Starting phenix.real_space_refine on Tue Aug 26 20:40:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u8t_8519/08_2025/5u8t_8519_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u8t_8519/08_2025/5u8t_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 { model { file = "/net/cci-nas-00/data/ceres_data/5u8t_8519/08_2025/5u8t_8519_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u8t_8519/08_2025/5u8t_8519_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5u8t_8519/08_2025/5u8t_8519.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u8t_8519/08_2025/5u8t_8519.map" } 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-2.0-5787/lib/python3.9/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: 8.25, per 1000 atoms: 0.20 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: 2.95 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.43 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: 6.92 Time building geometry restraints manager: 3.83 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: 1.090 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.960 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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= 0.484 Angle : 1.605 60.587 56112 Z= 1.036 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 aren 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 covalent geometry : bond 0.00766 (41467) covalent geometry : angle 1.56731 (56108) SS BOND : bond 0.00299 ( 2) SS BOND : angle 41.22048 ( 4) hydrogen bonds : bond 0.20091 ( 1354) hydrogen bonds : angle 11.13085 ( 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 : 1.100 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: 0.7646 (OUTLIER) cc_final: 0.7060 (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: 0.8741 (t) REVERT: 3 454 GLU cc_start: 0.8695 (tp30) cc_final: 0.8490 (tm-30) REVERT: 3 475 PHE cc_start: 0.8418 (t80) cc_final: 0.8045 (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: 0.9101 (tp) REVERT: 4 271 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9243 (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: 0.8123 (mm) REVERT: 4 688 VAL cc_start: 0.4523 (OUTLIER) cc_final: 0.4076 (t) REVERT: 4 864 ASP cc_start: 0.8839 (m-30) cc_final: 0.8157 (p0) REVERT: 5 21 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8977 (t0) REVERT: 5 41 ASP cc_start: 0.9442 (m-30) cc_final: 0.9186 (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: 0.9235 (tt) REVERT: 5 204 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7546 (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: 0.2491 (ttm) REVERT: 5 426 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9203 (mm) REVERT: 5 462 PHE cc_start: 0.8612 (OUTLIER) cc_final: 0.8252 (m-80) REVERT: 5 502 ILE cc_start: 0.9275 (mt) cc_final: 0.8955 (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: 0.8516 (mt) REVERT: 5 526 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (pp) REVERT: 5 595 SER cc_start: 0.8505 (OUTLIER) cc_final: 0.7643 (p) REVERT: 5 599 MET cc_start: 0.9167 (tpp) cc_final: 0.8689 (mmt) REVERT: 5 689 MET cc_start: 0.9087 (mmm) cc_final: 0.8861 (tpt) REVERT: 6 384 ASP cc_start: 0.9566 (t0) cc_final: 0.8894 (p0) REVERT: 6 387 GLU cc_start: 0.9182 (tp30) cc_final: 0.8947 (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: 0.8562 (tpt) REVERT: 6 629 MET cc_start: 0.7703 (ttp) cc_final: 0.7129 (tpt) REVERT: 6 656 MET cc_start: 0.9307 (mmm) cc_final: 0.9004 (mmm) REVERT: 6 662 SER cc_start: 0.7199 (OUTLIER) cc_final: 0.6883 (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: 0.7118 (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: 0.7749 (mmt180) REVERT: 6 803 MET cc_start: 0.9045 (tpp) cc_final: 0.8834 (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: 0.8431 (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: 0.8880 (mt) REVERT: 7 506 MET cc_start: 0.8304 (mmm) cc_final: 0.8091 (ppp) REVERT: 7 521 CYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8966 (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: 0.9194 (p0) REVERT: A 149 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8726 (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: 0.9401 (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: 0.8849 (p) REVERT: E 44 MET cc_start: 0.9826 (ptm) cc_final: 0.9536 (ptt) REVERT: E 267 LEU cc_start: 0.9440 (mt) cc_final: 0.9209 (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: 0.9080 (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: 0.9502 (tp-100) REVERT: E 536 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8515 (mm) REVERT: E 537 ASP cc_start: 0.9257 (m-30) cc_final: 0.8672 (p0) outliers start: 371 outliers final: 96 residues processed: 911 average time/residue: 0.2274 time to fit residues: 338.1338 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 : 1.230 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 2 238 ASN 2 561 HIS 2 615 GLN ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 760 GLN 2 780 GLN ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 351 ASN 3 417 GLN ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 532 ASN 3 564 HIS 4 400 GLN 4 447 ASN 4 582 HIS ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 5 581 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 7 585 ASN 7 615 HIS 7 657 ASN A 50 ASN 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.058120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049345 restraints weight = 397807.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.050629 restraints weight = 234905.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.051501 restraints weight = 157050.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052116 restraints weight = 115620.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.052534 restraints weight = 91093.794| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 41469 Z= 0.235 Angle : 1.016 18.709 56112 Z= 0.529 Chirality : 0.052 0.390 6492 Planarity : 0.006 0.124 7133 Dihedral : 11.051 179.793 5773 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 30.10 Ramachandran Plot: Outliers : 0.92 % Allowed : 8.71 % Favored : 90.37 % Rotamer: Outliers : 0.47 % Allowed : 5.85 % Favored : 93.68 % 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 aren not related in a simple way. whole: -3.39 (0.10), residues: 4995 helix: -2.39 (0.09), residues: 1917 sheet: -2.49 (0.18), residues: 517 loop : -2.02 (0.11), residues: 2561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 3 509 TYR 0.032 0.002 TYR 7 411 PHE 0.033 0.003 PHE 5 197 TRP 0.016 0.002 TRP B 74 HIS 0.019 0.002 HIS 7 112 Details of bonding type rmsd covalent geometry : bond 0.00495 (41467) covalent geometry : angle 1.01641 (56108) SS BOND : bond 0.01693 ( 2) SS BOND : angle 1.63664 ( 4) hydrogen bonds : bond 0.06114 ( 1354) hydrogen bonds : angle 7.32743 ( 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 492 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 471 time to evaluate : 1.477 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: 2 267 MET cc_start: 0.9221 (ptp) cc_final: 0.8653 (ptt) REVERT: 2 612 MET cc_start: 0.8685 (mtm) cc_final: 0.7753 (mtp) REVERT: 2 613 ASN cc_start: 0.9411 (m-40) cc_final: 0.9166 (m-40) REVERT: 2 677 PHE cc_start: 0.9490 (m-80) cc_final: 0.8941 (m-80) REVERT: 2 681 CYS cc_start: 0.9086 (m) cc_final: 0.8711 (m) REVERT: 3 136 MET cc_start: 0.9408 (mmm) cc_final: 0.9148 (tpp) REVERT: 3 179 LEU cc_start: 0.9809 (tt) cc_final: 0.9595 (tt) REVERT: 3 183 GLU cc_start: 0.9475 (pm20) cc_final: 0.9114 (pm20) REVERT: 3 367 LEU cc_start: 0.9012 (mt) cc_final: 0.8714 (mt) REVERT: 3 442 LEU cc_start: 0.9544 (mt) cc_final: 0.9245 (tt) REVERT: 3 454 GLU cc_start: 0.8989 (tp30) cc_final: 0.8590 (tm-30) REVERT: 3 551 ASP cc_start: 0.7318 (t70) cc_final: 0.6040 (m-30) REVERT: 4 272 MET cc_start: 0.9330 (mmp) cc_final: 0.8929 (tpp) REVERT: 4 382 MET cc_start: 0.9381 (ttt) cc_final: 0.9021 (ttm) REVERT: 4 554 LYS cc_start: 0.8277 (mttt) cc_final: 0.7886 (tptt) REVERT: 4 606 THR cc_start: 0.9254 (m) cc_final: 0.9041 (p) REVERT: 4 614 LEU cc_start: 0.9087 (mm) cc_final: 0.8748 (tp) REVERT: 4 651 GLN cc_start: 0.8351 (mt0) cc_final: 0.7856 (mp10) REVERT: 4 682 TYR cc_start: 0.9032 (p90) cc_final: 0.8804 (p90) REVERT: 4 801 MET cc_start: 0.9172 (ttm) cc_final: 0.8897 (mtp) REVERT: 4 902 ASP cc_start: 0.8441 (m-30) cc_final: 0.8187 (p0) REVERT: 5 41 ASP cc_start: 0.9312 (m-30) cc_final: 0.8909 (t0) REVERT: 5 48 ASP cc_start: 0.9221 (m-30) cc_final: 0.8977 (t0) REVERT: 5 65 MET cc_start: 0.9229 (mmp) cc_final: 0.8840 (mmm) REVERT: 5 68 LEU cc_start: 0.9845 (tt) cc_final: 0.9519 (mt) REVERT: 5 252 ASP cc_start: 0.7544 (t0) cc_final: 0.7125 (t0) REVERT: 5 260 GLU cc_start: 0.8062 (pt0) cc_final: 0.7758 (pt0) REVERT: 5 342 ILE cc_start: 0.8089 (pt) cc_final: 0.7837 (pt) REVERT: 5 362 ARG cc_start: 0.9174 (mtt180) cc_final: 0.8940 (mtt180) REVERT: 5 404 MET cc_start: 0.7154 (ptp) cc_final: 0.6388 (ppp) REVERT: 5 410 ILE cc_start: 0.8368 (pt) cc_final: 0.8057 (pt) REVERT: 5 449 LEU cc_start: 0.7973 (pp) cc_final: 0.7676 (pp) REVERT: 5 509 ILE cc_start: 0.9554 (pt) cc_final: 0.9335 (tp) REVERT: 5 511 THR cc_start: 0.9366 (p) cc_final: 0.9107 (p) REVERT: 5 543 GLN cc_start: 0.7416 (pt0) cc_final: 0.6989 (mm110) REVERT: 5 552 MET cc_start: 0.9425 (tpt) cc_final: 0.9187 (mmm) REVERT: 5 576 HIS cc_start: 0.9464 (m90) cc_final: 0.8926 (m90) REVERT: 5 599 MET cc_start: 0.9548 (tpp) cc_final: 0.9259 (tpp) REVERT: 5 689 MET cc_start: 0.8995 (mmm) cc_final: 0.8770 (ppp) REVERT: 6 384 ASP cc_start: 0.9460 (t0) cc_final: 0.8531 (p0) REVERT: 6 550 GLN cc_start: 0.9425 (mt0) cc_final: 0.8986 (mm-40) REVERT: 6 551 MET cc_start: 0.9281 (mtp) cc_final: 0.8914 (tpt) REVERT: 6 621 TYR cc_start: 0.8549 (p90) cc_final: 0.8063 (p90) REVERT: 6 629 MET cc_start: 0.6782 (ttp) cc_final: 0.6038 (tpp) REVERT: 6 652 ILE cc_start: 0.7558 (mt) cc_final: 0.7179 (mm) REVERT: 6 656 MET cc_start: 0.9278 (mmm) cc_final: 0.9053 (mmm) REVERT: 6 699 LEU cc_start: 0.9436 (mp) cc_final: 0.9146 (mt) REVERT: 6 720 ASN cc_start: 0.9526 (t0) cc_final: 0.8942 (m110) REVERT: 6 831 LEU cc_start: 0.9602 (mt) cc_final: 0.9002 (mt) REVERT: 7 20 GLU cc_start: 0.9527 (tt0) cc_final: 0.9247 (mm-30) REVERT: 7 147 ARG cc_start: 0.9301 (mtt-85) cc_final: 0.8748 (tpp80) REVERT: 7 459 MET cc_start: 0.9438 (mmp) cc_final: 0.9231 (mmm) REVERT: 7 498 MET cc_start: 0.8732 (pmm) cc_final: 0.8408 (pmm) REVERT: 7 529 MET cc_start: 0.8600 (ptt) cc_final: 0.7984 (ptt) REVERT: A 79 MET cc_start: 0.9216 (mmm) cc_final: 0.8782 (mmm) REVERT: A 164 ASP cc_start: 0.9254 (m-30) cc_final: 0.8876 (t0) REVERT: A 204 TYR cc_start: 0.9051 (m-80) cc_final: 0.8626 (m-10) REVERT: B 17 GLN cc_start: 0.9610 (pt0) cc_final: 0.9295 (pt0) REVERT: B 20 VAL cc_start: 0.9904 (m) cc_final: 0.9631 (p) REVERT: B 99 ASP cc_start: 0.9449 (m-30) cc_final: 0.9200 (m-30) REVERT: B 134 PHE cc_start: 0.8527 (m-80) cc_final: 0.8161 (m-80) REVERT: C 3 TYR cc_start: 0.8328 (t80) cc_final: 0.8040 (t80) REVERT: C 16 PHE cc_start: 0.9499 (m-80) cc_final: 0.9161 (m-80) REVERT: C 126 GLU cc_start: 0.9421 (tp30) cc_final: 0.8946 (tp30) REVERT: C 172 MET cc_start: 0.9225 (ppp) cc_final: 0.8900 (tmm) REVERT: C 176 ILE cc_start: 0.9600 (pt) cc_final: 0.9281 (pt) REVERT: D 70 GLU cc_start: 0.9380 (tp30) cc_final: 0.9177 (tm-30) REVERT: D 84 MET cc_start: 0.9420 (tmm) cc_final: 0.9008 (tmm) REVERT: D 93 MET cc_start: 0.9682 (mmp) cc_final: 0.9394 (mmm) REVERT: D 142 SER cc_start: 0.8891 (t) cc_final: 0.8479 (t) REVERT: D 277 MET cc_start: 0.8949 (mtt) cc_final: 0.8372 (mpp) REVERT: E 40 CYS cc_start: 0.9289 (m) cc_final: 0.8387 (p) REVERT: E 44 MET cc_start: 0.9621 (ptm) cc_final: 0.9248 (ptt) REVERT: E 241 TYR cc_start: 0.9307 (t80) cc_final: 0.9082 (t80) REVERT: E 366 MET cc_start: 0.9488 (mtt) cc_final: 0.9236 (mtt) REVERT: E 380 MET cc_start: 0.8782 (mmp) cc_final: 0.7979 (mmp) REVERT: E 387 GLU cc_start: 0.9668 (mm-30) cc_final: 0.9368 (tp30) REVERT: E 407 ASP cc_start: 0.9074 (m-30) cc_final: 0.7987 (t0) REVERT: E 485 ASP cc_start: 0.9002 (m-30) cc_final: 0.8715 (m-30) REVERT: E 537 ASP cc_start: 0.9167 (m-30) cc_final: 0.8500 (p0) REVERT: E 607 MET cc_start: 0.8789 (mtm) cc_final: 0.8281 (mtm) outliers start: 21 outliers final: 5 residues processed: 490 average time/residue: 0.2201 time to fit residues: 177.6779 Evaluate side-chains 351 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 346 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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: 9.9990 chunk 479 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 435 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 156 optimal weight: 30.0000 chunk 482 optimal weight: 4.9990 chunk 362 optimal weight: 9.9990 chunk 45 optimal weight: 0.0000 chunk 58 optimal weight: 1.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 282 HIS 2 613 ASN 2 651 ASN ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 507 ASN 3 691 ASN ** 4 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 524 ASN 5 561 ASN ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 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 ** 7 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN 7 538 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN B 22 ASN D 94 GLN D 183 HIS ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.057435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.048673 restraints weight = 400947.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.049956 restraints weight = 237291.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.050822 restraints weight = 159048.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051435 restraints weight = 117144.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.051857 restraints weight = 92460.957| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3786 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= 0.210 Angle : 0.909 15.863 56112 Z= 0.474 Chirality : 0.049 0.404 6492 Planarity : 0.005 0.060 7133 Dihedral : 10.381 175.865 5773 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.67 % Favored : 89.45 % Rotamer: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.48 % 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 aren not related in a simple way. whole: -2.77 (0.11), residues: 4995 helix: -1.62 (0.10), residues: 1935 sheet: -2.46 (0.18), residues: 563 loop : -1.78 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG 4 607 TYR 0.024 0.002 TYR 6 828 PHE 0.019 0.002 PHE 5 250 TRP 0.021 0.002 TRP B 74 HIS 0.015 0.002 HIS 5 560 Details of bonding type rmsd covalent geometry : bond 0.00431 (41467) covalent geometry : angle 0.90859 (56108) SS BOND : bond 0.00289 ( 2) SS BOND : angle 1.19898 ( 4) hydrogen bonds : bond 0.05269 ( 1354) hydrogen bonds : angle 6.69032 ( 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 434 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 427 time to evaluate : 1.663 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: 2 611 LYS cc_start: 0.9530 (mptt) cc_final: 0.9228 (tttp) REVERT: 2 624 MET cc_start: 0.7755 (ptm) cc_final: 0.7536 (ptm) REVERT: 2 677 PHE cc_start: 0.9585 (m-80) cc_final: 0.8960 (m-80) REVERT: 2 681 CYS cc_start: 0.9297 (m) cc_final: 0.8966 (m) REVERT: 2 823 MET cc_start: 0.8954 (ptp) cc_final: 0.8547 (ptp) REVERT: 3 179 LEU cc_start: 0.9816 (tt) cc_final: 0.9556 (tt) REVERT: 3 183 GLU cc_start: 0.9525 (pm20) cc_final: 0.9273 (pm20) REVERT: 3 367 LEU cc_start: 0.8988 (mt) cc_final: 0.8715 (mt) REVERT: 3 407 MET cc_start: 0.9204 (tpt) cc_final: 0.8931 (tpt) REVERT: 3 454 GLU cc_start: 0.9054 (tp30) cc_final: 0.8630 (tm-30) REVERT: 3 545 LEU cc_start: 0.9464 (mt) cc_final: 0.8760 (mp) REVERT: 4 272 MET cc_start: 0.9444 (mmp) cc_final: 0.9087 (ptt) REVERT: 4 382 MET cc_start: 0.9308 (ttt) cc_final: 0.8822 (ttm) REVERT: 4 554 LYS cc_start: 0.8336 (mttt) cc_final: 0.7870 (tptt) REVERT: 4 614 LEU cc_start: 0.9117 (mm) cc_final: 0.8809 (tp) REVERT: 4 649 MET cc_start: 0.9470 (ttt) cc_final: 0.9044 (ttt) REVERT: 4 651 GLN cc_start: 0.8481 (mt0) cc_final: 0.7971 (mp10) REVERT: 4 672 LEU cc_start: 0.9635 (tp) cc_final: 0.9356 (pp) REVERT: 4 682 TYR cc_start: 0.8930 (p90) cc_final: 0.8727 (p90) REVERT: 4 801 MET cc_start: 0.9242 (ttm) cc_final: 0.8929 (mtp) REVERT: 4 902 ASP cc_start: 0.8460 (m-30) cc_final: 0.8179 (p0) REVERT: 5 41 ASP cc_start: 0.9319 (m-30) cc_final: 0.8855 (t0) REVERT: 5 65 MET cc_start: 0.9311 (mmp) cc_final: 0.8832 (mmm) REVERT: 5 67 HIS cc_start: 0.9599 (m-70) cc_final: 0.9243 (m170) REVERT: 5 68 LEU cc_start: 0.9854 (tt) cc_final: 0.9493 (mt) REVERT: 5 252 ASP cc_start: 0.7802 (t0) cc_final: 0.7321 (t0) REVERT: 5 278 CYS cc_start: 0.8331 (m) cc_final: 0.7838 (m) REVERT: 5 362 ARG cc_start: 0.9325 (mtt180) cc_final: 0.8944 (mmm160) REVERT: 5 404 MET cc_start: 0.7245 (ptp) cc_final: 0.6492 (ppp) REVERT: 5 449 LEU cc_start: 0.7940 (pp) cc_final: 0.7570 (pp) REVERT: 5 511 THR cc_start: 0.9460 (p) cc_final: 0.9231 (p) REVERT: 5 543 GLN cc_start: 0.7265 (pt0) cc_final: 0.6855 (mm-40) REVERT: 5 552 MET cc_start: 0.9325 (tpt) cc_final: 0.9065 (mmm) REVERT: 5 576 HIS cc_start: 0.9550 (m90) cc_final: 0.8819 (m90) REVERT: 5 599 MET cc_start: 0.9413 (tpp) cc_final: 0.9150 (tpp) REVERT: 5 689 MET cc_start: 0.8997 (mmm) cc_final: 0.8745 (ppp) REVERT: 6 384 ASP cc_start: 0.9485 (t0) cc_final: 0.8591 (p0) REVERT: 6 519 MET cc_start: 0.9529 (mtt) cc_final: 0.8672 (mtp) REVERT: 6 551 MET cc_start: 0.9359 (mtp) cc_final: 0.9022 (tpt) REVERT: 6 621 TYR cc_start: 0.8634 (p90) cc_final: 0.8090 (p90) REVERT: 6 629 MET cc_start: 0.6739 (ttp) cc_final: 0.6050 (tpp) REVERT: 6 661 ILE cc_start: 0.8840 (mt) cc_final: 0.8453 (tt) REVERT: 6 679 LEU cc_start: 0.9683 (tt) cc_final: 0.9343 (tt) REVERT: 6 720 ASN cc_start: 0.9593 (t0) cc_final: 0.9239 (m110) REVERT: 6 803 MET cc_start: 0.9246 (mmp) cc_final: 0.8846 (mmm) REVERT: 7 20 GLU cc_start: 0.9549 (tt0) cc_final: 0.9223 (mm-30) REVERT: 7 457 CYS cc_start: 0.8238 (t) cc_final: 0.7154 (t) REVERT: 7 459 MET cc_start: 0.9376 (mmt) cc_final: 0.8869 (mmm) REVERT: 7 529 MET cc_start: 0.8774 (ptt) cc_final: 0.8301 (ptt) REVERT: A 164 ASP cc_start: 0.9257 (m-30) cc_final: 0.8935 (t0) REVERT: A 204 TYR cc_start: 0.9093 (m-80) cc_final: 0.8699 (m-10) REVERT: B 8 GLN cc_start: 0.9189 (pm20) cc_final: 0.8962 (pm20) REVERT: B 17 GLN cc_start: 0.9449 (pt0) cc_final: 0.9236 (pt0) REVERT: B 99 ASP cc_start: 0.9439 (m-30) cc_final: 0.9168 (m-30) REVERT: B 134 PHE cc_start: 0.8503 (m-80) cc_final: 0.8164 (m-80) REVERT: B 189 MET cc_start: 0.9736 (mmp) cc_final: 0.9491 (mmm) REVERT: C 8 ASP cc_start: 0.9185 (m-30) cc_final: 0.8984 (m-30) REVERT: C 126 GLU cc_start: 0.9454 (tp30) cc_final: 0.8931 (tp30) REVERT: C 134 GLU cc_start: 0.9515 (tm-30) cc_final: 0.8907 (tm-30) REVERT: D 64 MET cc_start: 0.9810 (tpp) cc_final: 0.9207 (tpp) REVERT: D 93 MET cc_start: 0.9799 (mmp) cc_final: 0.9267 (mmm) REVERT: D 277 MET cc_start: 0.9243 (mtt) cc_final: 0.8769 (mmt) REVERT: E 44 MET cc_start: 0.9601 (ptm) cc_final: 0.9236 (ptt) REVERT: E 241 TYR cc_start: 0.9304 (t80) cc_final: 0.9061 (t80) REVERT: E 362 MET cc_start: 0.9443 (tpt) cc_final: 0.8727 (tpp) REVERT: E 366 MET cc_start: 0.9478 (mtt) cc_final: 0.8968 (mtt) REVERT: E 380 MET cc_start: 0.8787 (mmp) cc_final: 0.8158 (mmp) REVERT: E 387 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9382 (tp30) REVERT: E 407 ASP cc_start: 0.9042 (m-30) cc_final: 0.7943 (t0) REVERT: E 537 ASP cc_start: 0.9252 (m-30) cc_final: 0.8707 (p0) outliers start: 7 outliers final: 3 residues processed: 433 average time/residue: 0.2119 time to fit residues: 152.6451 Evaluate side-chains 326 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 323 time to evaluate : 1.142 ------------------------------------------------------------------------------- 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: 0.5980 chunk 88 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 404 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 476 optimal weight: 5.9990 chunk 437 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 313 optimal weight: 30.0000 chunk 349 optimal weight: 6.9990 chunk 415 optimal weight: 8.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** 3 569 HIS 3 677 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** ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 658 GLN 6 669 HIS 6 750 GLN ** 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 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.048417 restraints weight = 399705.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.049689 restraints weight = 238023.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050560 restraints weight = 159925.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.051171 restraints weight = 118113.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.051599 restraints weight = 93266.476| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 41469 Z= 0.198 Angle : 0.879 18.675 56112 Z= 0.456 Chirality : 0.048 0.403 6492 Planarity : 0.005 0.059 7133 Dihedral : 10.115 176.883 5773 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.63 % Favored : 89.49 % Rotamer: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % Twisted Proline : 0.53 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.11), residues: 4995 helix: -1.20 (0.10), residues: 1954 sheet: -2.40 (0.19), residues: 544 loop : -1.77 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 4 909 TYR 0.024 0.002 TYR C 4 PHE 0.019 0.002 PHE 7 93 TRP 0.012 0.002 TRP E 551 HIS 0.012 0.001 HIS 5 560 Details of bonding type rmsd covalent geometry : bond 0.00406 (41467) covalent geometry : angle 0.87933 (56108) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.79176 ( 4) hydrogen bonds : bond 0.04706 ( 1354) hydrogen bonds : angle 6.32792 ( 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 402 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 398 time to evaluate : 1.658 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: 2 611 LYS cc_start: 0.9500 (mptt) cc_final: 0.9291 (tttp) REVERT: 2 612 MET cc_start: 0.8584 (mtm) cc_final: 0.7173 (mtp) REVERT: 2 677 PHE cc_start: 0.9608 (m-80) cc_final: 0.8918 (m-80) REVERT: 2 681 CYS cc_start: 0.9307 (m) cc_final: 0.9046 (m) REVERT: 2 764 MET cc_start: 0.9389 (ppp) cc_final: 0.9129 (ppp) REVERT: 3 136 MET cc_start: 0.8930 (tpp) cc_final: 0.8226 (tpp) REVERT: 3 183 GLU cc_start: 0.9542 (pm20) cc_final: 0.9284 (pm20) REVERT: 3 367 LEU cc_start: 0.9012 (mt) cc_final: 0.8737 (mt) REVERT: 3 454 GLU cc_start: 0.9014 (tp30) cc_final: 0.8600 (tm-30) REVERT: 3 545 LEU cc_start: 0.9313 (mt) cc_final: 0.8995 (mp) REVERT: 4 272 MET cc_start: 0.9384 (mmp) cc_final: 0.9003 (ptt) REVERT: 4 314 MET cc_start: 0.7023 (ttm) cc_final: 0.6458 (ttm) REVERT: 4 382 MET cc_start: 0.8925 (ttm) cc_final: 0.8279 (ttm) REVERT: 4 554 LYS cc_start: 0.8108 (mttt) cc_final: 0.7653 (tptt) REVERT: 4 614 LEU cc_start: 0.9037 (mm) cc_final: 0.8832 (tp) REVERT: 4 649 MET cc_start: 0.9398 (ttt) cc_final: 0.8948 (ttt) REVERT: 4 651 GLN cc_start: 0.8276 (mt0) cc_final: 0.7798 (mp10) REVERT: 4 682 TYR cc_start: 0.8875 (p90) cc_final: 0.8638 (p90) REVERT: 4 801 MET cc_start: 0.9294 (ttm) cc_final: 0.8926 (mtp) REVERT: 4 902 ASP cc_start: 0.8738 (m-30) cc_final: 0.8421 (p0) REVERT: 5 41 ASP cc_start: 0.9361 (m-30) cc_final: 0.8815 (t0) REVERT: 5 65 MET cc_start: 0.9250 (mmp) cc_final: 0.8909 (mmm) REVERT: 5 67 HIS cc_start: 0.9638 (m-70) cc_final: 0.9232 (m170) REVERT: 5 68 LEU cc_start: 0.9831 (tt) cc_final: 0.9615 (mt) REVERT: 5 252 ASP cc_start: 0.7951 (t0) cc_final: 0.7463 (t0) REVERT: 5 362 ARG cc_start: 0.9172 (mtt180) cc_final: 0.8896 (mmm160) REVERT: 5 393 MET cc_start: 0.8116 (mtp) cc_final: 0.7584 (mtt) REVERT: 5 410 ILE cc_start: 0.8211 (pt) cc_final: 0.7904 (pt) REVERT: 5 520 LEU cc_start: 0.9510 (tt) cc_final: 0.9056 (mt) REVERT: 5 576 HIS cc_start: 0.9562 (m90) cc_final: 0.8826 (m-70) REVERT: 5 599 MET cc_start: 0.9299 (tpp) cc_final: 0.9069 (tpp) REVERT: 6 384 ASP cc_start: 0.9526 (t0) cc_final: 0.8724 (p0) REVERT: 6 519 MET cc_start: 0.9445 (mtt) cc_final: 0.8705 (mtp) REVERT: 6 551 MET cc_start: 0.9446 (mtp) cc_final: 0.9061 (tpt) REVERT: 6 621 TYR cc_start: 0.8661 (p90) cc_final: 0.8072 (p90) REVERT: 6 661 ILE cc_start: 0.8905 (mt) cc_final: 0.8523 (tt) REVERT: 6 699 LEU cc_start: 0.9367 (mt) cc_final: 0.9145 (mt) REVERT: 6 719 CYS cc_start: 0.9433 (p) cc_final: 0.9087 (t) REVERT: 6 803 MET cc_start: 0.9319 (mmp) cc_final: 0.8874 (mmm) REVERT: 7 20 GLU cc_start: 0.9567 (tt0) cc_final: 0.9176 (mm-30) REVERT: 7 457 CYS cc_start: 0.8077 (t) cc_final: 0.6863 (t) REVERT: 7 459 MET cc_start: 0.9400 (mmt) cc_final: 0.8940 (mmm) REVERT: 7 529 MET cc_start: 0.8741 (ptt) cc_final: 0.8170 (ptt) REVERT: 7 707 MET cc_start: 0.7777 (mmp) cc_final: 0.7565 (pmm) REVERT: A 79 MET cc_start: 0.9342 (mmm) cc_final: 0.8858 (mmm) REVERT: A 164 ASP cc_start: 0.9255 (m-30) cc_final: 0.8961 (t0) REVERT: A 204 TYR cc_start: 0.9024 (m-80) cc_final: 0.8628 (m-10) REVERT: B 8 GLN cc_start: 0.9199 (pm20) cc_final: 0.8901 (pm20) REVERT: B 63 MET cc_start: 0.8399 (mpp) cc_final: 0.7925 (mpp) REVERT: B 99 ASP cc_start: 0.9407 (m-30) cc_final: 0.9150 (m-30) REVERT: B 134 PHE cc_start: 0.8448 (m-80) cc_final: 0.8069 (m-80) REVERT: B 189 MET cc_start: 0.9690 (mmp) cc_final: 0.9415 (mmm) REVERT: C 3 TYR cc_start: 0.8506 (t80) cc_final: 0.7701 (t80) REVERT: C 48 LEU cc_start: 0.9652 (tp) cc_final: 0.9398 (tt) REVERT: C 109 ILE cc_start: 0.9693 (pt) cc_final: 0.9473 (pt) REVERT: C 126 GLU cc_start: 0.9430 (tp30) cc_final: 0.9010 (tp30) REVERT: C 134 GLU cc_start: 0.9503 (tm-30) cc_final: 0.8897 (tm-30) REVERT: C 172 MET cc_start: 0.9530 (tmm) cc_final: 0.8881 (tmm) REVERT: C 176 ILE cc_start: 0.9626 (pt) cc_final: 0.9163 (pt) REVERT: C 186 ASP cc_start: 0.9713 (m-30) cc_final: 0.9509 (m-30) REVERT: D 68 LYS cc_start: 0.9662 (ptpp) cc_final: 0.9424 (ptmm) REVERT: D 84 MET cc_start: 0.9228 (tmm) cc_final: 0.8922 (tmm) REVERT: D 93 MET cc_start: 0.9783 (mmp) cc_final: 0.9234 (mmm) REVERT: D 218 MET cc_start: 0.9285 (mmm) cc_final: 0.8920 (mmm) REVERT: D 220 ASP cc_start: 0.9381 (m-30) cc_final: 0.8529 (m-30) REVERT: D 277 MET cc_start: 0.9201 (mtt) cc_final: 0.8727 (mmm) REVERT: E 44 MET cc_start: 0.9565 (ptm) cc_final: 0.9210 (ptt) REVERT: E 362 MET cc_start: 0.9398 (tpt) cc_final: 0.8705 (tpt) REVERT: E 366 MET cc_start: 0.9439 (mtt) cc_final: 0.9132 (mmm) REVERT: E 380 MET cc_start: 0.8824 (mmp) cc_final: 0.8155 (mmp) REVERT: E 407 ASP cc_start: 0.8955 (m-30) cc_final: 0.7935 (t0) REVERT: E 485 ASP cc_start: 0.9269 (m-30) cc_final: 0.8978 (t0) REVERT: E 537 ASP cc_start: 0.9249 (m-30) cc_final: 0.8647 (p0) REVERT: E 538 LEU cc_start: 0.9067 (mt) cc_final: 0.8804 (mt) outliers start: 4 outliers final: 3 residues processed: 402 average time/residue: 0.2075 time to fit residues: 140.1587 Evaluate side-chains 310 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 307 time to evaluate : 1.586 ------------------------------------------------------------------------------- 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: 1.9990 chunk 494 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 281 optimal weight: 7.9990 chunk 477 optimal weight: 9.9990 chunk 240 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 348 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 4 231 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS 6 698 ASN 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** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.056702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.047870 restraints weight = 398710.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049121 restraints weight = 238874.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050009 restraints weight = 162254.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.050622 restraints weight = 120015.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.051058 restraints weight = 94914.629| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 41469 Z= 0.200 Angle : 0.864 18.973 56112 Z= 0.449 Chirality : 0.048 0.408 6492 Planarity : 0.005 0.072 7133 Dihedral : 9.954 179.813 5773 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.90 % Allowed : 9.81 % Favored : 89.29 % Rotamer: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % Twisted Proline : 0.53 % 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 aren not related in a simple way. whole: -2.29 (0.11), residues: 4995 helix: -0.91 (0.11), residues: 1963 sheet: -2.42 (0.18), residues: 562 loop : -1.75 (0.13), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG 4 827 TYR 0.028 0.002 TYR 6 828 PHE 0.016 0.002 PHE 7 93 TRP 0.011 0.002 TRP C 190 HIS 0.012 0.001 HIS 5 560 Details of bonding type rmsd covalent geometry : bond 0.00412 (41467) covalent geometry : angle 0.86348 (56108) SS BOND : bond 0.00965 ( 2) SS BOND : angle 1.55196 ( 4) hydrogen bonds : bond 0.04528 ( 1354) hydrogen bonds : angle 6.17463 ( 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 394 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 390 time to evaluate : 1.453 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: 0.9054 (mmp) cc_final: 0.8822 (mmm) REVERT: 2 611 LYS cc_start: 0.9512 (mptt) cc_final: 0.9180 (tttp) REVERT: 2 612 MET cc_start: 0.8513 (mtm) cc_final: 0.7241 (mtp) REVERT: 2 640 LEU cc_start: 0.9418 (tp) cc_final: 0.8904 (tt) REVERT: 2 677 PHE cc_start: 0.9613 (m-80) cc_final: 0.9008 (m-80) REVERT: 2 681 CYS cc_start: 0.9352 (m) cc_final: 0.9076 (m) REVERT: 3 179 LEU cc_start: 0.9786 (tp) cc_final: 0.9552 (tp) REVERT: 3 252 ASP cc_start: 0.8908 (p0) cc_final: 0.8696 (t0) REVERT: 3 421 PHE cc_start: 0.9090 (t80) cc_final: 0.8781 (t80) REVERT: 3 454 GLU cc_start: 0.9047 (tp30) cc_final: 0.8656 (tm-30) REVERT: 3 545 LEU cc_start: 0.9303 (mt) cc_final: 0.9005 (mp) REVERT: 4 184 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7530 (p0) REVERT: 4 272 MET cc_start: 0.9355 (mmp) cc_final: 0.8905 (ptt) REVERT: 4 314 MET cc_start: 0.7162 (ttm) cc_final: 0.6877 (ttm) REVERT: 4 382 MET cc_start: 0.8814 (ttm) cc_final: 0.8329 (ttm) REVERT: 4 554 LYS cc_start: 0.8137 (mttt) cc_final: 0.7644 (tptt) REVERT: 4 649 MET cc_start: 0.9397 (ttt) cc_final: 0.8941 (ttt) REVERT: 4 651 GLN cc_start: 0.8249 (mt0) cc_final: 0.7941 (mp10) REVERT: 4 682 TYR cc_start: 0.8910 (p90) cc_final: 0.8702 (p90) REVERT: 4 801 MET cc_start: 0.9322 (ttm) cc_final: 0.8967 (mtp) REVERT: 4 902 ASP cc_start: 0.9007 (m-30) cc_final: 0.8637 (p0) REVERT: 4 903 ILE cc_start: 0.8806 (mt) cc_final: 0.8438 (mm) REVERT: 4 913 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7072 (mm-30) REVERT: 5 41 ASP cc_start: 0.9382 (m-30) cc_final: 0.8878 (t0) REVERT: 5 65 MET cc_start: 0.9326 (mmp) cc_final: 0.8951 (mmm) REVERT: 5 67 HIS cc_start: 0.9641 (m-70) cc_final: 0.9417 (m-70) REVERT: 5 252 ASP cc_start: 0.7870 (t0) cc_final: 0.7387 (t0) REVERT: 5 393 MET cc_start: 0.8158 (mtp) cc_final: 0.7491 (mtt) REVERT: 5 404 MET cc_start: 0.7501 (ptp) cc_final: 0.6681 (ppp) REVERT: 5 410 ILE cc_start: 0.8464 (pt) cc_final: 0.8129 (pt) REVERT: 5 552 MET cc_start: 0.9486 (mmp) cc_final: 0.9053 (mmm) REVERT: 5 576 HIS cc_start: 0.9578 (m90) cc_final: 0.9130 (m-70) REVERT: 5 599 MET cc_start: 0.9134 (tpp) cc_final: 0.8620 (mmt) REVERT: 6 373 MET cc_start: 0.7926 (tmm) cc_final: 0.7702 (tmm) REVERT: 6 384 ASP cc_start: 0.9585 (t0) cc_final: 0.8819 (p0) REVERT: 6 519 MET cc_start: 0.9447 (mtt) cc_final: 0.8823 (mtp) REVERT: 6 551 MET cc_start: 0.9453 (mtp) cc_final: 0.9054 (tpt) REVERT: 6 621 TYR cc_start: 0.8662 (p90) cc_final: 0.8042 (p90) REVERT: 6 656 MET cc_start: 0.8703 (mtp) cc_final: 0.8303 (mtp) REVERT: 6 661 ILE cc_start: 0.8916 (mt) cc_final: 0.8563 (tt) REVERT: 6 699 LEU cc_start: 0.9305 (mt) cc_final: 0.9072 (mt) REVERT: 6 719 CYS cc_start: 0.9541 (p) cc_final: 0.9183 (t) REVERT: 6 803 MET cc_start: 0.9422 (mmp) cc_final: 0.9068 (mmm) REVERT: 7 29 LYS cc_start: 0.6939 (tptt) cc_final: 0.6642 (tppt) REVERT: 7 457 CYS cc_start: 0.8175 (t) cc_final: 0.7011 (t) REVERT: 7 459 MET cc_start: 0.9418 (mmt) cc_final: 0.8969 (mmm) REVERT: 7 529 MET cc_start: 0.8887 (ptt) cc_final: 0.8413 (ptt) REVERT: 7 707 MET cc_start: 0.7864 (mmp) cc_final: 0.7608 (pmm) REVERT: A 79 MET cc_start: 0.9397 (mmm) cc_final: 0.8897 (mmm) REVERT: A 164 ASP cc_start: 0.9305 (m-30) cc_final: 0.8979 (t0) REVERT: A 204 TYR cc_start: 0.9060 (m-80) cc_final: 0.8694 (m-10) REVERT: B 63 MET cc_start: 0.8552 (mpp) cc_final: 0.8218 (mpp) REVERT: B 134 PHE cc_start: 0.8350 (m-80) cc_final: 0.7973 (m-80) REVERT: C 3 TYR cc_start: 0.8368 (t80) cc_final: 0.7458 (t80) REVERT: C 48 LEU cc_start: 0.9667 (tp) cc_final: 0.9409 (tt) REVERT: C 109 ILE cc_start: 0.9694 (pt) cc_final: 0.9490 (pt) REVERT: C 126 GLU cc_start: 0.9468 (tp30) cc_final: 0.9048 (tp30) REVERT: C 134 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9041 (tm-30) REVERT: C 176 ILE cc_start: 0.9558 (pt) cc_final: 0.9353 (pt) REVERT: D 68 LYS cc_start: 0.9669 (ptpp) cc_final: 0.9463 (ptmm) REVERT: D 93 MET cc_start: 0.9790 (mmp) cc_final: 0.9248 (mmm) REVERT: D 129 MET cc_start: 0.9272 (mmt) cc_final: 0.8886 (mmt) REVERT: D 218 MET cc_start: 0.9223 (mmm) cc_final: 0.8893 (mmm) REVERT: D 220 ASP cc_start: 0.9456 (m-30) cc_final: 0.8671 (m-30) REVERT: D 277 MET cc_start: 0.9269 (mtt) cc_final: 0.8725 (mmt) REVERT: E 44 MET cc_start: 0.9552 (ptm) cc_final: 0.9206 (ptt) REVERT: E 366 MET cc_start: 0.9515 (mtt) cc_final: 0.9127 (mtt) REVERT: E 380 MET cc_start: 0.8780 (mmp) cc_final: 0.7989 (mmp) REVERT: E 407 ASP cc_start: 0.9086 (m-30) cc_final: 0.8071 (t0) REVERT: E 537 ASP cc_start: 0.9275 (m-30) cc_final: 0.8688 (p0) REVERT: E 538 LEU cc_start: 0.9023 (mt) cc_final: 0.8784 (mt) outliers start: 4 outliers final: 2 residues processed: 394 average time/residue: 0.2195 time to fit residues: 145.7047 Evaluate side-chains 306 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 303 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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: 9.9990 chunk 434 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 178 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 386 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 442 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 392 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 51 ASN ** 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** ** 4 354 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 ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 359 GLN ** 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** 6 182 GLN ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS 6 750 GLN ** 7 72 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 167 HIS ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 GLN ** D 217 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 269 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 = 0.3216 r_free = 0.3216 target = 0.054689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.046035 restraints weight = 407238.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.047252 restraints weight = 244356.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048099 restraints weight = 165972.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.048696 restraints weight = 123467.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049116 restraints weight = 97966.036| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4860 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= 0.242 Angle : 0.895 19.332 56112 Z= 0.466 Chirality : 0.048 0.428 6492 Planarity : 0.005 0.080 7133 Dihedral : 9.934 177.826 5773 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 29.91 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.29 % Favored : 88.81 % Rotamer: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.87 % 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 aren not related in a simple way. whole: -2.35 (0.11), residues: 4995 helix: -0.89 (0.11), residues: 1977 sheet: -2.51 (0.19), residues: 553 loop : -1.84 (0.13), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 5 486 TYR 0.046 0.002 TYR 6 772 PHE 0.016 0.002 PHE B 184 TRP 0.031 0.002 TRP 6 939 HIS 0.012 0.002 HIS 5 560 Details of bonding type rmsd covalent geometry : bond 0.00491 (41467) covalent geometry : angle 0.89460 (56108) SS BOND : bond 0.00140 ( 2) SS BOND : angle 1.19330 ( 4) hydrogen bonds : bond 0.04533 ( 1354) hydrogen bonds : angle 6.17058 ( 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 373 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 370 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8423 (mtm) cc_final: 0.7107 (mtp) REVERT: 2 629 ILE cc_start: 0.7560 (tt) cc_final: 0.7129 (tt) REVERT: 2 677 PHE cc_start: 0.9653 (m-80) cc_final: 0.9038 (m-80) REVERT: 2 681 CYS cc_start: 0.9365 (m) cc_final: 0.9104 (m) REVERT: 3 136 MET cc_start: 0.9066 (tpp) cc_final: 0.8363 (tpp) REVERT: 3 179 LEU cc_start: 0.9776 (tp) cc_final: 0.9554 (tp) REVERT: 3 367 LEU cc_start: 0.8995 (mt) cc_final: 0.8696 (mt) REVERT: 3 384 MET cc_start: 0.9421 (tmm) cc_final: 0.8860 (tmm) REVERT: 3 454 GLU cc_start: 0.9126 (tp30) cc_final: 0.8741 (tm-30) REVERT: 3 545 LEU cc_start: 0.9373 (mt) cc_final: 0.9054 (mp) REVERT: 4 272 MET cc_start: 0.9285 (mmp) cc_final: 0.8854 (tpp) REVERT: 4 314 MET cc_start: 0.7280 (ttm) cc_final: 0.6992 (ttm) REVERT: 4 328 LEU cc_start: 0.9425 (mt) cc_final: 0.9209 (mt) REVERT: 4 382 MET cc_start: 0.8967 (ttm) cc_final: 0.8741 (ttm) REVERT: 4 554 LYS cc_start: 0.8175 (mttt) cc_final: 0.7700 (tptt) REVERT: 4 649 MET cc_start: 0.9383 (ttt) cc_final: 0.8943 (ttt) REVERT: 4 651 GLN cc_start: 0.8292 (mt0) cc_final: 0.8069 (mp10) REVERT: 4 682 TYR cc_start: 0.8907 (p90) cc_final: 0.8689 (p90) REVERT: 4 801 MET cc_start: 0.9356 (ttm) cc_final: 0.9026 (mtp) REVERT: 5 41 ASP cc_start: 0.9351 (m-30) cc_final: 0.8930 (t0) REVERT: 5 65 MET cc_start: 0.9374 (mmp) cc_final: 0.9148 (mmm) REVERT: 5 67 HIS cc_start: 0.9676 (m-70) cc_final: 0.9381 (m-70) REVERT: 5 252 ASP cc_start: 0.8028 (t0) cc_final: 0.7611 (t0) REVERT: 5 362 ARG cc_start: 0.9156 (mtt180) cc_final: 0.8913 (mmm160) REVERT: 5 393 MET cc_start: 0.8377 (mtp) cc_final: 0.7751 (mtt) REVERT: 5 404 MET cc_start: 0.7397 (ptp) cc_final: 0.6623 (ppp) REVERT: 5 410 ILE cc_start: 0.8658 (pt) cc_final: 0.8262 (pt) REVERT: 5 552 MET cc_start: 0.9491 (mmp) cc_final: 0.8965 (mmm) REVERT: 5 576 HIS cc_start: 0.9544 (m90) cc_final: 0.8775 (m90) REVERT: 6 168 MET cc_start: 0.9658 (mmp) cc_final: 0.9457 (mmm) REVERT: 6 373 MET cc_start: 0.8047 (tmm) cc_final: 0.7838 (tmm) REVERT: 6 384 ASP cc_start: 0.9657 (t0) cc_final: 0.8927 (p0) REVERT: 6 519 MET cc_start: 0.9433 (mtt) cc_final: 0.8746 (mtp) REVERT: 6 551 MET cc_start: 0.9428 (mtp) cc_final: 0.8983 (tpt) REVERT: 6 621 TYR cc_start: 0.8618 (p90) cc_final: 0.8025 (p90) REVERT: 6 661 ILE cc_start: 0.9025 (mt) cc_final: 0.8776 (tt) REVERT: 6 709 PHE cc_start: 0.8873 (m-80) cc_final: 0.8632 (m-80) REVERT: 6 719 CYS cc_start: 0.9551 (p) cc_final: 0.9209 (t) REVERT: 6 803 MET cc_start: 0.9404 (mmp) cc_final: 0.9043 (mmm) REVERT: 7 457 CYS cc_start: 0.8228 (t) cc_final: 0.7173 (t) REVERT: 7 529 MET cc_start: 0.8879 (ptt) cc_final: 0.8462 (ptt) REVERT: 7 707 MET cc_start: 0.7957 (mmp) cc_final: 0.7697 (pmm) REVERT: A 164 ASP cc_start: 0.9275 (m-30) cc_final: 0.8984 (t0) REVERT: A 204 TYR cc_start: 0.8855 (m-10) cc_final: 0.8533 (m-80) REVERT: B 63 MET cc_start: 0.8675 (mpp) cc_final: 0.8381 (mpp) REVERT: B 134 PHE cc_start: 0.8300 (m-80) cc_final: 0.7939 (m-80) REVERT: B 189 MET cc_start: 0.9665 (mmp) cc_final: 0.9455 (mmm) REVERT: C 3 TYR cc_start: 0.8643 (t80) cc_final: 0.7653 (t80) REVERT: C 126 GLU cc_start: 0.9458 (tp30) cc_final: 0.9040 (tp30) REVERT: C 134 GLU cc_start: 0.9565 (tm-30) cc_final: 0.9077 (tm-30) REVERT: C 172 MET cc_start: 0.9559 (tmm) cc_final: 0.9083 (tmm) REVERT: C 176 ILE cc_start: 0.9588 (pt) cc_final: 0.9138 (pt) REVERT: C 189 ARG cc_start: 0.9596 (mtp-110) cc_final: 0.9378 (ttp80) REVERT: D 93 MET cc_start: 0.9786 (mmp) cc_final: 0.9242 (mmm) REVERT: D 129 MET cc_start: 0.9329 (mmt) cc_final: 0.9056 (mmm) REVERT: D 218 MET cc_start: 0.9167 (mmm) cc_final: 0.8832 (mmm) REVERT: D 220 ASP cc_start: 0.9461 (m-30) cc_final: 0.8566 (m-30) REVERT: D 277 MET cc_start: 0.9324 (mtt) cc_final: 0.8818 (mmt) REVERT: E 44 MET cc_start: 0.9499 (ptm) cc_final: 0.9169 (ptt) REVERT: E 366 MET cc_start: 0.9468 (mtt) cc_final: 0.9163 (mmt) REVERT: E 380 MET cc_start: 0.8781 (mmp) cc_final: 0.8084 (mmp) REVERT: E 407 ASP cc_start: 0.9092 (m-30) cc_final: 0.8075 (t0) REVERT: E 482 ASP cc_start: 0.9538 (p0) cc_final: 0.9326 (t0) REVERT: E 485 ASP cc_start: 0.9345 (m-30) cc_final: 0.9004 (t0) REVERT: E 537 ASP cc_start: 0.9213 (m-30) cc_final: 0.8606 (p0) REVERT: E 538 LEU cc_start: 0.9074 (mt) cc_final: 0.8862 (mt) outliers start: 3 outliers final: 2 residues processed: 373 average time/residue: 0.2082 time to fit residues: 132.1305 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 : 1.328 ------------------------------------------------------------------------------- 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: 7.9990 chunk 418 optimal weight: 3.9990 chunk 338 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 464 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 496 optimal weight: 5.9990 chunk 374 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 196 ASN ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 359 GLN ** 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** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS 6 750 GLN ** 7 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS 7 585 ASN ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 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 ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.055804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.047217 restraints weight = 403693.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048457 restraints weight = 240729.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049295 restraints weight = 162378.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.049914 restraints weight = 120514.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.050334 restraints weight = 95443.714| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 41469 Z= 0.195 Angle : 0.861 19.926 56112 Z= 0.446 Chirality : 0.048 0.412 6492 Planarity : 0.005 0.078 7133 Dihedral : 9.843 177.735 5773 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 26.66 Ramachandran Plot: Outliers : 0.88 % Allowed : 9.89 % Favored : 89.23 % Rotamer: Outliers : 0.04 % Allowed : 2.31 % Favored : 97.64 % 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 aren not related in a simple way. whole: -2.17 (0.11), residues: 4995 helix: -0.69 (0.11), residues: 1991 sheet: -2.38 (0.19), residues: 575 loop : -1.78 (0.13), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 4 909 TYR 0.035 0.002 TYR 6 772 PHE 0.014 0.002 PHE B 184 TRP 0.018 0.002 TRP 6 939 HIS 0.009 0.001 HIS 6 653 Details of bonding type rmsd covalent geometry : bond 0.00399 (41467) covalent geometry : angle 0.86131 (56108) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.89145 ( 4) hydrogen bonds : bond 0.04176 ( 1354) hydrogen bonds : angle 5.98104 ( 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 373 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 1.685 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: 2 612 MET cc_start: 0.8678 (mtm) cc_final: 0.8128 (mtp) REVERT: 2 677 PHE cc_start: 0.9576 (m-80) cc_final: 0.8911 (m-80) REVERT: 3 179 LEU cc_start: 0.9760 (tp) cc_final: 0.9521 (tp) REVERT: 3 367 LEU cc_start: 0.8988 (mt) cc_final: 0.8700 (mt) REVERT: 3 384 MET cc_start: 0.9351 (tmm) cc_final: 0.8833 (tmm) REVERT: 3 545 LEU cc_start: 0.9329 (mt) cc_final: 0.9038 (mp) REVERT: 4 272 MET cc_start: 0.9279 (mmp) cc_final: 0.8850 (tpp) REVERT: 4 314 MET cc_start: 0.7506 (ttm) cc_final: 0.7212 (ttm) REVERT: 4 382 MET cc_start: 0.8819 (ttm) cc_final: 0.8053 (ttm) REVERT: 4 554 LYS cc_start: 0.8184 (mttt) cc_final: 0.7930 (tttt) REVERT: 4 649 MET cc_start: 0.9346 (ttt) cc_final: 0.8890 (ttt) REVERT: 4 651 GLN cc_start: 0.8344 (mt0) cc_final: 0.8120 (mp10) REVERT: 4 801 MET cc_start: 0.9421 (ttm) cc_final: 0.9048 (mtp) REVERT: 4 890 ILE cc_start: 0.9229 (mt) cc_final: 0.8889 (mt) REVERT: 4 897 ARG cc_start: 0.7377 (mtt180) cc_final: 0.7168 (mtp85) REVERT: 4 903 ILE cc_start: 0.8732 (mt) cc_final: 0.8523 (mt) REVERT: 5 41 ASP cc_start: 0.9366 (m-30) cc_final: 0.8921 (t0) REVERT: 5 67 HIS cc_start: 0.9664 (m-70) cc_final: 0.9287 (m90) REVERT: 5 252 ASP cc_start: 0.8024 (t0) cc_final: 0.7547 (t0) REVERT: 5 362 ARG cc_start: 0.9156 (mtt180) cc_final: 0.8895 (mmm160) REVERT: 5 393 MET cc_start: 0.8353 (mtp) cc_final: 0.8012 (mtp) REVERT: 5 404 MET cc_start: 0.7343 (ptp) cc_final: 0.6739 (ppp) REVERT: 5 410 ILE cc_start: 0.8656 (pt) cc_final: 0.8351 (pt) REVERT: 5 552 MET cc_start: 0.9517 (mmp) cc_final: 0.9001 (mmm) REVERT: 5 599 MET cc_start: 0.9221 (ttm) cc_final: 0.8731 (mtt) REVERT: 6 384 ASP cc_start: 0.9654 (t0) cc_final: 0.8946 (p0) REVERT: 6 519 MET cc_start: 0.9424 (mtt) cc_final: 0.8921 (mmm) REVERT: 6 551 MET cc_start: 0.9425 (mtp) cc_final: 0.9013 (mmm) REVERT: 6 621 TYR cc_start: 0.8636 (p90) cc_final: 0.8024 (p90) REVERT: 6 629 MET cc_start: 0.6811 (ttp) cc_final: 0.6252 (tpp) REVERT: 6 661 ILE cc_start: 0.9271 (mt) cc_final: 0.8938 (tt) REVERT: 6 709 PHE cc_start: 0.8951 (m-80) cc_final: 0.8590 (m-80) REVERT: 6 719 CYS cc_start: 0.9567 (p) cc_final: 0.9202 (t) REVERT: 6 726 GLU cc_start: 0.9515 (tp30) cc_final: 0.9080 (tp30) REVERT: 6 730 HIS cc_start: 0.8790 (t-90) cc_final: 0.8495 (t-90) REVERT: 6 735 HIS cc_start: 0.8264 (m90) cc_final: 0.8044 (m90) REVERT: 6 803 MET cc_start: 0.9387 (mmp) cc_final: 0.8962 (mmm) REVERT: 6 912 MET cc_start: 0.6711 (mmp) cc_final: 0.6409 (mmp) REVERT: 6 913 MET cc_start: 0.8957 (mmt) cc_final: 0.8756 (tmm) REVERT: 7 457 CYS cc_start: 0.8382 (t) cc_final: 0.7571 (t) REVERT: 7 459 MET cc_start: 0.9514 (mmp) cc_final: 0.9169 (mmm) REVERT: 7 529 MET cc_start: 0.8893 (ptt) cc_final: 0.8354 (ptt) REVERT: 7 707 MET cc_start: 0.7982 (mmp) cc_final: 0.7696 (pmm) REVERT: A 110 MET cc_start: 0.3456 (mmm) cc_final: 0.3225 (mmm) REVERT: A 164 ASP cc_start: 0.9305 (m-30) cc_final: 0.8950 (t0) REVERT: A 204 TYR cc_start: 0.8890 (m-10) cc_final: 0.8586 (m-80) REVERT: B 63 MET cc_start: 0.8624 (mpp) cc_final: 0.8359 (mpp) REVERT: B 134 PHE cc_start: 0.8267 (m-80) cc_final: 0.7921 (m-80) REVERT: B 187 GLU cc_start: 0.9584 (tt0) cc_final: 0.9147 (pt0) REVERT: B 189 MET cc_start: 0.9650 (mmp) cc_final: 0.9439 (mmm) REVERT: C 48 LEU cc_start: 0.9652 (tp) cc_final: 0.9420 (tt) REVERT: C 104 PHE cc_start: 0.9508 (t80) cc_final: 0.9283 (t80) REVERT: C 109 ILE cc_start: 0.9664 (pt) cc_final: 0.9458 (pt) REVERT: C 126 GLU cc_start: 0.9464 (tp30) cc_final: 0.9042 (tp30) REVERT: C 134 GLU cc_start: 0.9515 (tm-30) cc_final: 0.8997 (tm-30) REVERT: C 176 ILE cc_start: 0.9524 (pt) cc_final: 0.9094 (pt) REVERT: C 186 ASP cc_start: 0.9714 (m-30) cc_final: 0.9462 (m-30) REVERT: C 189 ARG cc_start: 0.9628 (mtp-110) cc_final: 0.9402 (ttp80) REVERT: D 93 MET cc_start: 0.9772 (mmp) cc_final: 0.9218 (mmm) REVERT: D 220 ASP cc_start: 0.9469 (m-30) cc_final: 0.8761 (m-30) REVERT: D 228 VAL cc_start: 0.9293 (m) cc_final: 0.9086 (t) REVERT: D 277 MET cc_start: 0.9334 (mtt) cc_final: 0.8724 (mmt) REVERT: E 44 MET cc_start: 0.9495 (ptm) cc_final: 0.9172 (ptt) REVERT: E 366 MET cc_start: 0.9491 (mtt) cc_final: 0.9128 (mtt) REVERT: E 380 MET cc_start: 0.8773 (mmp) cc_final: 0.8045 (mmp) REVERT: E 407 ASP cc_start: 0.9122 (m-30) cc_final: 0.8126 (t0) REVERT: E 485 ASP cc_start: 0.9251 (m-30) cc_final: 0.8909 (t0) REVERT: E 537 ASP cc_start: 0.9247 (m-30) cc_final: 0.8658 (p0) REVERT: E 538 LEU cc_start: 0.9001 (mt) cc_final: 0.8760 (mt) outliers start: 2 outliers final: 2 residues processed: 373 average time/residue: 0.2184 time to fit residues: 137.5015 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 : 1.551 ------------------------------------------------------------------------------- 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: 8.9990 chunk 235 optimal weight: 0.6980 chunk 359 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 490 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 440 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 chunk 445 optimal weight: 8.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 344 ASN 5 424 GLN ** 5 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS 6 750 GLN ** 7 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3253 r_free = 0.3253 target = 0.056061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.047353 restraints weight = 402068.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048601 restraints weight = 240935.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.049454 restraints weight = 163042.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.050065 restraints weight = 121029.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050497 restraints weight = 95855.027| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.5309 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= 0.187 Angle : 0.856 20.330 56112 Z= 0.442 Chirality : 0.048 0.396 6492 Planarity : 0.005 0.061 7133 Dihedral : 9.775 178.012 5773 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.86 % Allowed : 10.17 % Favored : 88.97 % Rotamer: Outliers : 0.07 % Allowed : 1.42 % Favored : 98.51 % 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 aren not related in a simple way. whole: -2.06 (0.12), residues: 4995 helix: -0.55 (0.11), residues: 1982 sheet: -2.36 (0.19), residues: 571 loop : -1.77 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG 4 909 TYR 0.033 0.002 TYR 6 772 PHE 0.015 0.002 PHE B 184 TRP 0.016 0.002 TRP 6 939 HIS 0.009 0.001 HIS 5 576 Details of bonding type rmsd covalent geometry : bond 0.00386 (41467) covalent geometry : angle 0.85562 (56108) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.79726 ( 4) hydrogen bonds : bond 0.04055 ( 1354) hydrogen bonds : angle 5.86868 ( 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 376 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 373 time to evaluate : 1.720 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: 2 612 MET cc_start: 0.8468 (mtm) cc_final: 0.7445 (mtp) REVERT: 2 677 PHE cc_start: 0.9567 (m-80) cc_final: 0.8902 (m-80) REVERT: 2 681 CYS cc_start: 0.9430 (m) cc_final: 0.9179 (m) REVERT: 3 136 MET cc_start: 0.9075 (tpp) cc_final: 0.8123 (tpp) REVERT: 3 179 LEU cc_start: 0.9742 (tp) cc_final: 0.9462 (tp) REVERT: 3 367 LEU cc_start: 0.8989 (mt) cc_final: 0.8706 (mt) REVERT: 3 384 MET cc_start: 0.9381 (tmm) cc_final: 0.8885 (tmm) REVERT: 3 545 LEU cc_start: 0.9312 (mt) cc_final: 0.9019 (mp) REVERT: 4 272 MET cc_start: 0.9265 (mmp) cc_final: 0.8797 (tpp) REVERT: 4 314 MET cc_start: 0.7517 (ttm) cc_final: 0.7213 (ttm) REVERT: 4 382 MET cc_start: 0.8761 (ttm) cc_final: 0.8445 (ttm) REVERT: 4 554 LYS cc_start: 0.8162 (mttt) cc_final: 0.7910 (tttt) REVERT: 4 649 MET cc_start: 0.9333 (ttt) cc_final: 0.8930 (ttt) REVERT: 4 651 GLN cc_start: 0.8304 (mt0) cc_final: 0.8062 (mp10) REVERT: 4 801 MET cc_start: 0.9431 (ttm) cc_final: 0.9004 (mtp) REVERT: 4 890 ILE cc_start: 0.9236 (mt) cc_final: 0.8882 (mt) REVERT: 4 903 ILE cc_start: 0.8696 (mt) cc_final: 0.8485 (mt) REVERT: 5 41 ASP cc_start: 0.9363 (m-30) cc_final: 0.8943 (t0) REVERT: 5 67 HIS cc_start: 0.9660 (m-70) cc_final: 0.9386 (m-70) REVERT: 5 252 ASP cc_start: 0.8012 (t0) cc_final: 0.7511 (t0) REVERT: 5 393 MET cc_start: 0.8369 (mtp) cc_final: 0.8007 (mtp) REVERT: 5 404 MET cc_start: 0.7221 (ptp) cc_final: 0.6717 (ppp) REVERT: 5 410 ILE cc_start: 0.8739 (pt) cc_final: 0.8445 (pt) REVERT: 5 552 MET cc_start: 0.9544 (mmp) cc_final: 0.9269 (mmm) REVERT: 5 599 MET cc_start: 0.9057 (ttm) cc_final: 0.8592 (mtt) REVERT: 6 384 ASP cc_start: 0.9659 (t0) cc_final: 0.8965 (p0) REVERT: 6 519 MET cc_start: 0.9449 (mtt) cc_final: 0.8787 (mtp) REVERT: 6 551 MET cc_start: 0.9413 (mtp) cc_final: 0.9006 (mmm) REVERT: 6 621 TYR cc_start: 0.8593 (p90) cc_final: 0.7972 (p90) REVERT: 6 661 ILE cc_start: 0.9096 (mt) cc_final: 0.8772 (tt) REVERT: 6 679 LEU cc_start: 0.9702 (tp) cc_final: 0.9488 (tp) REVERT: 6 709 PHE cc_start: 0.8933 (m-80) cc_final: 0.8581 (m-80) REVERT: 6 719 CYS cc_start: 0.9579 (p) cc_final: 0.9222 (t) REVERT: 6 726 GLU cc_start: 0.9511 (tp30) cc_final: 0.9070 (tp30) REVERT: 6 730 HIS cc_start: 0.8836 (t-90) cc_final: 0.8524 (t-90) REVERT: 6 735 HIS cc_start: 0.8290 (m90) cc_final: 0.8089 (m90) REVERT: 6 803 MET cc_start: 0.9390 (mmp) cc_final: 0.8961 (mmm) REVERT: 6 913 MET cc_start: 0.8899 (mmt) cc_final: 0.8687 (tmm) REVERT: 7 66 MET cc_start: 0.8676 (mmp) cc_final: 0.8219 (ptt) REVERT: 7 457 CYS cc_start: 0.8547 (t) cc_final: 0.7855 (t) REVERT: 7 459 MET cc_start: 0.9348 (mmp) cc_final: 0.9086 (mmm) REVERT: 7 707 MET cc_start: 0.8015 (mmp) cc_final: 0.7716 (pmm) REVERT: A 38 ARG cc_start: 0.9416 (mmp80) cc_final: 0.9109 (mmm160) REVERT: A 110 MET cc_start: 0.3364 (mmm) cc_final: 0.3056 (mmm) REVERT: A 164 ASP cc_start: 0.9296 (m-30) cc_final: 0.8918 (t0) REVERT: B 63 MET cc_start: 0.8630 (mpp) cc_final: 0.8408 (mpp) REVERT: B 134 PHE cc_start: 0.8181 (m-80) cc_final: 0.7818 (m-80) REVERT: B 187 GLU cc_start: 0.9526 (tt0) cc_final: 0.9247 (pt0) REVERT: C 3 TYR cc_start: 0.8003 (t80) cc_final: 0.7671 (t80) REVERT: C 48 LEU cc_start: 0.9648 (tp) cc_final: 0.9416 (tt) REVERT: C 104 PHE cc_start: 0.9534 (t80) cc_final: 0.9281 (t80) REVERT: C 109 ILE cc_start: 0.9659 (pt) cc_final: 0.9443 (pt) REVERT: C 126 GLU cc_start: 0.9461 (tp30) cc_final: 0.9049 (tp30) REVERT: C 134 GLU cc_start: 0.9513 (tm-30) cc_final: 0.9145 (tm-30) REVERT: C 165 PHE cc_start: 0.9325 (t80) cc_final: 0.8628 (t80) REVERT: C 172 MET cc_start: 0.9516 (tmm) cc_final: 0.9085 (tmm) REVERT: C 176 ILE cc_start: 0.9664 (pt) cc_final: 0.9277 (pt) REVERT: C 186 ASP cc_start: 0.9721 (m-30) cc_final: 0.9435 (m-30) REVERT: C 189 ARG cc_start: 0.9654 (mtp-110) cc_final: 0.9427 (ttp80) REVERT: D 93 MET cc_start: 0.9778 (mmp) cc_final: 0.9241 (mmm) REVERT: D 228 VAL cc_start: 0.9247 (m) cc_final: 0.9045 (t) REVERT: D 277 MET cc_start: 0.9335 (mtt) cc_final: 0.8698 (mmt) REVERT: E 44 MET cc_start: 0.9473 (ptm) cc_final: 0.9123 (ptt) REVERT: E 366 MET cc_start: 0.9538 (mtt) cc_final: 0.9115 (mtt) REVERT: E 380 MET cc_start: 0.8782 (mmp) cc_final: 0.8057 (mmp) REVERT: E 407 ASP cc_start: 0.9127 (m-30) cc_final: 0.8153 (t0) REVERT: E 537 ASP cc_start: 0.9274 (m-30) cc_final: 0.8659 (p0) REVERT: E 538 LEU cc_start: 0.8987 (mt) cc_final: 0.8740 (mt) outliers start: 3 outliers final: 2 residues processed: 376 average time/residue: 0.2122 time to fit residues: 135.2830 Evaluate side-chains 295 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 293 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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: 0.5980 chunk 439 optimal weight: 0.5980 chunk 318 optimal weight: 5.9990 chunk 57 optimal weight: 0.0670 chunk 180 optimal weight: 20.0000 chunk 90 optimal weight: 0.0070 chunk 113 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 443 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 49 GLN ** 5 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 359 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** ** 6 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 669 HIS 6 750 GLN 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.058364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.049533 restraints weight = 389771.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050831 restraints weight = 232441.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.051711 restraints weight = 156638.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.052340 restraints weight = 115532.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.052788 restraints weight = 90942.285| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5567 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= 0.154 Angle : 0.856 20.815 56112 Z= 0.436 Chirality : 0.048 0.410 6492 Planarity : 0.004 0.059 7133 Dihedral : 9.654 178.639 5773 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.94 % Allowed : 9.15 % Favored : 89.91 % Rotamer: Outliers : 0.07 % Allowed : 0.80 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 3.85 % 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 aren not related in a simple way. whole: -1.86 (0.12), residues: 4995 helix: -0.40 (0.11), residues: 1971 sheet: -2.06 (0.20), residues: 579 loop : -1.68 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 435 TYR 0.027 0.001 TYR 6 772 PHE 0.016 0.001 PHE 3 543 TRP 0.035 0.002 TRP 3 111 HIS 0.007 0.001 HIS 2 531 Details of bonding type rmsd covalent geometry : bond 0.00317 (41467) covalent geometry : angle 0.85582 (56108) SS BOND : bond 0.00267 ( 2) SS BOND : angle 0.81026 ( 4) hydrogen bonds : bond 0.03736 ( 1354) hydrogen bonds : angle 5.64716 ( 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 399 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 396 time to evaluate : 1.630 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: 2 612 MET cc_start: 0.8460 (mtm) cc_final: 0.7618 (mtp) REVERT: 2 677 PHE cc_start: 0.9489 (m-80) cc_final: 0.8678 (m-80) REVERT: 3 367 LEU cc_start: 0.9031 (mt) cc_final: 0.8735 (mt) REVERT: 3 384 MET cc_start: 0.9243 (tmm) cc_final: 0.8814 (tmm) REVERT: 3 545 LEU cc_start: 0.9312 (mt) cc_final: 0.9039 (mp) REVERT: 3 551 ASP cc_start: 0.7791 (t70) cc_final: 0.6330 (m-30) REVERT: 4 272 MET cc_start: 0.9201 (mmp) cc_final: 0.8786 (tpp) REVERT: 4 314 MET cc_start: 0.7580 (ttm) cc_final: 0.7226 (ttm) REVERT: 4 382 MET cc_start: 0.8529 (ttm) cc_final: 0.7687 (ttm) REVERT: 4 554 LYS cc_start: 0.8064 (mttt) cc_final: 0.7803 (tttt) REVERT: 4 649 MET cc_start: 0.9278 (ttt) cc_final: 0.8931 (ttt) REVERT: 4 651 GLN cc_start: 0.8441 (mt0) cc_final: 0.8208 (mp10) REVERT: 4 801 MET cc_start: 0.9358 (ttm) cc_final: 0.8927 (mtp) REVERT: 4 903 ILE cc_start: 0.8555 (mt) cc_final: 0.8318 (mt) REVERT: 5 41 ASP cc_start: 0.9349 (m-30) cc_final: 0.8764 (t0) REVERT: 5 49 GLN cc_start: 0.9104 (tp-100) cc_final: 0.8776 (tp-100) REVERT: 5 67 HIS cc_start: 0.9644 (m-70) cc_final: 0.9355 (m-70) REVERT: 5 252 ASP cc_start: 0.8126 (t0) cc_final: 0.7475 (t0) REVERT: 5 362 ARG cc_start: 0.9188 (mtt180) cc_final: 0.8855 (ptp-110) REVERT: 5 393 MET cc_start: 0.8347 (mtp) cc_final: 0.8002 (mtp) REVERT: 5 404 MET cc_start: 0.6864 (ptp) cc_final: 0.6550 (ppp) REVERT: 5 410 ILE cc_start: 0.8690 (pt) cc_final: 0.8396 (pt) REVERT: 5 552 MET cc_start: 0.9519 (mmp) cc_final: 0.9220 (mmm) REVERT: 5 599 MET cc_start: 0.9056 (ttm) cc_final: 0.8676 (mtt) REVERT: 6 384 ASP cc_start: 0.9607 (t0) cc_final: 0.8938 (p0) REVERT: 6 519 MET cc_start: 0.9507 (mtt) cc_final: 0.8889 (mtp) REVERT: 6 621 TYR cc_start: 0.8483 (p90) cc_final: 0.7885 (p90) REVERT: 6 629 MET cc_start: 0.6866 (ttp) cc_final: 0.6389 (tpp) REVERT: 6 709 PHE cc_start: 0.8776 (m-80) cc_final: 0.8524 (m-80) REVERT: 6 719 CYS cc_start: 0.9424 (p) cc_final: 0.9156 (t) REVERT: 6 726 GLU cc_start: 0.9445 (tp30) cc_final: 0.9024 (tp30) REVERT: 6 730 HIS cc_start: 0.8734 (t-90) cc_final: 0.8475 (t-90) REVERT: 6 803 MET cc_start: 0.9280 (mmp) cc_final: 0.8818 (mmm) REVERT: 7 29 LYS cc_start: 0.6725 (tptt) cc_final: 0.6426 (tppt) REVERT: 7 66 MET cc_start: 0.8880 (mmp) cc_final: 0.8226 (ptt) REVERT: 7 457 CYS cc_start: 0.8576 (t) cc_final: 0.7798 (t) REVERT: 7 707 MET cc_start: 0.7786 (mmp) cc_final: 0.7573 (pmm) REVERT: A 38 ARG cc_start: 0.9346 (mmp80) cc_final: 0.9124 (mmm160) REVERT: A 79 MET cc_start: 0.9500 (mmm) cc_final: 0.9039 (mmm) REVERT: A 110 MET cc_start: 0.2624 (mmm) cc_final: 0.2343 (mmm) REVERT: A 164 ASP cc_start: 0.9317 (m-30) cc_final: 0.8855 (t0) REVERT: A 204 TYR cc_start: 0.9085 (m-80) cc_final: 0.8787 (m-80) REVERT: B 20 VAL cc_start: 0.9822 (m) cc_final: 0.9599 (p) REVERT: B 134 PHE cc_start: 0.8094 (m-80) cc_final: 0.7720 (m-80) REVERT: C 8 ASP cc_start: 0.9154 (m-30) cc_final: 0.8950 (m-30) REVERT: C 104 PHE cc_start: 0.9457 (t80) cc_final: 0.9165 (t80) REVERT: C 109 ILE cc_start: 0.9627 (pt) cc_final: 0.9368 (pt) REVERT: C 126 GLU cc_start: 0.9410 (tp30) cc_final: 0.9026 (tp30) REVERT: C 134 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9146 (tm-30) REVERT: C 165 PHE cc_start: 0.9209 (t80) cc_final: 0.8902 (t80) REVERT: C 186 ASP cc_start: 0.9694 (m-30) cc_final: 0.9405 (m-30) REVERT: D 64 MET cc_start: 0.9755 (tpp) cc_final: 0.9112 (tpp) REVERT: D 68 LYS cc_start: 0.9699 (ptpp) cc_final: 0.9455 (ptpp) REVERT: D 93 MET cc_start: 0.9721 (mmp) cc_final: 0.9152 (mmm) REVERT: D 228 VAL cc_start: 0.9055 (m) cc_final: 0.8822 (t) REVERT: D 277 MET cc_start: 0.9203 (mtt) cc_final: 0.8641 (mmt) REVERT: E 44 MET cc_start: 0.9460 (ptm) cc_final: 0.9208 (ptt) REVERT: E 45 LEU cc_start: 0.9855 (mt) cc_final: 0.9651 (pp) REVERT: E 366 MET cc_start: 0.9486 (mtt) cc_final: 0.9068 (mtt) REVERT: E 380 MET cc_start: 0.8872 (mmp) cc_final: 0.8071 (mmp) REVERT: E 407 ASP cc_start: 0.8887 (m-30) cc_final: 0.8012 (t0) REVERT: E 537 ASP cc_start: 0.9219 (m-30) cc_final: 0.8591 (p0) REVERT: E 538 LEU cc_start: 0.8910 (mt) cc_final: 0.8685 (mt) outliers start: 3 outliers final: 2 residues processed: 399 average time/residue: 0.2177 time to fit residues: 146.3633 Evaluate side-chains 308 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 306 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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: 10.0000 chunk 280 optimal weight: 5.9990 chunk 502 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 431 optimal weight: 7.9990 chunk 441 optimal weight: 0.8980 chunk 227 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 5 359 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** 6 156 GLN 6 669 HIS 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** ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.056735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.047874 restraints weight = 396258.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049142 restraints weight = 239047.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.049997 restraints weight = 162386.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.050609 restraints weight = 120791.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.051049 restraints weight = 95666.051| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41469 Z= 0.183 Angle : 0.859 20.865 56112 Z= 0.442 Chirality : 0.047 0.422 6492 Planarity : 0.005 0.112 7133 Dihedral : 9.635 176.486 5773 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.89 % Favored : 89.15 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.49 % 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 aren not related in a simple way. whole: -1.83 (0.12), residues: 4995 helix: -0.31 (0.11), residues: 1980 sheet: -2.11 (0.20), residues: 562 loop : -1.73 (0.13), residues: 2453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 4 897 TYR 0.030 0.002 TYR 6 772 PHE 0.019 0.002 PHE 7 355 TRP 0.073 0.002 TRP D 190 HIS 0.006 0.001 HIS 2 531 Details of bonding type rmsd covalent geometry : bond 0.00376 (41467) covalent geometry : angle 0.85872 (56108) SS BOND : bond 0.00093 ( 2) SS BOND : angle 0.72251 ( 4) hydrogen bonds : bond 0.03832 ( 1354) hydrogen bonds : angle 5.68783 ( 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 : 1.508 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: 2 612 MET cc_start: 0.8800 (mtm) cc_final: 0.8407 (mtp) REVERT: 2 677 PHE cc_start: 0.9455 (m-80) cc_final: 0.8653 (m-80) REVERT: 3 367 LEU cc_start: 0.9038 (mt) cc_final: 0.8751 (mt) REVERT: 3 384 MET cc_start: 0.9326 (tmm) cc_final: 0.8917 (tmm) REVERT: 3 462 MET cc_start: 0.9461 (mmp) cc_final: 0.9256 (mmm) REVERT: 3 545 LEU cc_start: 0.9333 (mt) cc_final: 0.9074 (mp) REVERT: 4 272 MET cc_start: 0.9190 (mmp) cc_final: 0.8744 (tpp) REVERT: 4 314 MET cc_start: 0.7647 (ttm) cc_final: 0.7314 (ttm) REVERT: 4 382 MET cc_start: 0.8607 (ttm) cc_final: 0.8267 (ttm) REVERT: 4 554 LYS cc_start: 0.8109 (mttt) cc_final: 0.7906 (tttt) REVERT: 4 649 MET cc_start: 0.9289 (ttt) cc_final: 0.8791 (ttt) REVERT: 4 801 MET cc_start: 0.9401 (ttm) cc_final: 0.8973 (mtp) REVERT: 5 41 ASP cc_start: 0.9345 (m-30) cc_final: 0.8866 (t0) REVERT: 5 67 HIS cc_start: 0.9647 (m-70) cc_final: 0.9358 (m-70) REVERT: 5 252 ASP cc_start: 0.7993 (t0) cc_final: 0.7439 (t0) REVERT: 5 282 LEU cc_start: 0.9457 (mt) cc_final: 0.9248 (mt) REVERT: 5 362 ARG cc_start: 0.9202 (mtt180) cc_final: 0.8849 (ptp-110) REVERT: 5 393 MET cc_start: 0.8382 (mtp) cc_final: 0.8050 (mtp) REVERT: 5 404 MET cc_start: 0.7068 (ptp) cc_final: 0.6767 (ppp) REVERT: 5 410 ILE cc_start: 0.8741 (pt) cc_final: 0.8421 (pt) REVERT: 5 430 GLU cc_start: 0.8993 (pm20) cc_final: 0.8784 (pm20) REVERT: 5 552 MET cc_start: 0.9555 (mmp) cc_final: 0.9241 (mmm) REVERT: 5 599 MET cc_start: 0.9098 (ttm) cc_final: 0.8646 (mtt) REVERT: 6 384 ASP cc_start: 0.9617 (t0) cc_final: 0.8973 (p0) REVERT: 6 519 MET cc_start: 0.9521 (mtt) cc_final: 0.9100 (mmm) REVERT: 6 550 GLN cc_start: 0.9032 (mt0) cc_final: 0.8806 (mm-40) REVERT: 6 621 TYR cc_start: 0.8483 (p90) cc_final: 0.7876 (p90) REVERT: 6 709 PHE cc_start: 0.8877 (m-80) cc_final: 0.8630 (m-80) REVERT: 6 719 CYS cc_start: 0.9500 (p) cc_final: 0.9208 (t) REVERT: 6 726 GLU cc_start: 0.9393 (tp30) cc_final: 0.9008 (tp30) REVERT: 6 730 HIS cc_start: 0.8828 (t-90) cc_final: 0.8507 (t-90) REVERT: 6 735 HIS cc_start: 0.8215 (m90) cc_final: 0.8012 (m90) REVERT: 6 803 MET cc_start: 0.9315 (mmp) cc_final: 0.8872 (mmm) REVERT: 7 29 LYS cc_start: 0.6740 (tptt) cc_final: 0.6438 (tppt) REVERT: 7 66 MET cc_start: 0.8900 (mmp) cc_final: 0.8222 (ptt) REVERT: 7 300 MET cc_start: 0.8890 (mmm) cc_final: 0.8584 (tmm) REVERT: 7 457 CYS cc_start: 0.8684 (t) cc_final: 0.7468 (t) REVERT: 7 458 LEU cc_start: 0.9473 (mt) cc_final: 0.9249 (mt) REVERT: 7 707 MET cc_start: 0.7895 (mmp) cc_final: 0.7651 (pmm) REVERT: A 38 ARG cc_start: 0.9391 (mmp80) cc_final: 0.9048 (mmm160) REVERT: A 79 MET cc_start: 0.9511 (mmm) cc_final: 0.9116 (mmm) REVERT: A 164 ASP cc_start: 0.9338 (m-30) cc_final: 0.8914 (t0) REVERT: A 204 TYR cc_start: 0.9085 (m-80) cc_final: 0.8804 (m-80) REVERT: B 20 VAL cc_start: 0.9837 (m) cc_final: 0.9635 (p) REVERT: B 63 MET cc_start: 0.8737 (mpp) cc_final: 0.8516 (mpp) REVERT: B 134 PHE cc_start: 0.8151 (m-80) cc_final: 0.7772 (m-80) REVERT: C 3 TYR cc_start: 0.7592 (t80) cc_final: 0.6850 (t80) REVERT: C 8 ASP cc_start: 0.9129 (m-30) cc_final: 0.8644 (m-30) REVERT: C 48 LEU cc_start: 0.9676 (tp) cc_final: 0.9393 (tt) REVERT: C 88 ILE cc_start: 0.9503 (tp) cc_final: 0.9109 (tp) REVERT: C 95 LEU cc_start: 0.9444 (tt) cc_final: 0.9075 (pp) REVERT: C 104 PHE cc_start: 0.9529 (t80) cc_final: 0.8963 (t80) REVERT: C 109 ILE cc_start: 0.9646 (pt) cc_final: 0.9399 (pt) REVERT: C 134 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9141 (tm-30) REVERT: C 165 PHE cc_start: 0.9298 (t80) cc_final: 0.8783 (t80) REVERT: C 176 ILE cc_start: 0.9658 (pt) cc_final: 0.9322 (pt) REVERT: D 93 MET cc_start: 0.9707 (mmp) cc_final: 0.9129 (mmm) REVERT: D 228 VAL cc_start: 0.9104 (m) cc_final: 0.8884 (t) REVERT: D 277 MET cc_start: 0.9254 (mtt) cc_final: 0.8668 (mmt) REVERT: E 44 MET cc_start: 0.9418 (ptm) cc_final: 0.9034 (ptt) REVERT: E 366 MET cc_start: 0.9464 (mtt) cc_final: 0.9042 (mtt) REVERT: E 380 MET cc_start: 0.8792 (mmp) cc_final: 0.7843 (mmp) REVERT: E 407 ASP cc_start: 0.8947 (m-30) cc_final: 0.8083 (t0) REVERT: E 537 ASP cc_start: 0.9218 (m-30) cc_final: 0.8579 (p0) REVERT: E 538 LEU cc_start: 0.8925 (mt) cc_final: 0.8660 (mt) outliers start: 3 outliers final: 2 residues processed: 379 average time/residue: 0.2103 time to fit residues: 135.4885 Evaluate side-chains 293 residues out of total 4555 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 1.404 ------------------------------------------------------------------------------- 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: 0.8980 chunk 224 optimal weight: 30.0000 chunk 475 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 492 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 351 optimal weight: 40.0000 chunk 297 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 856 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** ** 5 359 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** 6 669 HIS 6 750 GLN 7 320 GLN ** 7 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 538 HIS ** 7 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN ** B 17 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** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.046628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.035520 restraints weight = 375138.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.036691 restraints weight = 254213.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037551 restraints weight = 189802.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.038213 restraints weight = 151546.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.038733 restraints weight = 126822.030| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5844 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= 0.166 Angle : 0.849 20.871 56112 Z= 0.436 Chirality : 0.047 0.404 6492 Planarity : 0.004 0.059 7133 Dihedral : 9.613 177.791 5773 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 23.63 Ramachandran Plot: Outliers : 0.96 % Allowed : 9.55 % Favored : 89.49 % Rotamer: Outliers : 0.07 % Allowed : 0.38 % Favored : 99.56 % 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 aren not related in a simple way. whole: -1.80 (0.12), residues: 4995 helix: -0.29 (0.11), residues: 1984 sheet: -1.99 (0.20), residues: 552 loop : -1.73 (0.13), residues: 2459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 909 TYR 0.027 0.001 TYR 6 772 PHE 0.017 0.001 PHE 2 609 TRP 0.041 0.002 TRP D 190 HIS 0.006 0.001 HIS 2 531 Details of bonding type rmsd covalent geometry : bond 0.00343 (41467) covalent geometry : angle 0.84893 (56108) SS BOND : bond 0.00162 ( 2) SS BOND : angle 0.72141 ( 4) hydrogen bonds : bond 0.03677 ( 1354) hydrogen bonds : angle 5.59760 ( 3861) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5597.01 seconds wall clock time: 98 minutes 52.91 seconds (5932.91 seconds total)