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Proline residue: B 183 - end of helix removed outlier: 3.762A pdb=" N ILE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 3.837A pdb=" N VAL C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP C 12 " --> pdb=" O ASP C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.782A pdb=" N ILE C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 91 removed outlier: 3.613A pdb=" N LYS C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.797A pdb=" N ILE C 100 " --> pdb=" O ASP C 96 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 101' Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 118 through 137 removed outlier: 4.101A pdb=" N ASN C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS C 137 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.184A pdb=" N LEU C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 192 removed outlier: 3.904A pdb=" N TYR C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 removed outlier: 3.598A pdb=" N PHE D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS D 72 " --> pdb=" O LYS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 104 removed outlier: 4.911A pdb=" N ARG D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 163 removed outlier: 3.519A pdb=" N GLU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER D 142 " --> pdb=" O PHE D 138 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR D 157 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 199 Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.989A pdb=" N ALA D 208 " --> pdb=" O GLU D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 4.423A pdb=" N ASP D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 18 removed outlier: 3.790A pdb=" N ALA E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.854A pdb=" N CYS E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 removed outlier: 3.924A pdb=" N ARG E 68 " --> pdb=" O TYR E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 130 through 135 removed outlier: 4.326A pdb=" N ILE E 134 " --> pdb=" O ASN E 130 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 130 through 135' Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 222 through 240 removed outlier: 3.740A pdb=" N GLU E 239 " --> pdb=" O GLY E 235 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 removed outlier: 3.878A pdb=" N GLN E 254 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 279 Processing helix chain 'E' and resid 287 through 302 Proline residue: E 293 - end of helix removed outlier: 4.759A pdb=" N GLU E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 341 removed outlier: 3.686A pdb=" N SER E 341 " --> pdb=" O SER E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 349 removed outlier: 3.860A pdb=" N ALA E 346 " --> pdb=" O ASN E 342 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS E 347 " --> pdb=" O TYR E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 365 Processing helix chain 'E' and resid 369 through 375 Processing helix chain 'E' and resid 381 through 396 removed outlier: 4.541A pdb=" N GLY E 389 " --> pdb=" O LYS E 385 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE E 390 " --> pdb=" O ARG E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 421 through 429 removed outlier: 4.181A pdb=" N GLU E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU E 428 " --> pdb=" O PHE E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 434 removed outlier: 4.410A pdb=" N GLU E 433 " --> pdb=" O THR E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 485 removed outlier: 3.860A pdb=" N TRP E 478 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU E 479 " --> pdb=" O SER E 475 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER E 480 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP E 485 " --> pdb=" O TRP E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 515 removed outlier: 3.639A pdb=" N ARG E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY E 495 " --> pdb=" O LEU E 491 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLN E 500 " --> pdb=" O ILE E 496 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN E 508 " --> pdb=" O ARG E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 557 Processing helix chain 'E' and resid 604 through 614 removed outlier: 3.644A pdb=" N GLN E 610 " --> pdb=" O SER E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 633 through 646 removed outlier: 3.642A pdb=" N SER E 638 " --> pdb=" O ARG E 634 " (cutoff:3.500A) Proline residue: E 639 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 331 through 333 removed outlier: 8.917A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 331 through 333 removed outlier: 7.963A pdb=" N ARG 2 387 " --> pdb=" O ARG 2 327 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG 2 327 " --> pdb=" O ARG 2 387 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N THR 2 389 " --> pdb=" O THR 2 325 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR 2 325 " --> pdb=" O THR 2 389 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 563 through 565 removed outlier: 6.619A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN 2 538 " --> pdb=" O ILE 2 679 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS 2 681 " --> pdb=" O ASN 2 538 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU 2 540 " --> pdb=" O CYS 2 681 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 579 through 582 Processing sheet with id=AA5, first strand: chain '2' and resid 635 through 636 removed outlier: 3.759A pdb=" N ILE 2 636 " --> pdb=" O ALA 5 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 193 through 194 removed outlier: 3.969A pdb=" N ARG 3 193 " --> pdb=" O HIS 3 253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 193 through 194 removed outlier: 3.969A pdb=" N ARG 3 193 " --> pdb=" O HIS 3 253 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU 3 320 " --> pdb=" O LYS 3 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 210 through 213 removed outlier: 3.827A pdb=" N THR 3 242 " --> pdb=" O TYR 3 202 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 431 through 433 removed outlier: 5.923A pdb=" N VAL 3 470 " --> pdb=" O ILE 3 513 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ALA 3 515 " --> pdb=" O VAL 3 470 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE 3 472 " --> pdb=" O ALA 3 515 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU 3 545 " --> pdb=" O ASN 3 404 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 494 through 496 Processing sheet with id=AB2, first strand: chain '4' and resid 332 through 335 removed outlier: 7.249A pdb=" N LYS 4 398 " --> pdb=" O LEU 4 333 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '4' and resid 339 through 342 Processing sheet with id=AB4, first strand: chain '4' and resid 357 through 359 Processing sheet with id=AB5, first strand: chain '4' and resid 439 through 442 Processing sheet with id=AB6, first strand: chain '4' and resid 628 through 632 removed outlier: 6.492A pdb=" N CYS 4 629 " --> pdb=" O LEU 4 672 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER 4 674 " --> pdb=" O CYS 4 629 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE 4 631 " --> pdb=" O SER 4 674 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '4' and resid 653 through 656 Processing sheet with id=AB8, first strand: chain '4' and resid 880 through 881 Processing sheet with id=AB9, first strand: chain '5' and resid 60 through 64 removed outlier: 5.675A pdb=" N LEU 5 61 " --> pdb=" O ILE 5 138 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN 5 140 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N VAL 5 63 " --> pdb=" O ASN 5 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '5' and resid 165 through 168 removed outlier: 7.552A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU 5 258 " --> pdb=" O LEU 5 274 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N ASN 5 273 " --> pdb=" O PRO 5 326 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N ILE 5 328 " --> pdb=" O ASN 5 273 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR 5 275 " --> pdb=" O ILE 5 328 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '5' and resid 189 through 193 removed outlier: 6.022A pdb=" N LYS 5 249 " --> pdb=" O THR 5 177 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU 5 179 " --> pdb=" O SER 5 247 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N SER 5 247 " --> pdb=" O LEU 5 179 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N ILE 5 181 " --> pdb=" O HIS 5 245 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N HIS 5 245 " --> pdb=" O ILE 5 181 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '5' and resid 292 through 294 Processing sheet with id=AC4, first strand: chain '5' and resid 411 through 413 removed outlier: 6.187A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE 5 479 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '5' and resid 454 through 455 removed outlier: 3.670A pdb=" N TYR 5 463 " --> pdb=" O GLN 5 454 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '5' and resid 501 through 503 Processing sheet with id=AC7, first strand: chain '6' and resid 153 through 154 removed outlier: 7.108A pdb=" N ILE 6 153 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain '6' and resid 293 through 297 removed outlier: 5.020A pdb=" N THR 6 297 " --> pdb=" O LYS 6 358 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS 6 358 " --> pdb=" O THR 6 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '6' and resid 396 through 397 Processing sheet with id=AD1, first strand: chain '6' and resid 403 through 405 Processing sheet with id=AD2, first strand: chain '6' and resid 635 through 639 removed outlier: 5.625A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain '6' and resid 660 through 661 Processing sheet with id=AD4, first strand: chain '7' and resid 78 through 81 removed outlier: 6.217A pdb=" N VAL 7 78 " --> pdb=" O TYR 7 203 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LYS 7 205 " --> pdb=" O VAL 7 78 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE 7 80 " --> pdb=" O LYS 7 205 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain '7' and resid 314 through 316 removed outlier: 3.684A pdb=" N LYS 7 314 " --> pdb=" O THR 7 246 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN 7 237 " --> pdb=" O PHE 7 355 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE 7 355 " --> pdb=" O GLN 7 237 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY 7 243 " --> pdb=" O VAL 7 349 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL 7 349 " --> pdb=" O GLY 7 243 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 252 through 253 Processing sheet with id=AD7, first strand: chain '7' and resid 268 through 270 removed outlier: 4.314A pdb=" N VAL 7 269 " --> pdb=" O TYR 7 260 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR 7 260 " --> pdb=" O VAL 7 269 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '7' and resid 333 through 334 Processing sheet with id=AD9, first strand: chain '7' and resid 457 through 458 removed outlier: 7.050A pdb=" N CYS 7 457 " --> pdb=" O PHE 7 598 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain '7' and resid 481 through 482 removed outlier: 6.579A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 162 through 163 Processing sheet with id=AE3, first strand: chain 'B' and resid 24 through 27 Processing sheet with id=AE4, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AE5, first strand: chain 'D' and resid 227 through 228 removed outlier: 3.720A pdb=" N VAL D 228 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET D 277 " --> pdb=" O VAL D 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 231 through 232 Processing sheet with id=AE7, first strand: chain 'E' and resid 29 through 31 removed outlier: 3.595A pdb=" N VAL E 59 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.468A pdb=" N LEU E 81 " --> pdb=" O TYR E 121 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU E 123 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU E 83 " --> pdb=" O LEU E 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 319 through 320 removed outlier: 5.191A pdb=" N THR E 412 " --> pdb=" O ILE E 419 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE E 419 " --> pdb=" O THR E 412 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 567 through 571 1361 hydrogen bonds defined for protein. 3861 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: 8.64 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6864 1.32 - 1.44: 10346 1.44 - 1.57: 23879 1.57 - 1.69: 84 1.69 - 1.82: 294 Bond restraints: 41467 Sorted by residual: bond pdb=" O3A ANP 2 901 " pdb=" PB ANP 2 901 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" O3A ANP 5 801 " pdb=" PB ANP 5 801 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O3A ANP 31001 " pdb=" PB ANP 31001 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" CA ALA 6 664 " pdb=" CB ALA 6 664 " ideal model delta sigma weight residual 1.528 1.438 0.090 1.51e-02 4.39e+03 3.56e+01 bond pdb=" CA ILE 3 122 " pdb=" CB ILE 3 122 " ideal model delta sigma weight residual 1.534 1.575 -0.040 6.80e-03 2.16e+04 3.48e+01 ... (remaining 41462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 55068 4.66 - 9.32: 952 9.32 - 13.98: 78 13.98 - 18.64: 6 18.64 - 23.30: 4 Bond angle restraints: 56108 Sorted by residual: angle pdb=" N ASP 6 839 " pdb=" CA ASP 6 839 " pdb=" C ASP 6 839 " ideal model delta sigma weight residual 111.14 129.97 -18.83 1.08e+00 8.57e-01 3.04e+02 angle pdb=" N SER E 19 " pdb=" CA SER E 19 " pdb=" C SER E 19 " ideal model delta sigma weight residual 111.14 129.70 -18.56 1.08e+00 8.57e-01 2.95e+02 angle pdb=" N ASP 7 263 " pdb=" CA ASP 7 263 " pdb=" C ASP 7 263 " ideal model delta sigma weight residual 111.14 128.10 -16.96 1.08e+00 8.57e-01 2.46e+02 angle pdb=" N ILE 6 533 " pdb=" CA ILE 6 533 " pdb=" C ILE 6 533 " ideal model delta sigma weight residual 110.74 122.94 -12.20 9.10e-01 1.21e+00 1.80e+02 angle pdb=" N VAL 2 846 " pdb=" CA VAL 2 846 " pdb=" C VAL 2 846 " ideal model delta sigma weight residual 110.42 122.79 -12.37 9.60e-01 1.09e+00 1.66e+02 ... (remaining 56103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 24551 32.72 - 65.44: 890 65.44 - 98.16: 61 98.16 - 130.89: 1 130.89 - 163.61: 3 Dihedral angle restraints: 25506 sinusoidal: 10573 harmonic: 14933 Sorted by residual: 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 180.00 120.49 59.51 0 5.00e+00 4.00e-02 1.42e+02 dihedral pdb=" CA VAL 7 257 " pdb=" C VAL 7 257 " pdb=" N ILE 7 258 " pdb=" CA ILE 7 258 " ideal model delta harmonic sigma weight residual 0.00 40.36 -40.36 0 5.00e+00 4.00e-02 6.51e+01 dihedral pdb=" CA VAL 6 560 " pdb=" C VAL 6 560 " pdb=" N GLU 6 561 " pdb=" CA GLU 6 561 " ideal model delta harmonic sigma weight residual 0.00 -40.31 40.31 0 5.00e+00 4.00e-02 6.50e+01 ... (remaining 25503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 6146 0.120 - 0.240: 307 0.240 - 0.360: 27 0.360 - 0.480: 9 0.480 - 0.600: 3 Chirality restraints: 6492 Sorted by residual: chirality pdb=" CA ASP 6 839 " pdb=" N ASP 6 839 " pdb=" C ASP 6 839 " pdb=" CB ASP 6 839 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.99e+00 chirality pdb=" CA SER E 19 " pdb=" N SER E 19 " pdb=" C SER E 19 " pdb=" CB SER E 19 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" CA ASP 7 263 " pdb=" N ASP 7 263 " pdb=" C ASP 7 263 " pdb=" CB ASP 7 263 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.90e+00 ... (remaining 6489 not shown) Planarity restraints: 7133 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 18 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" C ASN E 18 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN E 18 " -0.020 2.00e-02 2.50e+03 pdb=" N SER E 19 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS 7 262 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.00e+00 pdb=" C CYS 7 262 " -0.049 2.00e-02 2.50e+03 pdb=" O CYS 7 262 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP 7 263 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN 4 676 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO 4 677 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO 4 677 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO 4 677 " -0.037 5.00e-02 4.00e+02 ... (remaining 7130 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 282 2.37 - 3.00: 24354 3.00 - 3.63: 66824 3.63 - 4.27: 98108 4.27 - 4.90: 150052 Nonbonded interactions: 339620 Sorted by model distance: nonbonded pdb=" CG1 ILE D 260 " pdb=" OE2 GLU D 266 " model vdw 1.737 3.440 nonbonded pdb=" O SER 4 624 " pdb=" O GLY 4 626 " model vdw 1.754 3.040 nonbonded pdb=" CD1 ILE D 260 " pdb=" OE2 GLU D 266 " model vdw 1.784 3.460 nonbonded pdb=" O ILE E 15 " pdb=" OG SER E 19 " model vdw 1.832 3.040 nonbonded pdb=" CG1 ILE D 260 " pdb=" CD GLU D 266 " model vdw 1.875 3.670 ... (remaining 339615 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: 1.430 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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 35.340 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 0.008 0.164 41469 Z= 0.491 Angle : 1.607 60.587 56112 Z= 1.042 Chirality : 0.062 0.600 6492 Planarity : 0.005 0.069 7133 Dihedral : 16.109 163.608 15784 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 40.34 Ramachandran Plot: Outliers : 1.02 % Allowed : 10.09 % Favored : 88.89 % Rotamer: Outliers : 8.25 % Allowed : 10.99 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.61 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.09), residues: 4995 helix: -3.79 (0.07), residues: 1786 sheet: -2.69 (0.17), residues: 486 loop : -2.20 (0.11), residues: 2723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 6 614 TYR 0.023 0.002 TYR 3 247 PHE 0.026 0.002 PHE 5 462 TRP 0.014 0.002 TRP C 49 HIS 0.015 0.002 HIS 5 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.49 (41467) covalent geometry : angle 1.56909 / 1.03 (56108) SS BOND : bond 0.00299 / 0.20 ( 2) SS BOND : angle 41.22048 / 32.15 ( 4) hydrogen bonds : bond 0.20091 / 13.25 ( 1354) hydrogen bonds : angle 11.13085 / 7.57 ( 3861) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 371 poor density : 595 time to evaluate : 1.472 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: 2 247 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.9067 (mmp80) REVERT: 2 567 THR cc_start: 0.7647 (OUTLIER) cc_final: 0.7058 (p) REVERT: 2 763 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9027 (pt) REVERT: 3 27 ARG cc_start: 0.9570 (tpp-160) cc_final: 0.9322 (ttp80) REVERT: 3 136 MET cc_start: 0.9366 (mmm) cc_final: 0.9046 (mmm) REVERT: 3 367 LEU cc_start: 0.9193 (mt) cc_final: 0.8919 (mt) REVERT: 3 433 THR cc_start: 0.8955 (p) cc_final: 0.8744 (t) REVERT: 3 454 GLU cc_start: 0.8694 (tp30) cc_final: 0.8490 (tm-30) REVERT: 3 475 PHE cc_start: 0.8418 (t80) cc_final: 0.8047 (t80) REVERT: 3 665 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8901 (pm20) REVERT: 3 732 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9100 (tp) REVERT: 4 271 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9244 (tt) REVERT: 4 416 SER cc_start: 0.9016 (OUTLIER) cc_final: 0.8814 (p) REVERT: 4 554 LYS cc_start: 0.7920 (mttt) cc_final: 0.7667 (mtmm) REVERT: 4 654 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8124 (mm) REVERT: 4 688 VAL cc_start: 0.4523 (OUTLIER) cc_final: 0.4078 (t) REVERT: 4 864 ASP cc_start: 0.8839 (m-30) cc_final: 0.8156 (p0) REVERT: 5 21 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8976 (t0) REVERT: 5 41 ASP cc_start: 0.9442 (m-30) cc_final: 0.9187 (t0) REVERT: 5 54 ILE cc_start: 0.9849 (OUTLIER) cc_final: 0.9586 (pt) REVERT: 5 67 HIS cc_start: 0.9428 (m170) cc_final: 0.9223 (m-70) REVERT: 5 68 LEU cc_start: 0.9798 (tt) cc_final: 0.9462 (mt) REVERT: 5 162 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9233 (tt) REVERT: 5 204 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7548 (m) REVERT: 5 251 ILE cc_start: 0.9412 (pt) cc_final: 0.8790 (mt) REVERT: 5 348 MET cc_start: 0.4260 (OUTLIER) cc_final: 0.2490 (ttm) REVERT: 5 426 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9205 (mm) REVERT: 5 462 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8254 (m-80) REVERT: 5 502 ILE cc_start: 0.9275 (mt) cc_final: 0.8954 (mm) REVERT: 5 513 LEU cc_start: 0.9169 (pp) cc_final: 0.8845 (tt) REVERT: 5 520 LEU cc_start: 0.9179 (tt) cc_final: 0.8513 (mt) REVERT: 5 526 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8594 (pp) REVERT: 5 595 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.7646 (p) REVERT: 5 599 MET cc_start: 0.9167 (tpp) cc_final: 0.8690 (mmt) REVERT: 5 689 MET cc_start: 0.9087 (mmm) cc_final: 0.8862 (tpt) REVERT: 6 384 ASP cc_start: 0.9566 (t0) cc_final: 0.8891 (p0) REVERT: 6 387 GLU cc_start: 0.9182 (tp30) cc_final: 0.8948 (mm-30) REVERT: 6 550 GLN cc_start: 0.9495 (mt0) cc_final: 0.9049 (tp-100) REVERT: 6 551 MET cc_start: 0.8936 (mtp) cc_final: 0.8561 (tpt) REVERT: 6 629 MET cc_start: 0.7703 (ttp) cc_final: 0.7132 (tpt) REVERT: 6 656 MET cc_start: 0.9307 (mmm) cc_final: 0.9003 (mmm) REVERT: 6 662 SER cc_start: 0.7199 (OUTLIER) cc_final: 0.6881 (p) REVERT: 6 699 LEU cc_start: 0.9036 (mp) cc_final: 0.8657 (mt) REVERT: 6 709 PHE cc_start: 0.7745 (m-10) cc_final: 0.7117 (m-10) REVERT: 6 720 ASN cc_start: 0.9627 (t0) cc_final: 0.9040 (m110) REVERT: 6 752 ARG cc_start: 0.9397 (OUTLIER) cc_final: 0.9032 (ttm-80) REVERT: 6 794 ARG cc_start: 0.7950 (mmt-90) cc_final: 0.7750 (mmt180) REVERT: 6 803 MET cc_start: 0.9045 (tpp) cc_final: 0.8835 (mmm) REVERT: 6 824 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9345 (tp) REVERT: 6 831 LEU cc_start: 0.9607 (mt) cc_final: 0.9275 (mm) REVERT: 6 967 ARG cc_start: 0.4761 (OUTLIER) cc_final: 0.3958 (ppt90) REVERT: 7 86 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8816 (tt) REVERT: 7 125 MET cc_start: 0.8999 (ttm) cc_final: 0.8681 (tmm) REVERT: 7 147 ARG cc_start: 0.8796 (mtt-85) cc_final: 0.8430 (tpp80) REVERT: 7 372 THR cc_start: 0.9017 (p) cc_final: 0.8726 (p) REVERT: 7 454 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8536 (mm) REVERT: 7 458 LEU cc_start: 0.9230 (mt) cc_final: 0.8879 (mt) REVERT: 7 506 MET cc_start: 0.8304 (mmm) cc_final: 0.8090 (ppp) REVERT: 7 521 CYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8967 (p) REVERT: 7 527 ASP cc_start: 0.9327 (OUTLIER) cc_final: 0.9034 (t0) REVERT: A 15 ARG cc_start: 0.9731 (ptm160) cc_final: 0.9335 (ptm-80) REVERT: A 79 MET cc_start: 0.9424 (mmm) cc_final: 0.9080 (mmm) REVERT: A 104 ASN cc_start: 0.9470 (OUTLIER) cc_final: 0.9193 (p0) REVERT: A 149 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 151 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8683 (tp) REVERT: A 164 ASP cc_start: 0.9648 (m-30) cc_final: 0.9400 (t0) REVERT: A 204 TYR cc_start: 0.9178 (m-80) cc_final: 0.8800 (m-10) REVERT: B 8 GLN cc_start: 0.9313 (pt0) cc_final: 0.8596 (tp40) REVERT: B 147 ASP cc_start: 0.9568 (t0) cc_final: 0.9363 (t0) REVERT: B 160 LEU cc_start: 0.9735 (OUTLIER) cc_final: 0.9307 (tt) REVERT: B 169 GLN cc_start: 0.8846 (mt0) cc_final: 0.8267 (pm20) REVERT: C 4 TYR cc_start: 0.8590 (m-10) cc_final: 0.8283 (m-80) REVERT: C 8 ASP cc_start: 0.9528 (m-30) cc_final: 0.9169 (m-30) REVERT: C 126 GLU cc_start: 0.9765 (tp30) cc_final: 0.9397 (tp30) REVERT: C 172 MET cc_start: 0.9687 (ptm) cc_final: 0.9302 (tmm) REVERT: C 184 TYR cc_start: 0.9556 (m-80) cc_final: 0.9282 (m-80) REVERT: D 64 MET cc_start: 0.9674 (mmm) cc_final: 0.9446 (tpp) REVERT: D 93 MET cc_start: 0.9741 (mmp) cc_final: 0.9327 (mmm) REVERT: D 142 SER cc_start: 0.9589 (t) cc_final: 0.8743 (t) REVERT: E 32 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8476 (p) REVERT: E 34 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8725 (mt) REVERT: E 40 CYS cc_start: 0.9259 (m) cc_final: 0.8848 (p) REVERT: E 44 MET cc_start: 0.9826 (ptm) cc_final: 0.9535 (ptt) REVERT: E 267 LEU cc_start: 0.9440 (mt) cc_final: 0.9210 (pp) REVERT: E 284 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.7031 (p90) REVERT: E 366 MET cc_start: 0.9599 (mtt) cc_final: 0.9081 (mtt) REVERT: E 387 GLU cc_start: 0.9837 (mm-30) cc_final: 0.9578 (tp30) REVERT: E 407 ASP cc_start: 0.9226 (m-30) cc_final: 0.8315 (t0) REVERT: E 485 ASP cc_start: 0.9155 (OUTLIER) cc_final: 0.8906 (t0) REVERT: E 497 GLN cc_start: 0.9745 (mt0) cc_final: 0.9503 (tp-100) REVERT: E 536 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8514 (mm) REVERT: E 537 ASP cc_start: 0.9258 (m-30) cc_final: 0.8672 (p0) outliers start: 371 outliers final: 96 residues processed: 911 average time/residue: 0.2370 time to fit residues: 354.1225 Evaluate side-chains 514 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 383 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 6.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 238 ASN 2 561 HIS 2 615 GLN 2 651 ASN 2 760 GLN ** 2 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 51 ASN 3 351 ASN 3 417 GLN 3 532 ASN 3 564 HIS 4 400 GLN 4 447 ASN 4 582 HIS ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 862 GLN ** 5 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 254 GLN ** 5 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 676 HIS ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 583 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 6 914 ASN 7 112 HIS 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 543 GLN 7 544 GLN 7 615 HIS 7 657 ASN A 50 ASN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 GLN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 141 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.046585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.035744 restraints weight = 386556.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.036891 restraints weight = 261539.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.037738 restraints weight = 195007.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.038390 restraints weight = 155541.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.038882 restraints weight = 129932.479| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 41469 Z= 0.255 Angle : 1.028 18.479 56112 Z= 0.538 Chirality : 0.052 0.390 6492 Planarity : 0.007 0.170 7133 Dihedral : 11.087 178.698 5773 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 31.01 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.79 % Favored : 90.29 % Rotamer: Outliers : 0.38 % Allowed : 5.65 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.81 % Twisted Proline : 0.53 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.10), residues: 4995 helix: -2.48 (0.09), residues: 1916 sheet: -2.58 (0.18), residues: 528 loop : -2.00 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG 3 435 TYR 0.031 0.002 TYR 7 411 PHE 0.032 0.003 PHE 5 197 TRP 0.014 0.002 TRP E 478 HIS 0.022 0.002 HIS 7 112 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.26 (41467) covalent geometry : angle 1.02736 / 0.54 (56108) SS BOND : bond 0.00500 / 0.34 ( 2) SS BOND : angle 2.50702 / 2.03 ( 4) hydrogen bonds : bond 0.06530 / 4.31 ( 1354) hydrogen bonds : angle 7.49449 / 5.06 ( 3861) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 467 time to evaluate : 1.311 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: 2 267 MET cc_start: 0.9262 (ptp) cc_final: 0.8744 (ptm) REVERT: 2 612 MET cc_start: 0.8790 (mtm) cc_final: 0.8096 (mpp) REVERT: 2 613 ASN cc_start: 0.9388 (m-40) cc_final: 0.9111 (m-40) REVERT: 2 677 PHE cc_start: 0.9455 (m-80) cc_final: 0.8974 (m-80) REVERT: 2 681 CYS cc_start: 0.9126 (m) cc_final: 0.8767 (m) REVERT: 2 764 MET cc_start: 0.9227 (ppp) cc_final: 0.8946 (ppp) REVERT: 2 767 ILE cc_start: 0.9772 (mt) cc_final: 0.9503 (tt) REVERT: 3 136 MET cc_start: 0.9475 (mmm) cc_final: 0.9194 (tpp) REVERT: 3 183 GLU cc_start: 0.9462 (pm20) cc_final: 0.9085 (pm20) REVERT: 3 367 LEU cc_start: 0.9019 (mt) cc_final: 0.8739 (mt) REVERT: 3 454 GLU cc_start: 0.9040 (tp30) cc_final: 0.8629 (tm-30) REVERT: 3 479 THR cc_start: 0.8978 (p) cc_final: 0.8414 (p) REVERT: 3 551 ASP cc_start: 0.7660 (t70) cc_final: 0.6428 (m-30) REVERT: 4 272 MET cc_start: 0.9443 (mmp) cc_final: 0.9048 (tpp) REVERT: 4 382 MET cc_start: 0.9435 (ttt) cc_final: 0.9087 (ttm) REVERT: 4 554 LYS cc_start: 0.8355 (mttt) cc_final: 0.7987 (tptt) REVERT: 4 651 GLN cc_start: 0.8435 (mt0) cc_final: 0.7944 (mp10) REVERT: 4 682 TYR cc_start: 0.9036 (p90) cc_final: 0.8801 (p90) REVERT: 4 801 MET cc_start: 0.9134 (ttm) cc_final: 0.8881 (mtp) REVERT: 5 41 ASP cc_start: 0.9324 (m-30) cc_final: 0.9052 (t0) REVERT: 5 48 ASP cc_start: 0.9182 (m-30) cc_final: 0.8939 (t0) REVERT: 5 65 MET cc_start: 0.9173 (mmp) cc_final: 0.8842 (mmm) REVERT: 5 68 LEU cc_start: 0.9842 (tt) cc_final: 0.9505 (mt) REVERT: 5 252 ASP cc_start: 0.7522 (t0) cc_final: 0.7065 (t0) REVERT: 5 260 GLU cc_start: 0.8206 (pt0) cc_final: 0.7678 (pt0) REVERT: 5 342 ILE cc_start: 0.8184 (pt) cc_final: 0.7906 (pt) REVERT: 5 393 MET cc_start: 0.8388 (mmm) cc_final: 0.7603 (mtp) REVERT: 5 449 LEU cc_start: 0.8152 (pp) cc_final: 0.7910 (pp) REVERT: 5 509 ILE cc_start: 0.9579 (pt) cc_final: 0.9331 (tp) REVERT: 5 511 THR cc_start: 0.9272 (p) cc_final: 0.9043 (p) REVERT: 5 543 GLN cc_start: 0.7552 (pt0) cc_final: 0.7114 (mm-40) REVERT: 5 552 MET cc_start: 0.9307 (tpt) cc_final: 0.9095 (mmm) REVERT: 5 576 HIS cc_start: 0.9546 (m90) cc_final: 0.8950 (m90) REVERT: 5 599 MET cc_start: 0.9608 (tpp) cc_final: 0.8878 (mmt) REVERT: 5 689 MET cc_start: 0.9076 (mmm) cc_final: 0.8826 (ppp) REVERT: 6 384 ASP cc_start: 0.9447 (t0) cc_final: 0.8530 (p0) REVERT: 6 550 GLN cc_start: 0.9435 (mt0) cc_final: 0.9115 (tp-100) REVERT: 6 551 MET cc_start: 0.9316 (mtp) cc_final: 0.8924 (tpt) REVERT: 6 621 TYR cc_start: 0.8567 (p90) cc_final: 0.8012 (p90) REVERT: 6 629 MET cc_start: 0.6878 (ttp) cc_final: 0.6153 (tpp) REVERT: 6 652 ILE cc_start: 0.7073 (mt) cc_final: 0.6608 (mm) REVERT: 6 656 MET cc_start: 0.9358 (mmm) cc_final: 0.8972 (mmm) REVERT: 6 699 LEU cc_start: 0.9408 (mp) cc_final: 0.9187 (mt) REVERT: 6 720 ASN cc_start: 0.9542 (t0) cc_final: 0.9235 (m110) REVERT: 6 831 LEU cc_start: 0.9602 (mt) cc_final: 0.8892 (mt) REVERT: 7 20 GLU cc_start: 0.9610 (tt0) cc_final: 0.9354 (mm-30) REVERT: 7 147 ARG cc_start: 0.9337 (mtt-85) cc_final: 0.8770 (tpp80) REVERT: 7 529 MET cc_start: 0.8706 (ptt) cc_final: 0.8152 (ptt) REVERT: A 2 TYR cc_start: 0.8033 (t80) cc_final: 0.7756 (t80) REVERT: A 79 MET cc_start: 0.9299 (mmm) cc_final: 0.8893 (mmm) REVERT: A 164 ASP cc_start: 0.9292 (m-30) cc_final: 0.8931 (t0) REVERT: A 204 TYR cc_start: 0.9049 (m-80) cc_final: 0.8677 (m-10) REVERT: B 17 GLN cc_start: 0.9625 (pt0) cc_final: 0.9354 (pt0) REVERT: B 20 VAL cc_start: 0.9919 (m) cc_final: 0.9636 (p) REVERT: B 99 ASP cc_start: 0.9520 (m-30) cc_final: 0.9296 (m-30) REVERT: B 134 PHE cc_start: 0.8559 (m-80) cc_final: 0.8291 (m-80) REVERT: B 189 MET cc_start: 0.9701 (mmt) cc_final: 0.9483 (mmp) REVERT: C 3 TYR cc_start: 0.8289 (t80) cc_final: 0.8048 (t80) REVERT: C 16 PHE cc_start: 0.9443 (m-80) cc_final: 0.9139 (m-80) REVERT: C 126 GLU cc_start: 0.9459 (tp30) cc_final: 0.8971 (tp30) REVERT: C 172 MET cc_start: 0.9238 (ppp) cc_final: 0.8835 (tmm) REVERT: C 176 ILE cc_start: 0.9608 (pt) cc_final: 0.9284 (pt) REVERT: D 93 MET cc_start: 0.9710 (mmp) cc_final: 0.9324 (mmm) REVERT: D 142 SER cc_start: 0.8926 (t) cc_final: 0.8537 (t) REVERT: D 277 MET cc_start: 0.8788 (mtt) cc_final: 0.8302 (mpp) REVERT: E 40 CYS cc_start: 0.9422 (m) cc_final: 0.8554 (p) REVERT: E 44 MET cc_start: 0.9661 (ptm) cc_final: 0.9274 (ptt) REVERT: E 241 TYR cc_start: 0.9321 (t80) cc_final: 0.9104 (t80) REVERT: E 366 MET cc_start: 0.9488 (mtt) cc_final: 0.9195 (mtt) REVERT: E 380 MET cc_start: 0.8838 (mmp) cc_final: 0.8017 (mmp) REVERT: E 387 GLU cc_start: 0.9668 (mm-30) cc_final: 0.9407 (tp30) REVERT: E 407 ASP cc_start: 0.9013 (m-30) cc_final: 0.8012 (t0) REVERT: E 485 ASP cc_start: 0.9039 (m-30) cc_final: 0.8759 (m-30) REVERT: E 537 ASP cc_start: 0.9201 (m-30) cc_final: 0.8588 (p0) REVERT: E 607 MET cc_start: 0.8917 (mtm) cc_final: 0.8441 (mtm) outliers start: 17 outliers final: 5 residues processed: 482 average time/residue: 0.2355 time to fit residues: 187.2769 Evaluate side-chains 356 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 351 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 8 optimal weight: 10.0000 chunk 479 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 435 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 156 optimal weight: 50.0000 chunk 482 optimal weight: 4.9990 chunk 362 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 780 GLN ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 677 ASN 3 691 ASN ** 4 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 862 GLN ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 524 ASN 5 561 ASN ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 735 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 6 799 GLN ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN ** 7 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 585 ASN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 HIS E 476 ASN E 610 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.056674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.048019 restraints weight = 403369.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049289 restraints weight = 238760.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050145 restraints weight = 160105.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.050758 restraints weight = 118173.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.051194 restraints weight = 93249.963| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 41469 Z= 0.233 Angle : 0.928 15.788 56112 Z= 0.485 Chirality : 0.049 0.413 6492 Planarity : 0.005 0.063 7133 Dihedral : 10.470 175.469 5773 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 29.17 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.59 % Favored : 89.53 % Rotamer: Outliers : 0.18 % Allowed : 5.43 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.79 % 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 are not related in a simple way. whole: -2.86 (0.11), residues: 4995 helix: -1.69 (0.10), residues: 1936 sheet: -2.48 (0.18), residues: 543 loop : -1.86 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG 4 701 TYR 0.027 0.002 TYR 6 777 PHE 0.021 0.002 PHE 5 250 TRP 0.017 0.002 TRP B 117 HIS 0.015 0.002 HIS 5 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 (41467) covalent geometry : angle 0.92768 / 0.49 (56108) SS BOND : bond 0.00262 / 0.18 ( 2) SS BOND : angle 1.14484 / 0.90 ( 4) hydrogen bonds : bond 0.05441 / 3.58 ( 1354) hydrogen bonds : angle 6.77504 / 4.59 ( 3861) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 433 time to evaluate : 1.544 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: 2 237 MET cc_start: 0.9407 (tpt) cc_final: 0.9200 (mmp) REVERT: 2 611 LYS cc_start: 0.9522 (mptt) cc_final: 0.9167 (tttp) REVERT: 2 612 MET cc_start: 0.8613 (mtm) cc_final: 0.8106 (mtm) REVERT: 2 613 ASN cc_start: 0.9368 (m-40) cc_final: 0.9052 (p0) REVERT: 2 624 MET cc_start: 0.7827 (ptm) cc_final: 0.7599 (ptm) REVERT: 2 677 PHE cc_start: 0.9601 (m-80) cc_final: 0.8965 (m-80) REVERT: 2 681 CYS cc_start: 0.9327 (m) cc_final: 0.8992 (m) REVERT: 3 179 LEU cc_start: 0.9833 (tt) cc_final: 0.9531 (mt) REVERT: 3 183 GLU cc_start: 0.9534 (pm20) cc_final: 0.9282 (pm20) REVERT: 3 367 LEU cc_start: 0.9015 (mt) cc_final: 0.8752 (mt) REVERT: 3 407 MET cc_start: 0.9118 (tpt) cc_final: 0.8903 (tpt) REVERT: 3 454 GLU cc_start: 0.9061 (tp30) cc_final: 0.8676 (tm-30) REVERT: 4 272 MET cc_start: 0.9461 (mmp) cc_final: 0.9088 (ptt) REVERT: 4 382 MET cc_start: 0.9318 (ttt) cc_final: 0.8876 (ttm) REVERT: 4 554 LYS cc_start: 0.8358 (mttt) cc_final: 0.7892 (tptt) REVERT: 4 614 LEU cc_start: 0.9011 (mm) cc_final: 0.8794 (tp) REVERT: 4 649 MET cc_start: 0.9387 (ttt) cc_final: 0.9178 (ttt) REVERT: 4 651 GLN cc_start: 0.8341 (mt0) cc_final: 0.7839 (mp10) REVERT: 4 672 LEU cc_start: 0.9634 (tp) cc_final: 0.9331 (pp) REVERT: 4 682 TYR cc_start: 0.8968 (p90) cc_final: 0.8724 (p90) REVERT: 4 801 MET cc_start: 0.9266 (ttm) cc_final: 0.8946 (mtp) REVERT: 4 834 LYS cc_start: 0.9472 (mmtt) cc_final: 0.9097 (pptt) REVERT: 5 41 ASP cc_start: 0.9326 (m-30) cc_final: 0.8920 (t0) REVERT: 5 65 MET cc_start: 0.9324 (mmp) cc_final: 0.8855 (mmm) REVERT: 5 67 HIS cc_start: 0.9606 (m-70) cc_final: 0.9258 (m90) REVERT: 5 68 LEU cc_start: 0.9859 (tt) cc_final: 0.9516 (mt) REVERT: 5 252 ASP cc_start: 0.7821 (t0) cc_final: 0.7395 (t0) REVERT: 5 278 CYS cc_start: 0.8357 (m) cc_final: 0.7906 (m) REVERT: 5 404 MET cc_start: 0.7154 (ptp) cc_final: 0.6261 (ppp) REVERT: 5 449 LEU cc_start: 0.7957 (pp) cc_final: 0.7601 (pp) REVERT: 5 511 THR cc_start: 0.9462 (p) cc_final: 0.9236 (p) REVERT: 5 520 LEU cc_start: 0.9471 (tt) cc_final: 0.9032 (mt) REVERT: 5 543 GLN cc_start: 0.7374 (pt0) cc_final: 0.6911 (mm-40) REVERT: 5 552 MET cc_start: 0.9329 (tpt) cc_final: 0.9091 (mmm) REVERT: 5 576 HIS cc_start: 0.9563 (m90) cc_final: 0.8841 (m90) REVERT: 5 599 MET cc_start: 0.9427 (tpp) cc_final: 0.9158 (tpp) REVERT: 5 689 MET cc_start: 0.9007 (mmm) cc_final: 0.8750 (ppp) REVERT: 6 384 ASP cc_start: 0.9520 (t0) cc_final: 0.8620 (p0) REVERT: 6 519 MET cc_start: 0.9541 (mtt) cc_final: 0.9030 (mmm) REVERT: 6 551 MET cc_start: 0.9448 (mtp) cc_final: 0.8985 (tpt) REVERT: 6 621 TYR cc_start: 0.8560 (p90) cc_final: 0.8078 (p90) REVERT: 6 629 MET cc_start: 0.6806 (ttp) cc_final: 0.6089 (tpp) REVERT: 6 652 ILE cc_start: 0.7621 (mt) cc_final: 0.7274 (mm) REVERT: 6 656 MET cc_start: 0.9239 (mmm) cc_final: 0.8905 (mmm) REVERT: 6 661 ILE cc_start: 0.8839 (mt) cc_final: 0.8470 (tt) REVERT: 6 679 LEU cc_start: 0.9697 (tt) cc_final: 0.9408 (tt) REVERT: 6 720 ASN cc_start: 0.9593 (t0) cc_final: 0.9206 (m110) REVERT: 6 803 MET cc_start: 0.9202 (mmp) cc_final: 0.8846 (mmm) REVERT: 7 20 GLU cc_start: 0.9551 (tt0) cc_final: 0.9233 (mm-30) REVERT: 7 125 MET cc_start: 0.8950 (tmm) cc_final: 0.8414 (tmm) REVERT: 7 459 MET cc_start: 0.9533 (mmp) cc_final: 0.9278 (mmm) REVERT: 7 529 MET cc_start: 0.8811 (ptt) cc_final: 0.8295 (ptt) REVERT: 7 707 MET cc_start: 0.8005 (mmp) cc_final: 0.7714 (pmm) REVERT: A 164 ASP cc_start: 0.9224 (m-30) cc_final: 0.8990 (t0) REVERT: A 204 TYR cc_start: 0.9119 (m-80) cc_final: 0.8693 (m-80) REVERT: B 8 GLN cc_start: 0.9202 (pm20) cc_final: 0.8999 (pm20) REVERT: B 17 GLN cc_start: 0.9440 (pt0) cc_final: 0.9191 (pt0) REVERT: B 99 ASP cc_start: 0.9427 (m-30) cc_final: 0.9141 (m-30) REVERT: B 134 PHE cc_start: 0.8525 (m-80) cc_final: 0.8170 (m-80) REVERT: C 3 TYR cc_start: 0.8204 (t80) cc_final: 0.7693 (t80) REVERT: C 8 ASP cc_start: 0.9180 (m-30) cc_final: 0.8884 (m-30) REVERT: C 126 GLU cc_start: 0.9464 (tp30) cc_final: 0.8906 (tp30) REVERT: C 134 GLU cc_start: 0.9542 (tm-30) cc_final: 0.9139 (tm-30) REVERT: C 171 GLU cc_start: 0.9250 (mm-30) cc_final: 0.8965 (pm20) REVERT: D 93 MET cc_start: 0.9678 (mmp) cc_final: 0.9227 (mmm) REVERT: D 277 MET cc_start: 0.9314 (mtt) cc_final: 0.8825 (mmt) REVERT: E 44 MET cc_start: 0.9594 (ptm) cc_final: 0.9230 (ptt) REVERT: E 241 TYR cc_start: 0.9326 (t80) cc_final: 0.9055 (t80) REVERT: E 362 MET cc_start: 0.9426 (tpt) cc_final: 0.8708 (tpp) REVERT: E 366 MET cc_start: 0.9509 (mtt) cc_final: 0.9036 (mtt) REVERT: E 380 MET cc_start: 0.8803 (mmp) cc_final: 0.8051 (mmp) REVERT: E 387 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9382 (tp30) REVERT: E 407 ASP cc_start: 0.9074 (m-30) cc_final: 0.7970 (t0) REVERT: E 485 ASP cc_start: 0.9040 (m-30) cc_final: 0.8780 (m-30) REVERT: E 537 ASP cc_start: 0.9216 (m-30) cc_final: 0.8636 (p0) outliers start: 8 outliers final: 3 residues processed: 440 average time/residue: 0.2384 time to fit residues: 173.1531 Evaluate side-chains 324 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 321 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 115 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 404 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 476 optimal weight: 8.9990 chunk 437 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 313 optimal weight: 20.0000 chunk 349 optimal weight: 8.9990 chunk 415 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 231 ASN ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 579 GLN ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 254 GLN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 182 GLN ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 658 GLN 6 698 ASN 6 750 GLN 6 799 GLN ** 7 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.047183 restraints weight = 404817.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048430 restraints weight = 239699.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049278 restraints weight = 161575.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049835 restraints weight = 119594.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.050291 restraints weight = 95732.117| |-----------------------------------------------------------------------------| r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 41469 Z= 0.227 Angle : 0.899 18.547 56112 Z= 0.468 Chirality : 0.049 0.408 6492 Planarity : 0.005 0.065 7133 Dihedral : 10.232 178.805 5773 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 28.58 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.91 % Favored : 89.21 % Rotamer: Outliers : 0.18 % Allowed : 4.54 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % Twisted Proline : 0.53 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.11), residues: 4995 helix: -1.24 (0.10), residues: 1953 sheet: -2.43 (0.19), residues: 534 loop : -1.84 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 4 607 TYR 0.025 0.002 TYR 6 828 PHE 0.017 0.002 PHE B 184 TRP 0.029 0.002 TRP B 74 HIS 0.014 0.002 HIS 5 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.23 (41467) covalent geometry : angle 0.89871 / 0.47 (56108) SS BOND : bond 0.00166 / 0.12 ( 2) SS BOND : angle 0.81120 / 0.61 ( 4) hydrogen bonds : bond 0.04922 / 3.26 ( 1354) hydrogen bonds : angle 6.45255 / 4.37 ( 3861) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 390 time to evaluate : 1.413 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: 2 612 MET cc_start: 0.8672 (mtm) cc_final: 0.8044 (ttp) REVERT: 2 613 ASN cc_start: 0.9419 (m-40) cc_final: 0.9113 (p0) REVERT: 2 629 ILE cc_start: 0.7478 (tt) cc_final: 0.6651 (tt) REVERT: 2 677 PHE cc_start: 0.9615 (m-80) cc_final: 0.8883 (m-80) REVERT: 2 681 CYS cc_start: 0.9333 (m) cc_final: 0.9079 (m) REVERT: 2 764 MET cc_start: 0.9372 (ppp) cc_final: 0.9160 (ppp) REVERT: 3 136 MET cc_start: 0.9019 (tpp) cc_final: 0.8293 (tpp) REVERT: 3 367 LEU cc_start: 0.9008 (mt) cc_final: 0.8742 (mt) REVERT: 4 272 MET cc_start: 0.9445 (mmp) cc_final: 0.9012 (ptt) REVERT: 4 314 MET cc_start: 0.7045 (ttm) cc_final: 0.6574 (ttm) REVERT: 4 382 MET cc_start: 0.8962 (ttm) cc_final: 0.8395 (ttm) REVERT: 4 554 LYS cc_start: 0.8146 (mttt) cc_final: 0.7687 (tptt) REVERT: 4 614 LEU cc_start: 0.9091 (mm) cc_final: 0.8860 (tp) REVERT: 4 649 MET cc_start: 0.9344 (ttt) cc_final: 0.9121 (ttt) REVERT: 4 651 GLN cc_start: 0.8396 (mt0) cc_final: 0.7900 (mp10) REVERT: 4 682 TYR cc_start: 0.8965 (p90) cc_final: 0.8753 (p90) REVERT: 4 913 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7034 (mm-30) REVERT: 5 41 ASP cc_start: 0.9376 (m-30) cc_final: 0.8914 (t0) REVERT: 5 65 MET cc_start: 0.9286 (mmp) cc_final: 0.8934 (mmm) REVERT: 5 67 HIS cc_start: 0.9653 (m-70) cc_final: 0.9295 (m90) REVERT: 5 68 LEU cc_start: 0.9845 (tt) cc_final: 0.9622 (mt) REVERT: 5 252 ASP cc_start: 0.7858 (t0) cc_final: 0.7402 (t0) REVERT: 5 278 CYS cc_start: 0.8386 (m) cc_final: 0.8115 (m) REVERT: 5 393 MET cc_start: 0.8504 (mmm) cc_final: 0.7227 (ttm) REVERT: 5 404 MET cc_start: 0.7411 (ptp) cc_final: 0.6551 (ppp) REVERT: 5 410 ILE cc_start: 0.8384 (pt) cc_final: 0.8100 (pt) REVERT: 5 576 HIS cc_start: 0.9551 (m90) cc_final: 0.8816 (m-70) REVERT: 5 599 MET cc_start: 0.9245 (tpp) cc_final: 0.8995 (tpp) REVERT: 6 384 ASP cc_start: 0.9607 (t0) cc_final: 0.8843 (p0) REVERT: 6 551 MET cc_start: 0.9406 (mtp) cc_final: 0.9013 (tpt) REVERT: 6 621 TYR cc_start: 0.8635 (p90) cc_final: 0.8131 (p90) REVERT: 6 652 ILE cc_start: 0.7505 (mt) cc_final: 0.7064 (mm) REVERT: 6 656 MET cc_start: 0.9127 (mmm) cc_final: 0.8822 (mmm) REVERT: 6 661 ILE cc_start: 0.8902 (mt) cc_final: 0.8541 (tt) REVERT: 6 669 HIS cc_start: 0.8345 (t70) cc_final: 0.7992 (t-90) REVERT: 6 719 CYS cc_start: 0.9469 (p) cc_final: 0.9117 (t) REVERT: 6 803 MET cc_start: 0.9392 (mmp) cc_final: 0.9019 (mmm) REVERT: 7 20 GLU cc_start: 0.9575 (tt0) cc_final: 0.9174 (mm-30) REVERT: 7 457 CYS cc_start: 0.8158 (t) cc_final: 0.7042 (t) REVERT: 7 459 MET cc_start: 0.9504 (mmp) cc_final: 0.9015 (mmm) REVERT: 7 529 MET cc_start: 0.8855 (ptt) cc_final: 0.8321 (ptt) REVERT: 7 707 MET cc_start: 0.7905 (mmp) cc_final: 0.7683 (pmm) REVERT: A 38 ARG cc_start: 0.9316 (mmp80) cc_final: 0.9083 (mmm160) REVERT: A 79 MET cc_start: 0.9362 (mmm) cc_final: 0.8847 (mmm) REVERT: A 164 ASP cc_start: 0.9280 (m-30) cc_final: 0.9032 (t0) REVERT: A 204 TYR cc_start: 0.9059 (m-80) cc_final: 0.8656 (m-10) REVERT: B 63 MET cc_start: 0.8430 (mpp) cc_final: 0.8025 (mpp) REVERT: B 134 PHE cc_start: 0.8491 (m-80) cc_final: 0.8145 (m-80) REVERT: B 189 MET cc_start: 0.9713 (mmp) cc_final: 0.9464 (mmm) REVERT: C 3 TYR cc_start: 0.8434 (t80) cc_final: 0.7994 (t80) REVERT: C 126 GLU cc_start: 0.9456 (tp30) cc_final: 0.9001 (tp30) REVERT: C 134 GLU cc_start: 0.9532 (tm-30) cc_final: 0.9102 (tm-30) REVERT: C 172 MET cc_start: 0.9626 (tmm) cc_final: 0.8950 (tmm) REVERT: C 176 ILE cc_start: 0.9695 (pt) cc_final: 0.9122 (pt) REVERT: C 186 ASP cc_start: 0.9702 (m-30) cc_final: 0.9454 (m-30) REVERT: D 84 MET cc_start: 0.9400 (tmm) cc_final: 0.9045 (tmm) REVERT: D 93 MET cc_start: 0.9618 (mmp) cc_final: 0.9162 (mmm) REVERT: D 220 ASP cc_start: 0.9398 (m-30) cc_final: 0.9073 (m-30) REVERT: D 277 MET cc_start: 0.9282 (mtt) cc_final: 0.8767 (mmm) REVERT: E 44 MET cc_start: 0.9559 (ptm) cc_final: 0.9206 (ptt) REVERT: E 241 TYR cc_start: 0.9307 (t80) cc_final: 0.9058 (t80) REVERT: E 362 MET cc_start: 0.9405 (tpt) cc_final: 0.8736 (tpt) REVERT: E 366 MET cc_start: 0.9469 (mtt) cc_final: 0.9182 (mmm) REVERT: E 380 MET cc_start: 0.8803 (mmp) cc_final: 0.8116 (mmp) REVERT: E 387 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9384 (tp30) REVERT: E 407 ASP cc_start: 0.9079 (m-30) cc_final: 0.8020 (t0) REVERT: E 537 ASP cc_start: 0.9225 (m-30) cc_final: 0.8617 (p0) REVERT: E 538 LEU cc_start: 0.9099 (mt) cc_final: 0.8887 (mt) outliers start: 8 outliers final: 4 residues processed: 398 average time/residue: 0.2285 time to fit residues: 152.8665 Evaluate side-chains 307 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 303 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 399 optimal weight: 0.3980 chunk 494 optimal weight: 9.9990 chunk 166 optimal weight: 0.0030 chunk 158 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 477 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 overall best weight: 4.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 184 ASN ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 196 ASN 5 359 GLN ** 5 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN ** 7 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 ASN 7 320 GLN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047649 restraints weight = 399205.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048900 restraints weight = 237446.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.049788 restraints weight = 159949.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050386 restraints weight = 118480.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050815 restraints weight = 93854.621| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 41469 Z= 0.198 Angle : 0.867 17.167 56112 Z= 0.451 Chirality : 0.048 0.419 6492 Planarity : 0.005 0.056 7133 Dihedral : 10.044 175.750 5773 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 27.10 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.59 % Favored : 89.51 % Rotamer: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.11), residues: 4995 helix: -0.95 (0.11), residues: 1965 sheet: -2.48 (0.18), residues: 562 loop : -1.77 (0.13), residues: 2468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 189 TYR 0.023 0.002 TYR 6 828 PHE 0.024 0.002 PHE 3 543 TRP 0.013 0.002 TRP B 117 HIS 0.012 0.001 HIS 5 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (41467) covalent geometry : angle 0.86745 / 0.45 (56108) SS BOND : bond 0.01167 / 0.83 ( 2) SS BOND : angle 1.23382 / 1.02 ( 4) hydrogen bonds : bond 0.04550 / 3.04 ( 1354) hydrogen bonds : angle 6.21388 / 4.21 ( 3861) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 380 time to evaluate : 2.117 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: 2 613 ASN cc_start: 0.9440 (m-40) cc_final: 0.9201 (m-40) REVERT: 2 640 LEU cc_start: 0.9454 (tp) cc_final: 0.8933 (tt) REVERT: 2 677 PHE cc_start: 0.9617 (m-80) cc_final: 0.8989 (m-80) REVERT: 2 823 MET cc_start: 0.9023 (mtt) cc_final: 0.8814 (mtp) REVERT: 3 367 LEU cc_start: 0.8975 (mt) cc_final: 0.8690 (mt) REVERT: 4 184 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7515 (p0) REVERT: 4 272 MET cc_start: 0.9288 (mmp) cc_final: 0.8794 (ptt) REVERT: 4 314 MET cc_start: 0.7197 (ttm) cc_final: 0.6926 (ttm) REVERT: 4 382 MET cc_start: 0.8839 (ttm) cc_final: 0.8368 (ttm) REVERT: 4 554 LYS cc_start: 0.8191 (mttt) cc_final: 0.7710 (tptt) REVERT: 4 649 MET cc_start: 0.9354 (ttt) cc_final: 0.9153 (ttt) REVERT: 4 651 GLN cc_start: 0.8312 (mt0) cc_final: 0.8052 (mp10) REVERT: 4 801 MET cc_start: 0.9408 (ttm) cc_final: 0.8992 (mtp) REVERT: 5 41 ASP cc_start: 0.9351 (m-30) cc_final: 0.8916 (t0) REVERT: 5 65 MET cc_start: 0.9349 (mmp) cc_final: 0.9022 (mmm) REVERT: 5 67 HIS cc_start: 0.9646 (m-70) cc_final: 0.9425 (m-70) REVERT: 5 252 ASP cc_start: 0.7932 (t0) cc_final: 0.7435 (t0) REVERT: 5 393 MET cc_start: 0.8511 (mmm) cc_final: 0.7123 (ttm) REVERT: 5 404 MET cc_start: 0.7482 (ptp) cc_final: 0.6612 (ppp) REVERT: 5 410 ILE cc_start: 0.8600 (pt) cc_final: 0.8213 (pt) REVERT: 5 552 MET cc_start: 0.9512 (mmp) cc_final: 0.8986 (mmm) REVERT: 5 576 HIS cc_start: 0.9578 (m90) cc_final: 0.8811 (m-70) REVERT: 5 599 MET cc_start: 0.9199 (tpp) cc_final: 0.8960 (tpp) REVERT: 6 168 MET cc_start: 0.9678 (mmp) cc_final: 0.9474 (mmm) REVERT: 6 384 ASP cc_start: 0.9617 (t0) cc_final: 0.8861 (p0) REVERT: 6 519 MET cc_start: 0.9440 (mtt) cc_final: 0.8790 (mtp) REVERT: 6 551 MET cc_start: 0.9485 (mtp) cc_final: 0.9072 (tpt) REVERT: 6 621 TYR cc_start: 0.8624 (p90) cc_final: 0.8121 (p90) REVERT: 6 629 MET cc_start: 0.6815 (ttp) cc_final: 0.5964 (tpp) REVERT: 6 652 ILE cc_start: 0.7550 (mt) cc_final: 0.7209 (mt) REVERT: 6 656 MET cc_start: 0.9276 (mmm) cc_final: 0.9009 (mmm) REVERT: 6 661 ILE cc_start: 0.8913 (mt) cc_final: 0.8549 (tt) REVERT: 6 669 HIS cc_start: 0.8379 (t70) cc_final: 0.7982 (t-90) REVERT: 6 679 LEU cc_start: 0.9682 (tp) cc_final: 0.9474 (tp) REVERT: 6 719 CYS cc_start: 0.9528 (p) cc_final: 0.9171 (t) REVERT: 6 803 MET cc_start: 0.9419 (mmp) cc_final: 0.9065 (mmm) REVERT: 6 912 MET cc_start: 0.7009 (mmp) cc_final: 0.6769 (mmp) REVERT: 6 913 MET cc_start: 0.9004 (mmt) cc_final: 0.8790 (tmm) REVERT: 7 29 LYS cc_start: 0.6773 (tptt) cc_final: 0.6474 (tppt) REVERT: 7 66 MET cc_start: 0.8670 (mmp) cc_final: 0.8076 (ptt) REVERT: 7 457 CYS cc_start: 0.8190 (t) cc_final: 0.7070 (t) REVERT: 7 459 MET cc_start: 0.9483 (mmt) cc_final: 0.9003 (mmm) REVERT: 7 529 MET cc_start: 0.8883 (ptt) cc_final: 0.8412 (ptt) REVERT: 7 707 MET cc_start: 0.7974 (mmp) cc_final: 0.7718 (pmm) REVERT: A 164 ASP cc_start: 0.9309 (m-30) cc_final: 0.9034 (t0) REVERT: A 204 TYR cc_start: 0.9087 (m-80) cc_final: 0.8724 (m-10) REVERT: B 63 MET cc_start: 0.8567 (mpp) cc_final: 0.8245 (mpp) REVERT: B 134 PHE cc_start: 0.8321 (m-80) cc_final: 0.7966 (m-80) REVERT: B 189 MET cc_start: 0.9690 (mmp) cc_final: 0.9456 (mmm) REVERT: C 3 TYR cc_start: 0.8327 (t80) cc_final: 0.8051 (t80) REVERT: C 48 LEU cc_start: 0.9672 (tp) cc_final: 0.9414 (tt) REVERT: C 109 ILE cc_start: 0.9701 (pt) cc_final: 0.9500 (pt) REVERT: C 126 GLU cc_start: 0.9461 (tp30) cc_final: 0.9259 (tm-30) REVERT: C 134 GLU cc_start: 0.9526 (tm-30) cc_final: 0.9110 (tm-30) REVERT: D 93 MET cc_start: 0.9665 (mmp) cc_final: 0.9128 (mmm) REVERT: D 153 LYS cc_start: 0.9619 (ttpt) cc_final: 0.9269 (tppt) REVERT: D 277 MET cc_start: 0.9280 (mtt) cc_final: 0.8785 (mmt) REVERT: E 44 MET cc_start: 0.9547 (ptm) cc_final: 0.9206 (ptt) REVERT: E 241 TYR cc_start: 0.9227 (t80) cc_final: 0.8997 (t80) REVERT: E 362 MET cc_start: 0.9359 (tpt) cc_final: 0.8693 (tpt) REVERT: E 366 MET cc_start: 0.9466 (mtt) cc_final: 0.9211 (mmm) REVERT: E 380 MET cc_start: 0.8798 (mmp) cc_final: 0.8122 (mmp) REVERT: E 387 GLU cc_start: 0.9598 (mm-30) cc_final: 0.9364 (tp30) REVERT: E 407 ASP cc_start: 0.9126 (m-30) cc_final: 0.8068 (t0) REVERT: E 537 ASP cc_start: 0.9261 (m-30) cc_final: 0.8662 (p0) REVERT: E 538 LEU cc_start: 0.9050 (mt) cc_final: 0.8836 (mt) outliers start: 4 outliers final: 3 residues processed: 384 average time/residue: 0.2394 time to fit residues: 157.9362 Evaluate side-chains 301 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 297 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 436 optimal weight: 4.9990 chunk 434 optimal weight: 0.8980 chunk 239 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 386 optimal weight: 0.8980 chunk 156 optimal weight: 30.0000 chunk 442 optimal weight: 0.1980 chunk 197 optimal weight: 9.9990 chunk 392 optimal weight: 6.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 641 GLN ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 532 ASN ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 862 GLN 5 49 GLN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 196 ASN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS 7 585 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** 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 = 0.3291 r_free = 0.3291 target = 0.057627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.048879 restraints weight = 394178.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050168 restraints weight = 233822.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051038 restraints weight = 157062.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.051647 restraints weight = 115799.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.052082 restraints weight = 91667.363| |-----------------------------------------------------------------------------| r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41469 Z= 0.166 Angle : 0.851 16.624 56112 Z= 0.438 Chirality : 0.047 0.415 6492 Planarity : 0.004 0.057 7133 Dihedral : 9.909 178.126 5773 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 24.23 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.27 % Favored : 89.83 % Rotamer: Outliers : 0.07 % Allowed : 2.89 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.11), residues: 4995 helix: -0.68 (0.11), residues: 1978 sheet: -2.32 (0.19), residues: 572 loop : -1.68 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 5 486 TYR 0.045 0.002 TYR 6 772 PHE 0.016 0.002 PHE B 184 TRP 0.026 0.002 TRP 6 939 HIS 0.010 0.001 HIS 5 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (41467) covalent geometry : angle 0.85103 / 0.44 (56108) SS BOND : bond 0.00232 / 0.16 ( 2) SS BOND : angle 1.21867 / 1.06 ( 4) hydrogen bonds : bond 0.04095 / 2.73 ( 1354) hydrogen bonds : angle 5.95440 / 4.04 ( 3861) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 400 time to evaluate : 1.702 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: 2 613 ASN cc_start: 0.9357 (m-40) cc_final: 0.9006 (p0) REVERT: 2 677 PHE cc_start: 0.9609 (m-80) cc_final: 0.8985 (m-80) REVERT: 3 179 LEU cc_start: 0.9771 (tp) cc_final: 0.9546 (tp) REVERT: 3 252 ASP cc_start: 0.8669 (t0) cc_final: 0.8468 (p0) REVERT: 3 384 MET cc_start: 0.9342 (tmm) cc_final: 0.8782 (tmm) REVERT: 3 421 PHE cc_start: 0.9091 (t80) cc_final: 0.8789 (t80) REVERT: 3 551 ASP cc_start: 0.7127 (t70) cc_final: 0.5777 (m-30) REVERT: 4 272 MET cc_start: 0.9282 (mmp) cc_final: 0.8781 (ptt) REVERT: 4 314 MET cc_start: 0.7481 (ttm) cc_final: 0.7191 (ttm) REVERT: 4 651 GLN cc_start: 0.8279 (mt0) cc_final: 0.7989 (mp10) REVERT: 4 682 TYR cc_start: 0.8919 (p90) cc_final: 0.8699 (p90) REVERT: 4 801 MET cc_start: 0.9404 (ttm) cc_final: 0.8997 (mtp) REVERT: 5 41 ASP cc_start: 0.9385 (m-30) cc_final: 0.8879 (t0) REVERT: 5 49 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8877 (tp-100) REVERT: 5 65 MET cc_start: 0.9369 (mmp) cc_final: 0.9134 (mmm) REVERT: 5 67 HIS cc_start: 0.9672 (m-70) cc_final: 0.9407 (m-70) REVERT: 5 252 ASP cc_start: 0.7868 (t0) cc_final: 0.7288 (t0) REVERT: 5 393 MET cc_start: 0.8520 (mmm) cc_final: 0.7308 (ttm) REVERT: 5 404 MET cc_start: 0.7186 (ptp) cc_final: 0.6481 (ppp) REVERT: 5 410 ILE cc_start: 0.8580 (pt) cc_final: 0.8262 (pt) REVERT: 5 552 MET cc_start: 0.9472 (mmp) cc_final: 0.8976 (mmm) REVERT: 5 576 HIS cc_start: 0.9508 (m90) cc_final: 0.8701 (m90) REVERT: 6 384 ASP cc_start: 0.9591 (t0) cc_final: 0.8821 (p0) REVERT: 6 519 MET cc_start: 0.9420 (mtt) cc_final: 0.8695 (mtp) REVERT: 6 551 MET cc_start: 0.9470 (mtp) cc_final: 0.9036 (tpt) REVERT: 6 621 TYR cc_start: 0.8581 (p90) cc_final: 0.8017 (p90) REVERT: 6 629 MET cc_start: 0.6684 (ttp) cc_final: 0.5843 (tpp) REVERT: 6 652 ILE cc_start: 0.8116 (mt) cc_final: 0.7747 (mt) REVERT: 6 656 MET cc_start: 0.9231 (mmm) cc_final: 0.9014 (mmm) REVERT: 6 661 ILE cc_start: 0.9071 (mt) cc_final: 0.8843 (tt) REVERT: 6 669 HIS cc_start: 0.8296 (t70) cc_final: 0.7875 (t-90) REVERT: 6 679 LEU cc_start: 0.9708 (tp) cc_final: 0.9459 (tp) REVERT: 6 719 CYS cc_start: 0.9547 (p) cc_final: 0.9169 (t) REVERT: 6 726 GLU cc_start: 0.9520 (tp30) cc_final: 0.9139 (tp30) REVERT: 6 803 MET cc_start: 0.9392 (mmp) cc_final: 0.8981 (mmm) REVERT: 7 29 LYS cc_start: 0.6774 (tptt) cc_final: 0.6491 (tppt) REVERT: 7 457 CYS cc_start: 0.8285 (t) cc_final: 0.7193 (t) REVERT: 7 459 MET cc_start: 0.9403 (mmt) cc_final: 0.9018 (mmm) REVERT: 7 529 MET cc_start: 0.8878 (ptt) cc_final: 0.8384 (ptt) REVERT: 7 707 MET cc_start: 0.7936 (mmp) cc_final: 0.7665 (pmm) REVERT: A 15 ARG cc_start: 0.9553 (ttt180) cc_final: 0.9158 (ptm-80) REVERT: A 164 ASP cc_start: 0.9325 (m-30) cc_final: 0.9052 (t0) REVERT: A 198 ARG cc_start: 0.9412 (ptp-170) cc_final: 0.9055 (mtm180) REVERT: B 20 VAL cc_start: 0.9781 (m) cc_final: 0.9456 (p) REVERT: B 63 MET cc_start: 0.8537 (mpp) cc_final: 0.8249 (mpp) REVERT: B 73 LEU cc_start: 0.9701 (tp) cc_final: 0.9333 (mt) REVERT: B 134 PHE cc_start: 0.8275 (m-80) cc_final: 0.7905 (m-80) REVERT: B 150 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8499 (mt-10) REVERT: B 189 MET cc_start: 0.9646 (mmp) cc_final: 0.9418 (mmm) REVERT: C 3 TYR cc_start: 0.8245 (t80) cc_final: 0.7596 (t80) REVERT: C 48 LEU cc_start: 0.9662 (tp) cc_final: 0.9443 (tt) REVERT: C 109 ILE cc_start: 0.9648 (pt) cc_final: 0.9411 (pt) REVERT: C 165 PHE cc_start: 0.9374 (t80) cc_final: 0.9058 (t80) REVERT: D 93 MET cc_start: 0.9660 (mmp) cc_final: 0.9107 (mmm) REVERT: D 220 ASP cc_start: 0.9325 (m-30) cc_final: 0.9063 (m-30) REVERT: D 277 MET cc_start: 0.9248 (mtt) cc_final: 0.8667 (mmt) REVERT: E 44 MET cc_start: 0.9496 (ptm) cc_final: 0.9162 (ptt) REVERT: E 241 TYR cc_start: 0.9176 (t80) cc_final: 0.8969 (t80) REVERT: E 362 MET cc_start: 0.9280 (tpt) cc_final: 0.8641 (tpt) REVERT: E 366 MET cc_start: 0.9493 (mtt) cc_final: 0.9229 (mmt) REVERT: E 380 MET cc_start: 0.8793 (mmp) cc_final: 0.8076 (mmp) REVERT: E 407 ASP cc_start: 0.9087 (m-30) cc_final: 0.8070 (t0) REVERT: E 482 ASP cc_start: 0.9403 (p0) cc_final: 0.9178 (t0) REVERT: E 537 ASP cc_start: 0.9272 (m-30) cc_final: 0.8690 (p0) REVERT: E 538 LEU cc_start: 0.8999 (mt) cc_final: 0.8763 (mt) outliers start: 3 outliers final: 2 residues processed: 403 average time/residue: 0.2344 time to fit residues: 160.4259 Evaluate side-chains 302 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 300 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 182 optimal weight: 5.9990 chunk 418 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 37 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 464 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 496 optimal weight: 7.9990 chunk 374 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 538 ASN ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 750 GLN 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.056946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.048176 restraints weight = 396293.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.049446 restraints weight = 237360.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.050316 restraints weight = 160574.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.050925 restraints weight = 119104.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.051365 restraints weight = 94332.791| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 41469 Z= 0.179 Angle : 0.845 16.248 56112 Z= 0.437 Chirality : 0.047 0.417 6492 Planarity : 0.005 0.073 7133 Dihedral : 9.833 177.372 5773 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.49 % Favored : 89.61 % Rotamer: Outliers : 0.04 % Allowed : 2.00 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.12), residues: 4995 helix: -0.54 (0.11), residues: 1982 sheet: -2.21 (0.19), residues: 572 loop : -1.69 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG 3 435 TYR 0.035 0.002 TYR 6 772 PHE 0.020 0.002 PHE 2 609 TRP 0.016 0.002 TRP 6 939 HIS 0.006 0.001 HIS 3 712 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (41467) covalent geometry : angle 0.84469 / 0.44 (56108) SS BOND : bond 0.00130 / 0.09 ( 2) SS BOND : angle 0.83176 / 0.72 ( 4) hydrogen bonds : bond 0.04034 / 2.70 ( 1354) hydrogen bonds : angle 5.87806 / 3.97 ( 3861) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 379 time to evaluate : 1.684 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: 2 613 ASN cc_start: 0.9343 (m-40) cc_final: 0.9045 (p0) REVERT: 2 677 PHE cc_start: 0.9532 (m-80) cc_final: 0.8859 (m-80) REVERT: 3 136 MET cc_start: 0.9069 (tpp) cc_final: 0.8706 (tpp) REVERT: 3 179 LEU cc_start: 0.9726 (tp) cc_final: 0.9489 (tp) REVERT: 3 367 LEU cc_start: 0.9035 (mt) cc_final: 0.8756 (mt) REVERT: 3 384 MET cc_start: 0.9205 (tmm) cc_final: 0.8731 (tmm) REVERT: 3 551 ASP cc_start: 0.7707 (t70) cc_final: 0.6318 (m-30) REVERT: 4 272 MET cc_start: 0.9238 (mmp) cc_final: 0.8740 (ptt) REVERT: 4 314 MET cc_start: 0.7434 (ttm) cc_final: 0.7126 (ttm) REVERT: 4 382 MET cc_start: 0.8454 (ttm) cc_final: 0.7417 (ttm) REVERT: 4 649 MET cc_start: 0.9412 (ttt) cc_final: 0.9197 (ttt) REVERT: 4 651 GLN cc_start: 0.8443 (mt0) cc_final: 0.8132 (mp10) REVERT: 4 801 MET cc_start: 0.9340 (ttm) cc_final: 0.8971 (mtp) REVERT: 5 41 ASP cc_start: 0.9363 (m-30) cc_final: 0.8878 (t0) REVERT: 5 49 GLN cc_start: 0.9142 (tp-100) cc_final: 0.8813 (tp-100) REVERT: 5 67 HIS cc_start: 0.9664 (m-70) cc_final: 0.9342 (m-70) REVERT: 5 252 ASP cc_start: 0.7977 (t0) cc_final: 0.7445 (t0) REVERT: 5 393 MET cc_start: 0.8601 (mmm) cc_final: 0.7362 (ttm) REVERT: 5 404 MET cc_start: 0.6983 (ptp) cc_final: 0.6587 (ppp) REVERT: 5 410 ILE cc_start: 0.8623 (pt) cc_final: 0.8354 (pt) REVERT: 5 485 MET cc_start: 0.6344 (ppp) cc_final: 0.6056 (ppp) REVERT: 5 552 MET cc_start: 0.9490 (mmp) cc_final: 0.9019 (mmm) REVERT: 5 576 HIS cc_start: 0.9495 (m90) cc_final: 0.8682 (m90) REVERT: 6 373 MET cc_start: 0.7984 (tmm) cc_final: 0.7765 (tmm) REVERT: 6 384 ASP cc_start: 0.9583 (t0) cc_final: 0.8862 (p0) REVERT: 6 519 MET cc_start: 0.9388 (mtt) cc_final: 0.8810 (mmm) REVERT: 6 551 MET cc_start: 0.9440 (mtp) cc_final: 0.8974 (tpt) REVERT: 6 621 TYR cc_start: 0.8523 (p90) cc_final: 0.7971 (p90) REVERT: 6 629 MET cc_start: 0.6761 (ttp) cc_final: 0.5984 (tpp) REVERT: 6 652 ILE cc_start: 0.8236 (mt) cc_final: 0.7953 (mt) REVERT: 6 669 HIS cc_start: 0.8405 (t70) cc_final: 0.7987 (t-90) REVERT: 6 719 CYS cc_start: 0.9506 (p) cc_final: 0.9190 (t) REVERT: 6 726 GLU cc_start: 0.9484 (tp30) cc_final: 0.9067 (tp30) REVERT: 6 803 MET cc_start: 0.9324 (mmp) cc_final: 0.8856 (mmm) REVERT: 7 29 LYS cc_start: 0.6650 (tptt) cc_final: 0.6342 (tppt) REVERT: 7 457 CYS cc_start: 0.8447 (t) cc_final: 0.7505 (t) REVERT: 7 459 MET cc_start: 0.9391 (mmt) cc_final: 0.8996 (mmm) REVERT: 7 529 MET cc_start: 0.8869 (ptt) cc_final: 0.8405 (ptt) REVERT: 7 707 MET cc_start: 0.7860 (mmp) cc_final: 0.7618 (pmm) REVERT: A 164 ASP cc_start: 0.9288 (m-30) cc_final: 0.8983 (t0) REVERT: A 204 TYR cc_start: 0.8992 (m-80) cc_final: 0.8731 (m-80) REVERT: B 20 VAL cc_start: 0.9802 (m) cc_final: 0.9446 (p) REVERT: B 63 MET cc_start: 0.8637 (mpp) cc_final: 0.8389 (mpp) REVERT: B 73 LEU cc_start: 0.9681 (tp) cc_final: 0.9329 (mt) REVERT: B 134 PHE cc_start: 0.8220 (m-80) cc_final: 0.7924 (m-80) REVERT: B 150 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8339 (mt-10) REVERT: B 189 MET cc_start: 0.9640 (mmp) cc_final: 0.9387 (mmm) REVERT: C 3 TYR cc_start: 0.8205 (t80) cc_final: 0.7534 (t80) REVERT: C 8 ASP cc_start: 0.9032 (m-30) cc_final: 0.8776 (m-30) REVERT: C 48 LEU cc_start: 0.9635 (tp) cc_final: 0.9345 (tt) REVERT: C 104 PHE cc_start: 0.9454 (t80) cc_final: 0.9116 (t80) REVERT: C 109 ILE cc_start: 0.9608 (pt) cc_final: 0.9376 (pt) REVERT: C 176 ILE cc_start: 0.9698 (pt) cc_final: 0.9433 (pt) REVERT: D 93 MET cc_start: 0.9635 (mmp) cc_final: 0.9074 (mmm) REVERT: D 220 ASP cc_start: 0.9373 (m-30) cc_final: 0.9110 (m-30) REVERT: D 277 MET cc_start: 0.9216 (mtt) cc_final: 0.8674 (mmt) REVERT: E 44 MET cc_start: 0.9480 (ptm) cc_final: 0.9127 (ptt) REVERT: E 366 MET cc_start: 0.9481 (mtt) cc_final: 0.9019 (mtt) REVERT: E 380 MET cc_start: 0.8761 (mmt) cc_final: 0.7857 (mmp) REVERT: E 407 ASP cc_start: 0.8992 (m-30) cc_final: 0.8064 (t0) REVERT: E 482 ASP cc_start: 0.9492 (p0) cc_final: 0.9177 (t0) REVERT: E 537 ASP cc_start: 0.9187 (m-30) cc_final: 0.8543 (p0) REVERT: E 538 LEU cc_start: 0.8939 (mt) cc_final: 0.8677 (mt) outliers start: 2 outliers final: 2 residues processed: 381 average time/residue: 0.2305 time to fit residues: 150.6593 Evaluate side-chains 290 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 288 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 487 optimal weight: 8.9990 chunk 419 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 488 optimal weight: 4.9990 chunk 490 optimal weight: 0.9980 chunk 254 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 338 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 344 ASN 5 424 GLN ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 690 ASN 6 750 GLN 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** 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 = 0.3241 r_free = 0.3241 target = 0.055616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.046938 restraints weight = 404544.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.048169 restraints weight = 242810.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.049012 restraints weight = 165007.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.049609 restraints weight = 122636.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.050041 restraints weight = 97390.056| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 41469 Z= 0.207 Angle : 0.864 20.389 56112 Z= 0.448 Chirality : 0.048 0.404 6492 Planarity : 0.005 0.073 7133 Dihedral : 9.846 178.620 5773 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 27.63 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.13 % Favored : 89.01 % Rotamer: Outliers : 0.07 % Allowed : 1.27 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.85 % 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 are not related in a simple way. whole: -2.05 (0.12), residues: 4995 helix: -0.55 (0.11), residues: 1983 sheet: -2.37 (0.19), residues: 584 loop : -1.73 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 3 435 TYR 0.033 0.002 TYR 6 772 PHE 0.031 0.002 PHE 3 121 TRP 0.029 0.002 TRP 3 111 HIS 0.009 0.001 HIS 5 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (41467) covalent geometry : angle 0.86384 / 0.45 (56108) SS BOND : bond 0.00029 / 0.02 ( 2) SS BOND : angle 0.69771 / 0.59 ( 4) hydrogen bonds : bond 0.04119 / 2.75 ( 1354) hydrogen bonds : angle 5.90003 / 3.98 ( 3861) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 358 time to evaluate : 1.780 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: 2 237 MET cc_start: 0.9065 (mmp) cc_final: 0.8851 (mmm) REVERT: 2 276 MET cc_start: 0.9559 (tpp) cc_final: 0.9320 (tmm) REVERT: 2 540 LEU cc_start: 0.9682 (tp) cc_final: 0.9475 (pp) REVERT: 2 677 PHE cc_start: 0.9567 (m-80) cc_final: 0.8910 (m-80) REVERT: 3 136 MET cc_start: 0.9048 (tpp) cc_final: 0.8658 (tpp) REVERT: 3 179 LEU cc_start: 0.9729 (tp) cc_final: 0.9461 (tp) REVERT: 3 367 LEU cc_start: 0.8990 (mt) cc_final: 0.8714 (mt) REVERT: 3 384 MET cc_start: 0.9355 (tmm) cc_final: 0.8870 (tmm) REVERT: 3 551 ASP cc_start: 0.7915 (t70) cc_final: 0.6333 (m-30) REVERT: 4 272 MET cc_start: 0.9253 (mmp) cc_final: 0.8812 (tpp) REVERT: 4 314 MET cc_start: 0.7562 (ttm) cc_final: 0.7256 (ttm) REVERT: 4 328 LEU cc_start: 0.9415 (mt) cc_final: 0.9159 (mt) REVERT: 4 382 MET cc_start: 0.8412 (ttm) cc_final: 0.7565 (ttm) REVERT: 4 649 MET cc_start: 0.9412 (ttt) cc_final: 0.9195 (ttt) REVERT: 4 651 GLN cc_start: 0.8458 (mt0) cc_final: 0.8178 (mp10) REVERT: 4 801 MET cc_start: 0.9407 (ttm) cc_final: 0.8996 (mtp) REVERT: 5 41 ASP cc_start: 0.9362 (m-30) cc_final: 0.8960 (t0) REVERT: 5 49 GLN cc_start: 0.9220 (tp-100) cc_final: 0.8868 (tp-100) REVERT: 5 67 HIS cc_start: 0.9666 (m-70) cc_final: 0.9384 (m-70) REVERT: 5 252 ASP cc_start: 0.7954 (t0) cc_final: 0.7467 (t0) REVERT: 5 393 MET cc_start: 0.8654 (mmm) cc_final: 0.7367 (ttm) REVERT: 5 404 MET cc_start: 0.7193 (ptp) cc_final: 0.6715 (ppp) REVERT: 5 410 ILE cc_start: 0.8814 (pt) cc_final: 0.8550 (pt) REVERT: 5 552 MET cc_start: 0.9624 (mmp) cc_final: 0.9372 (mmm) REVERT: 6 384 ASP cc_start: 0.9640 (t0) cc_final: 0.8944 (p0) REVERT: 6 519 MET cc_start: 0.9410 (mtt) cc_final: 0.8720 (mtp) REVERT: 6 551 MET cc_start: 0.9440 (mtp) cc_final: 0.9013 (mmm) REVERT: 6 621 TYR cc_start: 0.8530 (p90) cc_final: 0.7933 (p90) REVERT: 6 669 HIS cc_start: 0.8406 (t70) cc_final: 0.7998 (t-90) REVERT: 6 719 CYS cc_start: 0.9577 (p) cc_final: 0.9212 (t) REVERT: 6 726 GLU cc_start: 0.9507 (tp30) cc_final: 0.9082 (tp30) REVERT: 6 803 MET cc_start: 0.9367 (mmp) cc_final: 0.8926 (mmm) REVERT: 7 29 LYS cc_start: 0.6663 (tptt) cc_final: 0.6373 (tppt) REVERT: 7 457 CYS cc_start: 0.8588 (t) cc_final: 0.7703 (t) REVERT: 7 459 MET cc_start: 0.9384 (mmt) cc_final: 0.9105 (mmm) REVERT: 7 707 MET cc_start: 0.8054 (mmp) cc_final: 0.7810 (pmm) REVERT: A 164 ASP cc_start: 0.9311 (m-30) cc_final: 0.8970 (t0) REVERT: A 204 TYR cc_start: 0.9086 (m-80) cc_final: 0.8854 (m-80) REVERT: B 20 VAL cc_start: 0.9846 (m) cc_final: 0.9631 (p) REVERT: B 63 MET cc_start: 0.8648 (mpp) cc_final: 0.8417 (mpp) REVERT: B 134 PHE cc_start: 0.8141 (m-80) cc_final: 0.7714 (m-80) REVERT: B 150 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8410 (mt-10) REVERT: C 48 LEU cc_start: 0.9642 (tp) cc_final: 0.9366 (tt) REVERT: C 104 PHE cc_start: 0.9540 (t80) cc_final: 0.9294 (t80) REVERT: C 109 ILE cc_start: 0.9629 (pt) cc_final: 0.9424 (pt) REVERT: C 172 MET cc_start: 0.9558 (tmm) cc_final: 0.9080 (tmm) REVERT: C 176 ILE cc_start: 0.9715 (pt) cc_final: 0.9416 (pt) REVERT: D 93 MET cc_start: 0.9669 (mmp) cc_final: 0.9113 (mmm) REVERT: D 277 MET cc_start: 0.9334 (mtt) cc_final: 0.8779 (mmm) REVERT: E 44 MET cc_start: 0.9453 (ptm) cc_final: 0.9083 (ptt) REVERT: E 366 MET cc_start: 0.9505 (mtt) cc_final: 0.9113 (mtt) REVERT: E 380 MET cc_start: 0.8738 (mmt) cc_final: 0.7854 (mmp) REVERT: E 407 ASP cc_start: 0.9085 (m-30) cc_final: 0.8121 (t0) REVERT: E 482 ASP cc_start: 0.9531 (p0) cc_final: 0.9197 (t0) REVERT: E 490 GLU cc_start: 0.9520 (mp0) cc_final: 0.9304 (pm20) REVERT: E 537 ASP cc_start: 0.9269 (m-30) cc_final: 0.8647 (p0) REVERT: E 538 LEU cc_start: 0.8988 (mt) cc_final: 0.8735 (mt) outliers start: 3 outliers final: 2 residues processed: 361 average time/residue: 0.2308 time to fit residues: 142.7871 Evaluate side-chains 285 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 295 optimal weight: 20.0000 chunk 439 optimal weight: 6.9990 chunk 318 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 180 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 418 optimal weight: 6.9990 chunk 443 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 690 ASN 6 750 GLN 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 HIS D 217 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.055785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.047101 restraints weight = 404907.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.048319 restraints weight = 242408.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049177 restraints weight = 164731.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.049783 restraints weight = 122099.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.050211 restraints weight = 97038.264| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 41469 Z= 0.196 Angle : 0.856 20.615 56112 Z= 0.443 Chirality : 0.048 0.418 6492 Planarity : 0.005 0.058 7133 Dihedral : 9.822 178.292 5773 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.87 % Favored : 89.23 % Rotamer: Outliers : 0.07 % Allowed : 0.85 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.85 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 4995 helix: -0.46 (0.11), residues: 1980 sheet: -2.33 (0.19), residues: 581 loop : -1.75 (0.13), residues: 2434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 93 TYR 0.031 0.002 TYR 6 772 PHE 0.023 0.002 PHE 2 609 TRP 0.016 0.002 TRP 6 939 HIS 0.007 0.001 HIS 5 560 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.20 (41467) covalent geometry : angle 0.85570 / 0.44 (56108) SS BOND : bond 0.00091 / 0.06 ( 2) SS BOND : angle 0.73938 / 0.64 ( 4) hydrogen bonds : bond 0.04039 / 2.71 ( 1354) hydrogen bonds : angle 5.83887 / 3.95 ( 3861) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 363 time to evaluate : 1.691 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: 2 609 PHE cc_start: 0.8755 (m-80) cc_final: 0.8489 (m-80) REVERT: 2 677 PHE cc_start: 0.9539 (m-80) cc_final: 0.8898 (m-80) REVERT: 3 136 MET cc_start: 0.9036 (tpp) cc_final: 0.8658 (tpp) REVERT: 3 179 LEU cc_start: 0.9726 (tp) cc_final: 0.9458 (tp) REVERT: 3 367 LEU cc_start: 0.8988 (mt) cc_final: 0.8707 (mt) REVERT: 3 384 MET cc_start: 0.9337 (tmm) cc_final: 0.8856 (tmm) REVERT: 4 272 MET cc_start: 0.9255 (mmp) cc_final: 0.8807 (tpp) REVERT: 4 314 MET cc_start: 0.7556 (ttm) cc_final: 0.7249 (ttm) REVERT: 4 328 LEU cc_start: 0.9385 (mt) cc_final: 0.9133 (mt) REVERT: 4 382 MET cc_start: 0.8433 (ttm) cc_final: 0.7429 (ttm) REVERT: 4 649 MET cc_start: 0.9365 (ttt) cc_final: 0.9142 (ttt) REVERT: 4 651 GLN cc_start: 0.8470 (mt0) cc_final: 0.8204 (mp10) REVERT: 4 801 MET cc_start: 0.9435 (ttm) cc_final: 0.9000 (mtp) REVERT: 5 41 ASP cc_start: 0.9362 (m-30) cc_final: 0.8940 (t0) REVERT: 5 49 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8860 (tp-100) REVERT: 5 67 HIS cc_start: 0.9670 (m-70) cc_final: 0.9401 (m-70) REVERT: 5 252 ASP cc_start: 0.7972 (t0) cc_final: 0.7483 (t0) REVERT: 5 393 MET cc_start: 0.8606 (mmm) cc_final: 0.7411 (ttm) REVERT: 5 404 MET cc_start: 0.7092 (ptp) cc_final: 0.6662 (ppp) REVERT: 5 410 ILE cc_start: 0.8905 (pt) cc_final: 0.8640 (pt) REVERT: 5 552 MET cc_start: 0.9629 (mmp) cc_final: 0.9404 (mmm) REVERT: 6 384 ASP cc_start: 0.9658 (t0) cc_final: 0.8982 (p0) REVERT: 6 519 MET cc_start: 0.9517 (mtt) cc_final: 0.8885 (mtp) REVERT: 6 551 MET cc_start: 0.9435 (mtp) cc_final: 0.9008 (mmm) REVERT: 6 621 TYR cc_start: 0.8723 (p90) cc_final: 0.8191 (p90) REVERT: 6 669 HIS cc_start: 0.8435 (t70) cc_final: 0.8086 (t-90) REVERT: 6 719 CYS cc_start: 0.9552 (p) cc_final: 0.9186 (t) REVERT: 6 726 GLU cc_start: 0.9516 (tp30) cc_final: 0.9123 (tp30) REVERT: 6 803 MET cc_start: 0.9309 (mmp) cc_final: 0.8887 (mmm) REVERT: 7 29 LYS cc_start: 0.6823 (tptt) cc_final: 0.6525 (tppt) REVERT: 7 457 CYS cc_start: 0.8611 (t) cc_final: 0.7733 (t) REVERT: 7 459 MET cc_start: 0.9367 (mmt) cc_final: 0.9095 (mmm) REVERT: 7 707 MET cc_start: 0.8062 (mmp) cc_final: 0.7753 (pmm) REVERT: A 164 ASP cc_start: 0.9307 (m-30) cc_final: 0.8953 (t0) REVERT: A 204 TYR cc_start: 0.9114 (m-80) cc_final: 0.8886 (m-80) REVERT: B 134 PHE cc_start: 0.8101 (m-80) cc_final: 0.7660 (m-80) REVERT: B 150 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 3 TYR cc_start: 0.7723 (t80) cc_final: 0.7194 (t80) REVERT: C 8 ASP cc_start: 0.9137 (m-30) cc_final: 0.8693 (m-30) REVERT: C 48 LEU cc_start: 0.9649 (tp) cc_final: 0.9408 (tt) REVERT: C 104 PHE cc_start: 0.9557 (t80) cc_final: 0.9266 (t80) REVERT: C 109 ILE cc_start: 0.9626 (pt) cc_final: 0.9412 (pt) REVERT: C 134 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9175 (tm-30) REVERT: C 175 GLU cc_start: 0.9097 (pp20) cc_final: 0.8843 (pp20) REVERT: D 93 MET cc_start: 0.9670 (mmp) cc_final: 0.9066 (mmm) REVERT: D 129 MET cc_start: 0.9499 (mmp) cc_final: 0.9004 (mmm) REVERT: D 133 LEU cc_start: 0.9541 (tt) cc_final: 0.9275 (pp) REVERT: D 220 ASP cc_start: 0.9087 (m-30) cc_final: 0.8720 (m-30) REVERT: D 277 MET cc_start: 0.9348 (mtt) cc_final: 0.8731 (mmt) REVERT: E 44 MET cc_start: 0.9465 (ptm) cc_final: 0.9102 (ptt) REVERT: E 366 MET cc_start: 0.9528 (mtt) cc_final: 0.9133 (mtt) REVERT: E 380 MET cc_start: 0.8729 (mmt) cc_final: 0.7839 (mmp) REVERT: E 407 ASP cc_start: 0.9070 (m-30) cc_final: 0.8205 (t0) REVERT: E 482 ASP cc_start: 0.9578 (p0) cc_final: 0.9185 (t0) REVERT: E 490 GLU cc_start: 0.9515 (mp0) cc_final: 0.9315 (pm20) REVERT: E 537 ASP cc_start: 0.9263 (m-30) cc_final: 0.8651 (p0) REVERT: E 538 LEU cc_start: 0.8980 (mt) cc_final: 0.8726 (mt) outliers start: 3 outliers final: 2 residues processed: 366 average time/residue: 0.2371 time to fit residues: 147.5674 Evaluate side-chains 289 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 502 optimal weight: 5.9990 chunk 222 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 chunk 431 optimal weight: 2.9990 chunk 441 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 156 GLN 6 690 ASN 6 750 GLN 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** 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 = 0.3071 r_free = 0.3071 target = 0.046192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.035250 restraints weight = 376669.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.036393 restraints weight = 254552.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.037229 restraints weight = 189905.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.037894 restraints weight = 151780.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.038367 restraints weight = 126897.408| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 41469 Z= 0.173 Angle : 0.850 21.131 56112 Z= 0.437 Chirality : 0.048 0.422 6492 Planarity : 0.005 0.058 7133 Dihedral : 9.768 177.750 5773 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 24.79 Ramachandran Plot: Outliers : 0.94 % Allowed : 9.65 % Favored : 89.41 % Rotamer: Outliers : 0.07 % Allowed : 0.58 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % 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 are not related in a simple way. whole: -1.90 (0.12), residues: 4995 helix: -0.36 (0.11), residues: 2000 sheet: -2.20 (0.20), residues: 574 loop : -1.76 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 22 TYR 0.028 0.002 TYR 6 772 PHE 0.020 0.002 PHE 2 609 TRP 0.023 0.002 TRP E 478 HIS 0.007 0.001 HIS 2 779 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 (41467) covalent geometry : angle 0.84997 / 0.44 (56108) SS BOND : bond 0.00161 / 0.11 ( 2) SS BOND : angle 0.68880 / 0.60 ( 4) hydrogen bonds : bond 0.03835 / 2.58 ( 1354) hydrogen bonds : angle 5.72088 / 3.87 ( 3861) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9990 Ramachandran restraints generated. 4995 Oldfield, 0 Emsley, 4995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 376 time to evaluate : 1.472 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: 2 609 PHE cc_start: 0.8790 (m-80) cc_final: 0.8440 (m-80) REVERT: 2 677 PHE cc_start: 0.9486 (m-80) cc_final: 0.8851 (m-80) REVERT: 3 103 LEU cc_start: 0.9539 (tt) cc_final: 0.9304 (mm) REVERT: 3 367 LEU cc_start: 0.8956 (mt) cc_final: 0.8671 (mt) REVERT: 3 384 MET cc_start: 0.9394 (tmm) cc_final: 0.8920 (tmm) REVERT: 4 272 MET cc_start: 0.9323 (mmp) cc_final: 0.8885 (tpp) REVERT: 4 314 MET cc_start: 0.7647 (ttm) cc_final: 0.7339 (ttm) REVERT: 4 382 MET cc_start: 0.8489 (ttm) cc_final: 0.7592 (ttm) REVERT: 4 801 MET cc_start: 0.9428 (ttm) cc_final: 0.9008 (mtp) REVERT: 5 41 ASP cc_start: 0.9394 (m-30) cc_final: 0.9075 (t0) REVERT: 5 49 GLN cc_start: 0.9197 (tp-100) cc_final: 0.8812 (tp-100) REVERT: 5 67 HIS cc_start: 0.9667 (m-70) cc_final: 0.9310 (m90) REVERT: 5 252 ASP cc_start: 0.7999 (t0) cc_final: 0.7383 (t0) REVERT: 5 351 GLU cc_start: 0.8772 (tt0) cc_final: 0.8479 (mp0) REVERT: 5 362 ARG cc_start: 0.9437 (mpp80) cc_final: 0.9146 (mtt180) REVERT: 5 393 MET cc_start: 0.8479 (mmm) cc_final: 0.7460 (ttm) REVERT: 5 404 MET cc_start: 0.7158 (ptp) cc_final: 0.6811 (ppp) REVERT: 5 410 ILE cc_start: 0.8748 (pt) cc_final: 0.8463 (pt) REVERT: 5 430 GLU cc_start: 0.9031 (pm20) cc_final: 0.8599 (pm20) REVERT: 5 478 CYS cc_start: 0.7938 (m) cc_final: 0.7539 (m) REVERT: 5 552 MET cc_start: 0.9605 (mmp) cc_final: 0.9379 (mmm) REVERT: 6 384 ASP cc_start: 0.9641 (t0) cc_final: 0.8946 (p0) REVERT: 6 519 MET cc_start: 0.9532 (mtt) cc_final: 0.9114 (mmm) REVERT: 6 551 MET cc_start: 0.9424 (mtp) cc_final: 0.8951 (tpt) REVERT: 6 621 TYR cc_start: 0.8646 (p90) cc_final: 0.8176 (p90) REVERT: 6 669 HIS cc_start: 0.8508 (t70) cc_final: 0.8177 (t-90) REVERT: 6 719 CYS cc_start: 0.9621 (p) cc_final: 0.9259 (t) REVERT: 6 726 GLU cc_start: 0.9486 (tp30) cc_final: 0.9110 (tp30) REVERT: 6 803 MET cc_start: 0.9335 (mmp) cc_final: 0.8912 (mmm) REVERT: 7 29 LYS cc_start: 0.6604 (tptt) cc_final: 0.6357 (tppt) REVERT: 7 300 MET cc_start: 0.8940 (mmm) cc_final: 0.8581 (tmm) REVERT: 7 457 CYS cc_start: 0.8669 (t) cc_final: 0.7806 (t) REVERT: 7 707 MET cc_start: 0.8235 (mmp) cc_final: 0.7870 (pmm) REVERT: A 38 ARG cc_start: 0.9426 (mmp80) cc_final: 0.9218 (mmp80) REVERT: A 164 ASP cc_start: 0.9405 (m-30) cc_final: 0.8979 (t0) REVERT: A 204 TYR cc_start: 0.9190 (m-80) cc_final: 0.8962 (m-80) REVERT: B 63 MET cc_start: 0.8656 (mpp) cc_final: 0.8431 (mpp) REVERT: B 134 PHE cc_start: 0.8096 (m-80) cc_final: 0.7645 (m-80) REVERT: B 147 ASP cc_start: 0.9496 (t0) cc_final: 0.8701 (t0) REVERT: B 150 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8458 (mt-10) REVERT: C 3 TYR cc_start: 0.7891 (t80) cc_final: 0.7173 (t80) REVERT: C 8 ASP cc_start: 0.9270 (m-30) cc_final: 0.8910 (m-30) REVERT: C 48 LEU cc_start: 0.9633 (tp) cc_final: 0.9369 (tt) REVERT: C 104 PHE cc_start: 0.9586 (t80) cc_final: 0.9153 (t80) REVERT: C 109 ILE cc_start: 0.9606 (pt) cc_final: 0.9375 (pt) REVERT: C 134 GLU cc_start: 0.9546 (tm-30) cc_final: 0.9198 (tm-30) REVERT: C 175 GLU cc_start: 0.9117 (pp20) cc_final: 0.8859 (pp20) REVERT: D 93 MET cc_start: 0.9681 (mmp) cc_final: 0.9107 (mmm) REVERT: D 129 MET cc_start: 0.9505 (mmp) cc_final: 0.9237 (mmm) REVERT: D 220 ASP cc_start: 0.9267 (m-30) cc_final: 0.8867 (m-30) REVERT: D 277 MET cc_start: 0.9279 (mtt) cc_final: 0.8692 (mmt) REVERT: E 44 MET cc_start: 0.9484 (ptm) cc_final: 0.9139 (ptt) REVERT: E 366 MET cc_start: 0.9540 (mtt) cc_final: 0.9158 (mtt) REVERT: E 380 MET cc_start: 0.8730 (mmt) cc_final: 0.7906 (mmm) REVERT: E 407 ASP cc_start: 0.9068 (m-30) cc_final: 0.8215 (t0) REVERT: E 482 ASP cc_start: 0.9629 (p0) cc_final: 0.9296 (t0) REVERT: E 490 GLU cc_start: 0.9519 (mp0) cc_final: 0.9317 (pm20) REVERT: E 537 ASP cc_start: 0.9313 (m-30) cc_final: 0.8735 (p0) REVERT: E 538 LEU cc_start: 0.9040 (mt) cc_final: 0.8817 (mt) outliers start: 3 outliers final: 2 residues processed: 379 average time/residue: 0.2326 time to fit residues: 150.6248 Evaluate side-chains 294 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 506 random chunks: chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 30.0000 chunk 475 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 184 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 27 optimal weight: 0.0980 chunk 492 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 chunk 351 optimal weight: 20.0000 chunk 297 optimal weight: 0.6980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 627 GLN ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 690 ASN 6 750 GLN ** 7 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN D 217 ASN ** E 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.057877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049076 restraints weight = 392473.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050369 restraints weight = 234588.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.051248 restraints weight = 158186.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.051872 restraints weight = 116828.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.052315 restraints weight = 92041.063| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41469 Z= 0.154 Angle : 0.846 21.007 56112 Z= 0.433 Chirality : 0.048 0.415 6492 Planarity : 0.004 0.059 7133 Dihedral : 9.687 177.791 5773 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.47 % Favored : 89.57 % Rotamer: Outliers : 0.07 % Allowed : 0.53 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % 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 are not related in a simple way. whole: -1.76 (0.12), residues: 4995 helix: -0.25 (0.11), residues: 1994 sheet: -1.99 (0.20), residues: 561 loop : -1.72 (0.13), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 435 TYR 0.026 0.001 TYR 6 772 PHE 0.020 0.001 PHE 2 609 TRP 0.025 0.002 TRP E 478 HIS 0.006 0.001 HIS 2 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (41467) covalent geometry : angle 0.84599 / 0.43 (56108) SS BOND : bond 0.00225 / 0.15 ( 2) SS BOND : angle 0.72998 / 0.62 ( 4) hydrogen bonds : bond 0.03674 / 2.49 ( 1354) hydrogen bonds : angle 5.57574 / 3.77 ( 3861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6213.62 seconds wall clock time: 109 minutes 39.96 seconds (6579.96 seconds total)