Starting phenix.real_space_refine on Wed Nov 20 14:07:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5t_27919/11_2024/8e5t_27919_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5t_27919/11_2024/8e5t_27919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5t_27919/11_2024/8e5t_27919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5t_27919/11_2024/8e5t_27919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5t_27919/11_2024/8e5t_27919_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e5t_27919/11_2024/8e5t_27919_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 1.055 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 968 5.49 5 Mg 33 5.21 5 S 46 5.16 5 C 30824 2.51 5 N 10116 2.21 5 O 13137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 55125 Number of models: 1 Model: "" Number of chains: 32 Chain: "5" Number of atoms: 4332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4332 Classifications: {'peptide': 530} Link IDs: {'PTRANS': 19, 'TRANS': 510} Chain breaks: 3 Chain: "6" Number of atoms: 4156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4156 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 20, 'TRANS': 493} Chain breaks: 1 Chain: "C" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2166 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 268} Chain breaks: 1 Chain: "D" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1086 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "E" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1136 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 135} Chain breaks: 1 Chain: "F" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1941 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 11, 'TRANS': 230} Chain: "G" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 926 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 177} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 552 Unresolved non-hydrogen angles: 698 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 259 Chain: "K" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1263 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 234} Link IDs: {'PTRANS': 10, 'TRANS': 243} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 819 Unresolved non-hydrogen angles: 1040 Unresolved non-hydrogen dihedrals: 674 Unresolved non-hydrogen chiralities: 85 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 8, 'ASN:plan1': 15, 'TRP:plan': 2, 'ASP:plan': 15, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 389 Chain: "L" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 376 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 143 Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 733 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 552 Unresolved non-hydrogen angles: 698 Unresolved non-hydrogen dihedrals: 472 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 4, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 26} Unresolved non-hydrogen planarities: 350 Chain: "Q" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1015 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "S" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1394 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 6, 'TRANS': 159} Chain: "b" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1075 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 200} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 745 Unresolved non-hydrogen angles: 950 Unresolved non-hydrogen dihedrals: 629 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 8, 'TYR:plan': 8, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 11, 'GLU:plan': 13, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 411 Chain: "e" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 598 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "f" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 706 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 83} Chain breaks: 2 Chain: "i" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 376 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 126 Chain: "m" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 310 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 1, 'TRANS': 60} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 129 Chain: "n" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 1728 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 316} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 327} Chain breaks: 2 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1197 Unresolved non-hydrogen angles: 1529 Unresolved non-hydrogen dihedrals: 1020 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 18, 'ASN:plan1': 14, 'TRP:plan': 4, 'ASP:plan': 21, 'PHE:plan': 21, 'GLU:plan': 18, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 644 Chain: "o" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 656 Classifications: {'peptide': 133} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 128} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 474 Unresolved non-hydrogen angles: 589 Unresolved non-hydrogen dihedrals: 412 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 6, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 249 Chain: "p" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 2158 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 381} Link IDs: {'PTRANS': 21, 'TRANS': 415} Chain breaks: 1 Unresolved chain link angles: 21 Unresolved non-hydrogen bonds: 1396 Unresolved non-hydrogen angles: 1769 Unresolved non-hydrogen dihedrals: 1155 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'GLN:plan1': 20, 'ASP:plan': 20, 'TYR:plan': 14, 'ASN:plan1': 18, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 24, 'GLU:plan': 26, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 704 Chain: "s" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 682 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 129} Link IDs: {'PTRANS': 14, 'TRANS': 122} Chain breaks: 1 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 658 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 9, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 24, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 306 Chain: "t" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1168 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 209} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 723 Unresolved non-hydrogen angles: 911 Unresolved non-hydrogen dihedrals: 580 Unresolved non-hydrogen chiralities: 82 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 13, 'ASP:plan': 8, 'PHE:plan': 11, 'GLU:plan': 17, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 342 Chain: "z" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2058 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Chain: "O" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1440 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "1" Number of atoms: 15943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 15943 Classifications: {'RNA': 743} Modifications used: {'rna2p_pur': 65, 'rna2p_pyr': 34, 'rna3p_pur': 363, 'rna3p_pyr': 281} Link IDs: {'rna2p': 99, 'rna3p': 643} Chain breaks: 12 Chain: "2" Number of atoms: 2939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2939 Classifications: {'RNA': 138} Modifications used: {'rna2p_pur': 18, 'rna2p_pyr': 14, 'rna3p_pur': 54, 'rna3p_pyr': 52} Link IDs: {'rna2p': 31, 'rna3p': 106} Chain breaks: 2 Chain: "3" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1838 Classifications: {'RNA': 87} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 19, 'rna3p_pur': 32, 'rna3p_pyr': 28} Link IDs: {'rna2p': 26, 'rna3p': 60} Chain breaks: 1 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Unusual residues: {' MG': 30} Classifications: {'undetermined': 30} Link IDs: {None: 29} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10770 SG CYS D 15 58.164 184.072 98.531 1.00 99.81 S ATOM 10872 SG CYS D 28 55.718 185.060 96.092 1.00 98.20 S ATOM 10952 SG CYS D 38 57.563 187.342 97.153 1.00101.97 S ATOM 10991 SG CYS D 43 55.149 186.242 98.978 1.00 92.14 S Time building chain proxies: 28.17, per 1000 atoms: 0.51 Number of scatterers: 55125 At special positions: 0 Unit cell: (172.9, 306.8, 240.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 46 16.00 P 968 15.00 Mg 33 11.99 O 13137 8.00 N 10116 7.00 C 30824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 12.76 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 28 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 38 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 15 " Number of angles added : 6 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9874 Finding SS restraints... Secondary structure from input PDB file: 228 helices and 36 sheets defined 57.1% alpha, 10.1% beta 295 base pairs and 487 stacking pairs defined. Time for finding SS restraints: 21.51 Creating SS restraints... Processing helix chain '5' and resid 225 through 229 Processing helix chain '5' and resid 238 through 254 Processing helix chain '5' and resid 256 through 267 removed outlier: 3.929A pdb=" N ASP 5 267 " --> pdb=" O GLU 5 263 " (cutoff:3.500A) Processing helix chain '5' and resid 267 through 281 Processing helix chain '5' and resid 282 through 297 removed outlier: 3.749A pdb=" N SER 5 297 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) Processing helix chain '5' and resid 301 through 313 Processing helix chain '5' and resid 316 through 332 Processing helix chain '5' and resid 343 through 347 Processing helix chain '5' and resid 355 through 384 removed outlier: 3.552A pdb=" N HIS 5 384 " --> pdb=" O GLU 5 380 " (cutoff:3.500A) Processing helix chain '5' and resid 387 through 405 Processing helix chain '5' and resid 408 through 419 Processing helix chain '5' and resid 420 through 422 No H-bonds generated for 'chain '5' and resid 420 through 422' Processing helix chain '5' and resid 424 through 442 Processing helix chain '5' and resid 445 through 458 removed outlier: 3.544A pdb=" N ILE 5 456 " --> pdb=" O ALA 5 452 " (cutoff:3.500A) Processing helix chain '5' and resid 463 through 476 Processing helix chain '5' and resid 483 through 503 Processing helix chain '5' and resid 551 through 568 Processing helix chain '5' and resid 574 through 590 removed outlier: 4.228A pdb=" N TYR 5 578 " --> pdb=" O PRO 5 574 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HIS 5 581 " --> pdb=" O VAL 5 577 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU 5 583 " --> pdb=" O GLU 5 579 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N THR 5 584 " --> pdb=" O VAL 5 580 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N HIS 5 590 " --> pdb=" O PHE 5 586 " (cutoff:3.500A) Processing helix chain '5' and resid 593 through 612 removed outlier: 3.689A pdb=" N GLN 5 599 " --> pdb=" O ASN 5 595 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 626 Processing helix chain '5' and resid 627 through 635 removed outlier: 6.008A pdb=" N ARG 5 630 " --> pdb=" O PHE 5 627 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N SER 5 635 " --> pdb=" O VAL 5 632 " (cutoff:3.500A) Processing helix chain '5' and resid 636 through 651 Processing helix chain '5' and resid 654 through 670 Processing helix chain '5' and resid 674 through 692 Processing helix chain '5' and resid 693 through 700 Processing helix chain '5' and resid 745 through 751 removed outlier: 3.711A pdb=" N PHE 5 749 " --> pdb=" O GLU 5 745 " (cutoff:3.500A) Processing helix chain '5' and resid 754 through 767 Processing helix chain '5' and resid 781 through 790 Processing helix chain '5' and resid 847 through 849 No H-bonds generated for 'chain '5' and resid 847 through 849' Processing helix chain '5' and resid 850 through 861 Processing helix chain '6' and resid 179 through 191 Processing helix chain '6' and resid 195 through 212 Processing helix chain '6' and resid 227 through 250 Proline residue: 6 243 - end of helix Processing helix chain '6' and resid 264 through 276 Processing helix chain '6' and resid 277 through 287 Processing helix chain '6' and resid 290 through 303 Processing helix chain '6' and resid 304 through 309 Processing helix chain '6' and resid 314 through 329 Processing helix chain '6' and resid 331 through 350 removed outlier: 3.658A pdb=" N GLU 6 348 " --> pdb=" O ASN 6 344 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE 6 349 " --> pdb=" O THR 6 345 " (cutoff:3.500A) Processing helix chain '6' and resid 353 through 367 removed outlier: 3.590A pdb=" N LEU 6 358 " --> pdb=" O LEU 6 354 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS 6 359 " --> pdb=" O GLU 6 355 " (cutoff:3.500A) Processing helix chain '6' and resid 376 through 394 removed outlier: 3.996A pdb=" N GLU 6 389 " --> pdb=" O ASN 6 385 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU 6 390 " --> pdb=" O SER 6 386 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP 6 394 " --> pdb=" O LEU 6 390 " (cutoff:3.500A) Processing helix chain '6' and resid 394 through 422 removed outlier: 3.547A pdb=" N TYR 6 399 " --> pdb=" O GLU 6 395 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU 6 404 " --> pdb=" O GLN 6 400 " (cutoff:3.500A) Processing helix chain '6' and resid 432 through 437 removed outlier: 3.951A pdb=" N VAL 6 436 " --> pdb=" O ALA 6 432 " (cutoff:3.500A) Processing helix chain '6' and resid 438 through 456 Processing helix chain '6' and resid 457 through 462 Processing helix chain '6' and resid 466 through 470 Processing helix chain '6' and resid 471 through 484 Processing helix chain '6' and resid 488 through 490 No H-bonds generated for 'chain '6' and resid 488 through 490' Processing helix chain '6' and resid 491 through 510 Processing helix chain '6' and resid 515 through 523 Processing helix chain '6' and resid 556 through 578 removed outlier: 4.226A pdb=" N TYR 6 578 " --> pdb=" O TYR 6 574 " (cutoff:3.500A) Processing helix chain '6' and resid 583 through 602 Proline residue: 6 590 - end of helix Processing helix chain '6' and resid 604 through 630 Processing helix chain '6' and resid 638 through 643 Processing helix chain '6' and resid 650 through 653 Processing helix chain '6' and resid 654 through 692 removed outlier: 3.724A pdb=" N VAL 6 662 " --> pdb=" O SER 6 658 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS 6 670 " --> pdb=" O VAL 6 666 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU 6 680 " --> pdb=" O GLU 6 676 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU 6 689 " --> pdb=" O ARG 6 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 114 through 129 Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 161 through 173 Processing helix chain 'C' and resid 174 through 185 removed outlier: 3.748A pdb=" N LYS C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.551A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.281A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.783A pdb=" N ILE C 289 " --> pdb=" O ASP C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.657A pdb=" N SER C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.032A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 66 through 70 Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 85 through 97 Processing helix chain 'D' and resid 101 through 126 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.557A pdb=" N PHE E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 102 through 107' Processing helix chain 'E' and resid 136 through 152 removed outlier: 3.569A pdb=" N ALA E 144 " --> pdb=" O VAL E 140 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 9 through 73 removed outlier: 3.839A pdb=" N LYS F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.641A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.650A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.726A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'G' and resid 54 through 62 Processing helix chain 'G' and resid 64 through 69 Processing helix chain 'G' and resid 83 through 97 removed outlier: 3.747A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR G 97 " --> pdb=" O LEU G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 removed outlier: 3.692A pdb=" N GLU G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 164 through 174 removed outlier: 4.622A pdb=" N ALA G 168 " --> pdb=" O VAL G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.922A pdb=" N LEU G 186 " --> pdb=" O GLY G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 4.675A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 231 removed outlier: 3.698A pdb=" N ASP G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL G 229 " --> pdb=" O LYS G 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 50 removed outlier: 3.540A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 76 Processing helix chain 'K' and resid 106 through 115 Processing helix chain 'K' and resid 128 through 135 Processing helix chain 'K' and resid 136 through 148 removed outlier: 3.753A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER K 146 " --> pdb=" O ASP K 142 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU K 147 " --> pdb=" O GLN K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 177 removed outlier: 4.019A pdb=" N PHE K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 188 removed outlier: 3.743A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 190 through 195 removed outlier: 3.542A pdb=" N GLY K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.617A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 Processing helix chain 'K' and resid 255 through 274 Processing helix chain 'K' and resid 295 through 303 removed outlier: 3.998A pdb=" N ASP K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 83 removed outlier: 3.632A pdb=" N VAL L 80 " --> pdb=" O THR L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.682A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 123 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 97 through 112 Processing helix chain 'M' and resid 113 through 125 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.719A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.779A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.513A pdb=" N VAL N 106 " --> pdb=" O ALA N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix Processing helix chain 'N' and resid 159 through 163 Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 4.345A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 73 Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.839A pdb=" N LYS S 47 " --> pdb=" O TYR S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 115 Processing helix chain 'S' and resid 137 through 143 removed outlier: 3.546A pdb=" N LYS S 141 " --> pdb=" O ARG S 137 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE S 143 " --> pdb=" O TYR S 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 56 removed outlier: 3.995A pdb=" N LEU b 48 " --> pdb=" O ARG b 44 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE b 49 " --> pdb=" O HIS b 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 82 removed outlier: 3.854A pdb=" N GLU b 76 " --> pdb=" O GLN b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 161 Processing helix chain 'b' and resid 244 through 263 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 84 removed outlier: 3.605A pdb=" N THR e 84 " --> pdb=" O LYS e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.514A pdb=" N VAL e 106 " --> pdb=" O ALA e 102 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'i' and resid 27 through 31 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 77 removed outlier: 3.723A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N GLU i 66 " --> pdb=" O ARG i 62 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N LYS i 67 " --> pdb=" O ASN i 63 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) Processing helix chain 'i' and resid 80 through 99 Processing helix chain 'm' and resid 197 through 208 Processing helix chain 'm' and resid 234 through 257 removed outlier: 3.670A pdb=" N GLU m 241 " --> pdb=" O TYR m 237 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG m 242 " --> pdb=" O ASP m 238 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 71 Processing helix chain 'n' and resid 74 through 97 Processing helix chain 'n' and resid 98 through 108 removed outlier: 3.905A pdb=" N ALA n 102 " --> pdb=" O GLU n 98 " (cutoff:3.500A) Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 145 removed outlier: 4.393A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU n 139 " --> pdb=" O ALA n 135 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 removed outlier: 3.742A pdb=" N GLU n 173 " --> pdb=" O TYR n 169 " (cutoff:3.500A) Processing helix chain 'n' and resid 214 through 241 removed outlier: 4.437A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 258 through 262 Processing helix chain 'n' and resid 372 through 384 removed outlier: 3.846A pdb=" N LEU n 376 " --> pdb=" O PRO n 372 " (cutoff:3.500A) Processing helix chain 'n' and resid 389 through 394 Processing helix chain 'n' and resid 429 through 439 removed outlier: 3.699A pdb=" N ILE n 436 " --> pdb=" O ILE n 432 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN n 437 " --> pdb=" O PHE n 433 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 115 removed outlier: 3.618A pdb=" N LYS o 109 " --> pdb=" O LYS o 105 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR o 110 " --> pdb=" O GLU o 106 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN o 113 " --> pdb=" O LYS o 109 " (cutoff:3.500A) Processing helix chain 'o' and resid 141 through 151 Processing helix chain 'o' and resid 192 through 215 removed outlier: 3.895A pdb=" N LEU o 196 " --> pdb=" O PRO o 192 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP o 198 " --> pdb=" O LYS o 194 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS o 201 " --> pdb=" O LYS o 197 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU o 211 " --> pdb=" O ARG o 207 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY o 215 " --> pdb=" O LEU o 211 " (cutoff:3.500A) Processing helix chain 'p' and resid 50 through 61 Processing helix chain 'p' and resid 66 through 79 Proline residue: p 74 - end of helix Processing helix chain 'p' and resid 91 through 108 Proline residue: p 99 - end of helix Processing helix chain 'p' and resid 123 through 140 removed outlier: 4.533A pdb=" N GLU p 136 " --> pdb=" O GLY p 132 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU p 137 " --> pdb=" O VAL p 133 " (cutoff:3.500A) Processing helix chain 'p' and resid 153 through 164 removed outlier: 3.608A pdb=" N GLU p 157 " --> pdb=" O ASN p 153 " (cutoff:3.500A) Processing helix chain 'p' and resid 171 through 182 removed outlier: 3.694A pdb=" N LEU p 175 " --> pdb=" O THR p 171 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU p 176 " --> pdb=" O PRO p 172 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASP p 177 " --> pdb=" O GLY p 173 " (cutoff:3.500A) Processing helix chain 'p' and resid 197 through 205 removed outlier: 3.529A pdb=" N ILE p 201 " --> pdb=" O GLU p 197 " (cutoff:3.500A) Processing helix chain 'p' and resid 206 through 217 Processing helix chain 'p' and resid 232 through 243 Processing helix chain 'p' and resid 274 through 287 removed outlier: 4.290A pdb=" N LEU p 278 " --> pdb=" O ASP p 274 " (cutoff:3.500A) Processing helix chain 'p' and resid 298 through 312 Processing helix chain 'p' and resid 324 through 339 removed outlier: 3.581A pdb=" N GLU p 339 " --> pdb=" O PHE p 335 " (cutoff:3.500A) Processing helix chain 'p' and resid 347 through 352 Processing helix chain 'p' and resid 369 through 384 Processing helix chain 'p' and resid 395 through 397 No H-bonds generated for 'chain 'p' and resid 395 through 397' Processing helix chain 'p' and resid 398 through 409 removed outlier: 4.077A pdb=" N LEU p 402 " --> pdb=" O GLU p 398 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG p 403 " --> pdb=" O LEU p 399 " (cutoff:3.500A) Processing helix chain 'p' and resid 425 through 436 Processing helix chain 'p' and resid 436 through 457 Processing helix chain 'p' and resid 469 through 478 Processing helix chain 's' and resid 262 through 266 removed outlier: 3.659A pdb=" N ARG s 265 " --> pdb=" O PRO s 262 " (cutoff:3.500A) Processing helix chain 's' and resid 269 through 286 removed outlier: 3.741A pdb=" N ALA s 273 " --> pdb=" O SER s 269 " (cutoff:3.500A) Processing helix chain 's' and resid 290 through 308 removed outlier: 3.889A pdb=" N ILE s 303 " --> pdb=" O GLU s 299 " (cutoff:3.500A) Processing helix chain 's' and resid 342 through 347 Processing helix chain 's' and resid 350 through 357 Processing helix chain 's' and resid 358 through 366 removed outlier: 4.738A pdb=" N ARG s 364 " --> pdb=" O SER s 360 " (cutoff:3.500A) Processing helix chain 's' and resid 382 through 395 Processing helix chain 't' and resid 59 through 87 Processing helix chain 't' and resid 156 through 167 Processing helix chain 't' and resid 184 through 191 removed outlier: 4.217A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 229 through 243 removed outlier: 3.928A pdb=" N ASN t 233 " --> pdb=" O LEU t 229 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU t 236 " --> pdb=" O ASN t 232 " (cutoff:3.500A) Processing helix chain 't' and resid 247 through 257 Processing helix chain 't' and resid 260 through 268 removed outlier: 3.917A pdb=" N CYS t 264 " --> pdb=" O SER t 260 " (cutoff:3.500A) Processing helix chain 't' and resid 281 through 299 removed outlier: 4.166A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG t 287 " --> pdb=" O LEU t 283 " (cutoff:3.500A) Processing helix chain 't' and resid 313 through 322 Processing helix chain 'z' and resid 2 through 11 Processing helix chain 'z' and resid 14 through 30 removed outlier: 3.660A pdb=" N LYS z 27 " --> pdb=" O GLU z 23 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR z 30 " --> pdb=" O LYS z 26 " (cutoff:3.500A) Processing helix chain 'z' and resid 31 through 37 removed outlier: 3.584A pdb=" N LYS z 35 " --> pdb=" O ALA z 31 " (cutoff:3.500A) Processing helix chain 'z' and resid 38 through 55 removed outlier: 3.613A pdb=" N PHE z 42 " --> pdb=" O LYS z 38 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 76 removed outlier: 3.600A pdb=" N HIS z 73 " --> pdb=" O LEU z 69 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N TYR z 76 " --> pdb=" O LEU z 72 " (cutoff:3.500A) Processing helix chain 'z' and resid 78 through 85 removed outlier: 3.775A pdb=" N ASN z 82 " --> pdb=" O ASP z 78 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER z 83 " --> pdb=" O PRO z 79 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA z 85 " --> pdb=" O ASP z 81 " (cutoff:3.500A) Processing helix chain 'z' and resid 89 through 110 Processing helix chain 'z' and resid 114 through 140 removed outlier: 4.293A pdb=" N ASP z 119 " --> pdb=" O ARG z 115 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS z 120 " --> pdb=" O TYR z 116 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR z 121 " --> pdb=" O ARG z 117 " (cutoff:3.500A) Processing helix chain 'z' and resid 142 through 153 Processing helix chain 'z' and resid 167 through 186 removed outlier: 4.370A pdb=" N LEU z 178 " --> pdb=" O VAL z 174 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP z 179 " --> pdb=" O ASP z 175 " (cutoff:3.500A) Processing helix chain 'z' and resid 198 through 212 Processing helix chain 'z' and resid 213 through 227 removed outlier: 3.567A pdb=" N VAL z 217 " --> pdb=" O PRO z 213 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA z 219 " --> pdb=" O ALA z 215 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE z 220 " --> pdb=" O ASP z 216 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE z 221 " --> pdb=" O VAL z 217 " (cutoff:3.500A) Processing helix chain 'z' and resid 231 through 242 Processing helix chain 'z' and resid 245 through 251 removed outlier: 4.190A pdb=" N VAL z 249 " --> pdb=" O ASP z 245 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 37 through 40 removed outlier: 3.767A pdb=" N GLU O 40 " --> pdb=" O ARG O 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 40' Processing helix chain 'O' and resid 46 through 58 Processing helix chain 'O' and resid 75 through 88 removed outlier: 3.821A pdb=" N MET O 87 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 102 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 removed outlier: 3.526A pdb=" N ALA O 123 " --> pdb=" O VAL O 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 120 through 123' Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 187 removed outlier: 3.527A pdb=" N VAL O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU O 187 " --> pdb=" O ALA O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 198 removed outlier: 4.090A pdb=" N LYS O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '6' and resid 176 through 177 removed outlier: 6.841A pdb=" N ILE 6 176 " --> pdb=" O ALA 6 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '6' and resid 253 through 255 Processing sheet with id=AA3, first strand: chain 'C' and resid 5 through 9 removed outlier: 6.978A pdb=" N VAL C 6 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASN C 18 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL C 8 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 150 through 152 removed outlier: 6.574A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AA7, first strand: chain 'D' and resid 50 through 56 Processing sheet with id=AA8, first strand: chain 'E' and resid 77 through 79 removed outlier: 6.899A pdb=" N LEU E 64 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.472A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AB2, first strand: chain 'G' and resid 70 through 71 removed outlier: 3.689A pdb=" N GLY G 234 " --> pdb=" O VAL G 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 177 through 179 Processing sheet with id=AB4, first strand: chain 'K' and resid 243 through 250 removed outlier: 5.027A pdb=" N THR K 243 " --> pdb=" O ASN K 85 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASN K 85 " --> pdb=" O THR K 243 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASN K 245 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 83 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N HIS K 247 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE K 81 " --> pdb=" O HIS K 247 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY K 249 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR K 292 " --> pdb=" O ILE K 279 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE K 281 " --> pdb=" O PRO K 290 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 100 through 101 Processing sheet with id=AB6, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.271A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU K 124 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP K 183 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE K 126 " --> pdb=" O ASP K 183 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE K 180 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE K 209 " --> pdb=" O ILE K 180 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ALA K 182 " --> pdb=" O ILE K 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AB8, first strand: chain 'M' and resid 14 through 15 removed outlier: 3.623A pdb=" N PHE S 150 " --> pdb=" O VAL M 15 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 56 through 59 removed outlier: 6.340A pdb=" N ASP M 47 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE M 35 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.504A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N TYR N 127 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLN N 123 " --> pdb=" O TYR N 127 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL N 135 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N VAL N 115 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Q' and resid 102 through 106 removed outlier: 3.593A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY Q 85 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE Q 106 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL Q 87 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL Q 84 " --> pdb=" O LEU Q 140 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'S' and resid 25 through 31 removed outlier: 7.671A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 86 through 96 removed outlier: 3.560A pdb=" N TRP S 78 " --> pdb=" O LYS S 125 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LYS S 125 " --> pdb=" O TRP S 78 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ARG S 80 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE S 123 " --> pdb=" O ARG S 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 33 through 36 removed outlier: 6.170A pdb=" N LEU b 34 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE b 89 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE b 36 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA b 91 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE b 110 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE b 215 " --> pdb=" O THR b 190 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N THR b 190 " --> pdb=" O ILE b 215 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL b 188 " --> pdb=" O PRO b 217 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE b 219 " --> pdb=" O ILE b 186 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE b 186 " --> pdb=" O PHE b 219 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 33 through 36 removed outlier: 6.170A pdb=" N LEU b 34 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE b 89 " --> pdb=" O LEU b 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE b 36 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA b 91 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU b 97 " --> pdb=" O ILE b 114 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE b 110 " --> pdb=" O LEU b 101 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR b 109 " --> pdb=" O ILE b 226 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE b 226 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS b 111 " --> pdb=" O ILE b 224 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU b 117 " --> pdb=" O ARG b 218 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG b 218 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'b' and resid 137 through 139 removed outlier: 6.609A pdb=" N LEU b 137 " --> pdb=" O GLN m 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'e' and resid 72 through 76 removed outlier: 5.810A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'f' and resid 8 through 16 removed outlier: 5.304A pdb=" N HIS f 13 " --> pdb=" O LYS f 31 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS f 31 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER f 15 " --> pdb=" O LEU f 29 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'n' and resid 188 through 192 Processing sheet with id=AD2, first strand: chain 'n' and resid 366 through 367 removed outlier: 6.628A pdb=" N TYR n 366 " --> pdb=" O ILE n 411 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'o' and resid 117 through 124 removed outlier: 5.250A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU o 167 " --> pdb=" O SER o 90 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE o 92 " --> pdb=" O ARG o 165 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ARG o 165 " --> pdb=" O ILE o 92 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N TYR o 94 " --> pdb=" O GLN o 163 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN o 163 " --> pdb=" O TYR o 94 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N SER o 96 " --> pdb=" O LEU o 161 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU o 161 " --> pdb=" O SER o 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'p' and resid 145 through 148 removed outlier: 3.972A pdb=" N GLY p 146 " --> pdb=" O MET p 167 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE p 169 " --> pdb=" O GLY p 146 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE p 117 " --> pdb=" O LEU p 168 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA p 170 " --> pdb=" O ILE p 117 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL p 119 " --> pdb=" O ALA p 170 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU p 193 " --> pdb=" O MET p 225 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE p 227 " --> pdb=" O LEU p 193 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE p 195 " --> pdb=" O PHE p 227 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE p 250 " --> pdb=" O LEU p 83 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'p' and resid 316 through 319 removed outlier: 3.633A pdb=" N THR p 346 " --> pdb=" O LEU p 319 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE p 292 " --> pdb=" O LEU p 343 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS p 345 " --> pdb=" O ILE p 292 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL p 294 " --> pdb=" O CYS p 345 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE p 361 " --> pdb=" O LEU p 391 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE p 393 " --> pdb=" O ILE p 361 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN p 363 " --> pdb=" O PHE p 393 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLN p 266 " --> pdb=" O ASN p 413 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 't' and resid 130 through 134 Processing sheet with id=AD7, first strand: chain 't' and resid 174 through 179 Processing sheet with id=AD8, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.431A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 42 through 44 2140 hydrogen bonds defined for protein. 6177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 724 hydrogen bonds 1174 hydrogen bond angles 0 basepair planarities 295 basepair parallelities 487 stacking parallelities Total time for adding SS restraints: 32.42 Time building geometry restraints manager: 15.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 15614 1.34 - 1.48: 19169 1.48 - 1.61: 23091 1.61 - 1.74: 26 1.74 - 1.88: 76 Bond restraints: 57976 Sorted by residual: bond pdb=" C PRO s 331 " pdb=" N PRO s 332 " ideal model delta sigma weight residual 1.331 1.364 -0.033 7.90e-03 1.60e+04 1.73e+01 bond pdb=" N LYS G 120 " pdb=" CA LYS G 120 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.40e+00 bond pdb=" C LEU p 314 " pdb=" N PRO p 315 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.20e-02 6.94e+03 4.72e+00 bond pdb=" CG LYS 5 314 " pdb=" CD LYS 5 314 " ideal model delta sigma weight residual 1.520 1.585 -0.065 3.00e-02 1.11e+03 4.69e+00 bond pdb=" CB CYS D 15 " pdb=" SG CYS D 15 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.52e+00 ... (remaining 57971 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 82700 2.58 - 5.15: 771 5.15 - 7.73: 46 7.73 - 10.31: 9 10.31 - 12.88: 1 Bond angle restraints: 83527 Sorted by residual: angle pdb=" C GLY G 119 " pdb=" N LYS G 120 " pdb=" CA LYS G 120 " ideal model delta sigma weight residual 121.54 134.42 -12.88 1.91e+00 2.74e-01 4.55e+01 angle pdb=" O4' G 1 330 " pdb=" C1' G 1 330 " pdb=" N9 G 1 330 " ideal model delta sigma weight residual 108.50 117.62 -9.12 1.50e+00 4.44e-01 3.70e+01 angle pdb=" N PRO s 340 " pdb=" CA PRO s 340 " pdb=" C PRO s 340 " ideal model delta sigma weight residual 110.70 117.52 -6.82 1.22e+00 6.72e-01 3.13e+01 angle pdb=" C2' G 1 330 " pdb=" C1' G 1 330 " pdb=" N9 G 1 330 " ideal model delta sigma weight residual 112.00 119.75 -7.75 1.50e+00 4.44e-01 2.67e+01 angle pdb=" C SER C 292 " pdb=" CA SER C 292 " pdb=" CB SER C 292 " ideal model delta sigma weight residual 115.79 110.31 5.48 1.19e+00 7.06e-01 2.12e+01 ... (remaining 83522 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 33300 35.73 - 71.46: 2354 71.46 - 107.19: 290 107.19 - 142.91: 18 142.91 - 178.64: 19 Dihedral angle restraints: 35981 sinusoidal: 20889 harmonic: 15092 Sorted by residual: dihedral pdb=" CA GLY G 119 " pdb=" C GLY G 119 " pdb=" N LYS G 120 " pdb=" CA LYS G 120 " ideal model delta harmonic sigma weight residual 180.00 47.20 132.80 0 5.00e+00 4.00e-02 7.05e+02 dihedral pdb=" CA SER S 83 " pdb=" C SER S 83 " pdb=" N ARG S 84 " pdb=" CA ARG S 84 " ideal model delta harmonic sigma weight residual -180.00 -131.06 -48.94 0 5.00e+00 4.00e-02 9.58e+01 dihedral pdb=" O4' U 2 156 " pdb=" C1' U 2 156 " pdb=" N1 U 2 156 " pdb=" C2 U 2 156 " ideal model delta sinusoidal sigma weight residual 200.00 42.20 157.80 1 1.50e+01 4.44e-03 8.22e+01 ... (remaining 35978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.795: 10633 0.795 - 1.589: 0 1.589 - 2.384: 0 2.384 - 3.178: 0 3.178 - 3.973: 1 Chirality restraints: 10634 Sorted by residual: chirality pdb=" C1' G 1 330 " pdb=" O4' G 1 330 " pdb=" C2' G 1 330 " pdb=" N9 G 1 330 " both_signs ideal model delta sigma weight residual False 2.46 -1.51 3.97 2.00e-01 2.50e+01 3.95e+02 chirality pdb=" CA PRO G 176 " pdb=" N PRO G 176 " pdb=" C PRO G 176 " pdb=" CB PRO G 176 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE p 361 " pdb=" N ILE p 361 " pdb=" C ILE p 361 " pdb=" CB ILE p 361 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 10631 not shown) Planarity restraints: 7205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU z 157 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO z 158 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO z 158 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO z 158 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C 1 641 " 0.035 2.00e-02 2.50e+03 1.72e-02 6.66e+00 pdb=" N1 C 1 641 " -0.032 2.00e-02 2.50e+03 pdb=" C2 C 1 641 " -0.005 2.00e-02 2.50e+03 pdb=" O2 C 1 641 " -0.006 2.00e-02 2.50e+03 pdb=" N3 C 1 641 " 0.004 2.00e-02 2.50e+03 pdb=" C4 C 1 641 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C 1 641 " 0.010 2.00e-02 2.50e+03 pdb=" C5 C 1 641 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C 1 641 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 517 " -0.034 2.00e-02 2.50e+03 1.44e-02 6.24e+00 pdb=" N9 G 1 517 " 0.033 2.00e-02 2.50e+03 pdb=" C8 G 1 517 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 1 517 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 1 517 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 1 517 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G 1 517 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G 1 517 " -0.005 2.00e-02 2.50e+03 pdb=" C2 G 1 517 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G 1 517 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 1 517 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G 1 517 " 0.003 2.00e-02 2.50e+03 ... (remaining 7202 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 403 2.56 - 3.14: 43944 3.14 - 3.73: 98742 3.73 - 4.31: 125652 4.31 - 4.90: 184276 Nonbonded interactions: 453017 Sorted by model distance: nonbonded pdb=" O2' G 1 251 " pdb=" OP2 U 1 252 " model vdw 1.971 3.040 nonbonded pdb=" OP1 C 1 439 " pdb=" O2' A 1 440 " model vdw 1.985 3.040 nonbonded pdb=" O PHE 6 441 " pdb=" OG SER 6 444 " model vdw 1.997 3.040 nonbonded pdb=" O2' G 1 22 " pdb=" O2' A 2 96 " model vdw 2.021 3.040 nonbonded pdb=" OP2 C 11176 " pdb=" O2' G 11177 " model vdw 2.030 3.040 ... (remaining 453012 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: 4.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.970 Check model and map are aligned: 0.390 Set scattering table: 0.490 Process input model: 144.470 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 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 : 0.003 0.070 57976 Z= 0.216 Angle : 0.681 12.885 83527 Z= 0.390 Chirality : 0.055 3.973 10634 Planarity : 0.005 0.072 7205 Dihedral : 21.120 178.642 26107 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 5072 helix: 0.80 (0.10), residues: 2602 sheet: -0.93 (0.22), residues: 476 loop : -0.79 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 100 HIS 0.013 0.001 HIS D 99 PHE 0.034 0.002 PHE 5 681 TYR 0.026 0.002 TYR O 54 ARG 0.013 0.001 ARG S 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 4.468 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: 5 648 LEU cc_start: 0.7787 (mt) cc_final: 0.7477 (mt) REVERT: 5 842 LYS cc_start: 0.8042 (tptp) cc_final: 0.7766 (tptt) REVERT: 6 196 LEU cc_start: 0.8069 (mt) cc_final: 0.7548 (tp) REVERT: 6 581 ASN cc_start: 0.6117 (m-40) cc_final: 0.5795 (m-40) REVERT: 6 645 PHE cc_start: 0.5332 (t80) cc_final: 0.4919 (t80) REVERT: C 117 GLU cc_start: 0.8544 (tt0) cc_final: 0.8216 (tp30) REVERT: C 211 GLU cc_start: 0.6495 (tp30) cc_final: 0.6272 (tm-30) REVERT: E 97 ASN cc_start: 0.5628 (p0) cc_final: 0.5116 (p0) REVERT: Q 22 ASP cc_start: 0.7171 (p0) cc_final: 0.6747 (t70) REVERT: S 7 TYR cc_start: 0.6639 (m-80) cc_final: 0.6112 (m-10) REVERT: S 50 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8266 (mmtm) REVERT: S 150 PHE cc_start: 0.7685 (p90) cc_final: 0.7116 (p90) REVERT: e 90 LYS cc_start: 0.6759 (mptt) cc_final: 0.6543 (mmtt) REVERT: f 97 SER cc_start: 0.6503 (m) cc_final: 0.6182 (m) REVERT: z 119 ASP cc_start: 0.7386 (m-30) cc_final: 0.7151 (p0) REVERT: z 220 ILE cc_start: 0.8314 (mt) cc_final: 0.8032 (mt) REVERT: O 19 LEU cc_start: 0.7869 (tp) cc_final: 0.7603 (tt) REVERT: O 42 ASN cc_start: 0.6638 (m110) cc_final: 0.6073 (t0) outliers start: 0 outliers final: 0 residues processed: 570 average time/residue: 0.7263 time to fit residues: 667.3369 Evaluate side-chains 231 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 505 optimal weight: 10.0000 chunk 454 optimal weight: 9.9990 chunk 251 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 306 optimal weight: 0.0170 chunk 242 optimal weight: 0.9980 chunk 469 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 349 optimal weight: 0.9990 chunk 543 optimal weight: 10.0000 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 389 HIS 5 581 HIS ** 5 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 748 ASN 6 189 GLN 6 277 HIS 6 335 GLN 6 462 ASN 6 545 HIS C 160 GLN D 26 ASN D 47 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN F 172 ASN F 222 HIS ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 HIS ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 63 GLN z 73 HIS z 132 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 57976 Z= 0.248 Angle : 0.660 10.686 83527 Z= 0.346 Chirality : 0.040 0.342 10634 Planarity : 0.005 0.065 7205 Dihedral : 22.303 179.135 20344 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 2.20 % Allowed : 8.72 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.12), residues: 5072 helix: 1.41 (0.10), residues: 2681 sheet: -0.73 (0.23), residues: 485 loop : -0.67 (0.14), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP z 181 HIS 0.012 0.002 HIS e 88 PHE 0.027 0.002 PHE 6 403 TYR 0.039 0.002 TYR 5 311 ARG 0.010 0.001 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 241 time to evaluate : 4.552 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: 6 222 LYS cc_start: 0.8019 (tttt) cc_final: 0.7460 (ttpt) REVERT: 6 240 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7586 (tptp) REVERT: 6 431 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: 6 547 ILE cc_start: 0.7758 (tp) cc_final: 0.7558 (tp) REVERT: 6 686 GLU cc_start: 0.7347 (tt0) cc_final: 0.7122 (tm-30) REVERT: M 12 TRP cc_start: 0.5556 (OUTLIER) cc_final: 0.4971 (t-100) REVERT: Q 22 ASP cc_start: 0.7266 (p0) cc_final: 0.6497 (t70) REVERT: S 50 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8363 (mmtm) REVERT: S 80 ARG cc_start: 0.7287 (ptm160) cc_final: 0.6782 (tpt170) REVERT: S 125 LYS cc_start: 0.6137 (OUTLIER) cc_final: 0.5837 (tmmt) REVERT: e 81 ASP cc_start: 0.7407 (t0) cc_final: 0.7185 (t0) REVERT: e 90 LYS cc_start: 0.7323 (mptt) cc_final: 0.7079 (mmtt) REVERT: f 97 SER cc_start: 0.6970 (m) cc_final: 0.6683 (p) REVERT: z 119 ASP cc_start: 0.7555 (m-30) cc_final: 0.7346 (p0) REVERT: z 181 TRP cc_start: 0.5663 (m100) cc_final: 0.5254 (m100) REVERT: O 42 ASN cc_start: 0.6358 (m110) cc_final: 0.5983 (t0) REVERT: O 43 ILE cc_start: 0.8981 (mt) cc_final: 0.8673 (tt) REVERT: O 50 ASN cc_start: 0.6440 (m-40) cc_final: 0.6226 (m-40) REVERT: O 100 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7090 (pm20) outliers start: 55 outliers final: 32 residues processed: 288 average time/residue: 0.6494 time to fit residues: 319.9430 Evaluate side-chains 224 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 4.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 291 THR Chi-restraints excluded: chain 5 residue 589 THR Chi-restraints excluded: chain 5 residue 631 LEU Chi-restraints excluded: chain 5 residue 700 THR Chi-restraints excluded: chain 6 residue 240 LYS Chi-restraints excluded: chain 6 residue 260 THR Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 323 VAL Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 431 GLU Chi-restraints excluded: chain 6 residue 588 VAL Chi-restraints excluded: chain 6 residue 648 ASP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 125 LYS Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain z residue 78 ASP Chi-restraints excluded: chain z residue 246 THR Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 302 optimal weight: 20.0000 chunk 168 optimal weight: 0.4980 chunk 452 optimal weight: 5.9990 chunk 370 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 544 optimal weight: 10.0000 chunk 588 optimal weight: 30.0000 chunk 485 optimal weight: 6.9990 chunk 540 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 437 optimal weight: 9.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 671 HIS 5 747 ASN 6 400 GLN ** 6 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 490 GLN 6 566 GLN 6 620 GLN C 213 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 ASN ** D 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN M 56 GLN Q 78 ASN S 88 HIS S 114 HIS ** z 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.164 57976 Z= 0.549 Angle : 0.988 17.505 83527 Z= 0.512 Chirality : 0.051 0.355 10634 Planarity : 0.008 0.128 7205 Dihedral : 22.768 179.005 20344 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.26 % Favored : 94.62 % Rotamer: Outliers : 5.44 % Allowed : 12.32 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.11), residues: 5072 helix: -0.10 (0.09), residues: 2646 sheet: -1.01 (0.23), residues: 482 loop : -1.49 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.004 TRP S 78 HIS 0.015 0.004 HIS F 194 PHE 0.041 0.004 PHE z 111 TYR 0.050 0.004 TYR 5 220 ARG 0.024 0.002 ARG 6 375 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 184 time to evaluate : 4.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 274 MET cc_start: 0.3546 (OUTLIER) cc_final: 0.3092 (ptt) REVERT: 5 353 MET cc_start: 0.4077 (ptt) cc_final: 0.3832 (ptt) REVERT: 5 631 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6492 (tp) REVERT: 5 747 ASN cc_start: 0.6959 (OUTLIER) cc_final: 0.6421 (t0) REVERT: 6 211 ASN cc_start: 0.7753 (m-40) cc_final: 0.6836 (t0) REVERT: 6 222 LYS cc_start: 0.8531 (tttt) cc_final: 0.7704 (ttpt) REVERT: 6 240 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7516 (tptp) REVERT: 6 374 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6779 (tpt) REVERT: 6 542 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7102 (m-30) REVERT: 6 633 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: C 20 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7580 (mt) REVERT: C 36 HIS cc_start: 0.6017 (t-90) cc_final: 0.5197 (m170) REVERT: C 150 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5684 (tt) REVERT: D 119 MET cc_start: 0.8253 (tpp) cc_final: 0.7918 (tpt) REVERT: E 92 SER cc_start: 0.8139 (t) cc_final: 0.7444 (p) REVERT: E 102 ASN cc_start: 0.6097 (t0) cc_final: 0.5876 (t0) REVERT: S 35 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7637 (p) REVERT: e 81 ASP cc_start: 0.7834 (t0) cc_final: 0.7452 (t0) REVERT: z 119 ASP cc_start: 0.8090 (m-30) cc_final: 0.7680 (p0) REVERT: z 181 TRP cc_start: 0.7111 (m100) cc_final: 0.6703 (m100) outliers start: 136 outliers final: 83 residues processed: 304 average time/residue: 0.6346 time to fit residues: 333.9167 Evaluate side-chains 230 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 137 time to evaluate : 4.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 291 THR Chi-restraints excluded: chain 5 residue 398 VAL Chi-restraints excluded: chain 5 residue 472 ILE Chi-restraints excluded: chain 5 residue 589 THR Chi-restraints excluded: chain 5 residue 631 LEU Chi-restraints excluded: chain 5 residue 634 SER Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain 5 residue 644 LEU Chi-restraints excluded: chain 5 residue 661 PHE Chi-restraints excluded: chain 5 residue 662 VAL Chi-restraints excluded: chain 5 residue 699 LEU Chi-restraints excluded: chain 5 residue 700 THR Chi-restraints excluded: chain 5 residue 747 ASN Chi-restraints excluded: chain 5 residue 864 ASP Chi-restraints excluded: chain 6 residue 203 ILE Chi-restraints excluded: chain 6 residue 240 LYS Chi-restraints excluded: chain 6 residue 260 THR Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 289 THR Chi-restraints excluded: chain 6 residue 321 SER Chi-restraints excluded: chain 6 residue 323 VAL Chi-restraints excluded: chain 6 residue 328 THR Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 374 MET Chi-restraints excluded: chain 6 residue 431 GLU Chi-restraints excluded: chain 6 residue 468 LEU Chi-restraints excluded: chain 6 residue 483 ILE Chi-restraints excluded: chain 6 residue 494 LEU Chi-restraints excluded: chain 6 residue 529 THR Chi-restraints excluded: chain 6 residue 542 ASP Chi-restraints excluded: chain 6 residue 588 VAL Chi-restraints excluded: chain 6 residue 607 LEU Chi-restraints excluded: chain 6 residue 633 GLU Chi-restraints excluded: chain 6 residue 648 ASP Chi-restraints excluded: chain 6 residue 660 VAL Chi-restraints excluded: chain 6 residue 666 VAL Chi-restraints excluded: chain 6 residue 682 ASP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 173 LEU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 122 VAL Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 145 ASN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain e residue 87 MET Chi-restraints excluded: chain e residue 109 LEU Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 72 THR Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain z residue 35 LYS Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 78 ASP Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 246 THR Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 538 optimal weight: 10.0000 chunk 409 optimal weight: 0.4980 chunk 282 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 260 optimal weight: 0.1980 chunk 365 optimal weight: 4.9990 chunk 546 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 285 optimal weight: 0.9990 chunk 518 optimal weight: 10.0000 chunk 156 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 57976 Z= 0.179 Angle : 0.600 11.529 83527 Z= 0.314 Chirality : 0.038 0.288 10634 Planarity : 0.004 0.065 7205 Dihedral : 22.438 178.283 20344 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.98 % Favored : 96.90 % Rotamer: Outliers : 3.08 % Allowed : 14.79 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 5072 helix: 1.40 (0.10), residues: 2668 sheet: -0.87 (0.22), residues: 506 loop : -1.21 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 7 HIS 0.007 0.001 HIS e 88 PHE 0.024 0.002 PHE 6 341 TYR 0.030 0.002 TYR 5 311 ARG 0.008 0.001 ARG 5 414 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 189 time to evaluate : 4.643 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: 5 274 MET cc_start: 0.3729 (ttt) cc_final: 0.3476 (ptt) REVERT: 5 557 PHE cc_start: 0.7432 (m-80) cc_final: 0.7146 (m-80) REVERT: 5 644 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8335 (mm) REVERT: 5 688 LEU cc_start: 0.8341 (tp) cc_final: 0.7890 (tp) REVERT: 6 211 ASN cc_start: 0.8010 (m-40) cc_final: 0.7377 (t0) REVERT: 6 222 LYS cc_start: 0.8386 (tttt) cc_final: 0.7695 (ttpt) REVERT: 6 237 MET cc_start: 0.7534 (ppp) cc_final: 0.7091 (ppp) REVERT: 6 240 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7544 (tptp) REVERT: 6 282 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7362 (tt) REVERT: 6 353 MET cc_start: 0.6370 (pmm) cc_final: 0.5446 (ptp) REVERT: C 36 HIS cc_start: 0.5897 (t-90) cc_final: 0.5071 (m170) REVERT: C 147 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: D 119 MET cc_start: 0.7995 (tpp) cc_final: 0.7630 (tpt) REVERT: E 92 SER cc_start: 0.7578 (t) cc_final: 0.7286 (p) REVERT: E 94 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7836 (pm20) REVERT: M 107 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: S 27 MET cc_start: 0.7072 (mmt) cc_final: 0.5534 (mtt) REVERT: S 52 LYS cc_start: 0.8659 (ptpp) cc_final: 0.8239 (ptmt) REVERT: S 114 HIS cc_start: 0.7080 (OUTLIER) cc_final: 0.6235 (t70) REVERT: e 87 MET cc_start: 0.6204 (ptp) cc_final: 0.5978 (ptm) REVERT: f 67 MET cc_start: 0.6495 (tmm) cc_final: 0.6017 (tmm) REVERT: z 143 LYS cc_start: 0.7180 (mppt) cc_final: 0.6743 (mppt) REVERT: O 100 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6888 (pm20) outliers start: 77 outliers final: 37 residues processed: 252 average time/residue: 0.6332 time to fit residues: 284.5044 Evaluate side-chains 192 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 148 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 250 LYS Chi-restraints excluded: chain 5 residue 589 THR Chi-restraints excluded: chain 5 residue 631 LEU Chi-restraints excluded: chain 5 residue 644 LEU Chi-restraints excluded: chain 5 residue 661 PHE Chi-restraints excluded: chain 5 residue 840 THR Chi-restraints excluded: chain 5 residue 846 ILE Chi-restraints excluded: chain 6 residue 240 LYS Chi-restraints excluded: chain 6 residue 260 THR Chi-restraints excluded: chain 6 residue 273 ILE Chi-restraints excluded: chain 6 residue 282 LEU Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 431 GLU Chi-restraints excluded: chain 6 residue 588 VAL Chi-restraints excluded: chain 6 residue 648 ASP Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 114 HIS Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 97 SER Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain z residue 78 ASP Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 246 THR Chi-restraints excluded: chain O residue 100 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 482 optimal weight: 1.9990 chunk 328 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 431 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 494 optimal weight: 3.9990 chunk 400 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 519 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 346 ASN ** 5 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 599 GLN 5 747 ASN 6 277 HIS 6 373 ASN ** 6 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN D 85 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 HIS ** f 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 57976 Z= 0.535 Angle : 0.931 13.285 83527 Z= 0.482 Chirality : 0.050 0.315 10634 Planarity : 0.007 0.088 7205 Dihedral : 22.746 179.619 20344 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 19.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 5.72 % Allowed : 15.79 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.11), residues: 5072 helix: 0.02 (0.09), residues: 2651 sheet: -1.31 (0.23), residues: 480 loop : -1.72 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP z 181 HIS 0.015 0.003 HIS F 186 PHE 0.045 0.004 PHE z 111 TYR 0.040 0.004 TYR 6 437 ARG 0.013 0.001 ARG Q 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 145 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 274 MET cc_start: 0.3244 (OUTLIER) cc_final: 0.2914 (ptt) REVERT: 5 631 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6828 (tp) REVERT: 6 196 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7717 (tp) REVERT: 6 240 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7584 (tptp) REVERT: 6 366 ILE cc_start: 0.8348 (mp) cc_final: 0.8140 (mt) REVERT: 6 542 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6468 (m-30) REVERT: 6 547 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8108 (tp) REVERT: 6 633 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7408 (pm20) REVERT: C 20 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7464 (mt) REVERT: C 36 HIS cc_start: 0.6171 (t-90) cc_final: 0.5293 (m170) REVERT: C 290 ILE cc_start: 0.7014 (OUTLIER) cc_final: 0.6700 (tt) REVERT: D 49 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7685 (mtpt) REVERT: D 119 MET cc_start: 0.8140 (tpp) cc_final: 0.7762 (tpt) REVERT: E 92 SER cc_start: 0.8615 (t) cc_final: 0.8081 (p) REVERT: M 107 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: S 27 MET cc_start: 0.6949 (mmt) cc_final: 0.5493 (mtm) REVERT: S 53 LYS cc_start: 0.6855 (mttt) cc_final: 0.6555 (mttm) REVERT: S 114 HIS cc_start: 0.7341 (OUTLIER) cc_final: 0.6855 (t70) REVERT: e 81 ASP cc_start: 0.7750 (t0) cc_final: 0.7293 (t0) REVERT: f 5 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6472 (p-80) REVERT: f 67 MET cc_start: 0.6816 (tmm) cc_final: 0.6263 (tmm) REVERT: z 92 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8193 (m-30) REVERT: z 111 PHE cc_start: 0.6857 (OUTLIER) cc_final: 0.6504 (t80) REVERT: z 119 ASP cc_start: 0.7813 (m-30) cc_final: 0.7502 (p0) REVERT: z 169 ILE cc_start: 0.5955 (OUTLIER) cc_final: 0.5560 (mp) REVERT: z 181 TRP cc_start: 0.7458 (m100) cc_final: 0.7217 (m100) REVERT: O 100 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6811 (pm20) outliers start: 143 outliers final: 86 residues processed: 270 average time/residue: 0.6110 time to fit residues: 289.9102 Evaluate side-chains 236 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 133 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 213 ILE Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 291 THR Chi-restraints excluded: chain 5 residue 346 ASN Chi-restraints excluded: chain 5 residue 423 ILE Chi-restraints excluded: chain 5 residue 435 LEU Chi-restraints excluded: chain 5 residue 497 LEU Chi-restraints excluded: chain 5 residue 589 THR Chi-restraints excluded: chain 5 residue 604 ILE Chi-restraints excluded: chain 5 residue 631 LEU Chi-restraints excluded: chain 5 residue 634 SER Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain 5 residue 644 LEU Chi-restraints excluded: chain 5 residue 661 PHE Chi-restraints excluded: chain 5 residue 685 LEU Chi-restraints excluded: chain 5 residue 700 THR Chi-restraints excluded: chain 5 residue 846 ILE Chi-restraints excluded: chain 6 residue 191 HIS Chi-restraints excluded: chain 6 residue 196 LEU Chi-restraints excluded: chain 6 residue 240 LYS Chi-restraints excluded: chain 6 residue 242 VAL Chi-restraints excluded: chain 6 residue 260 THR Chi-restraints excluded: chain 6 residue 321 SER Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 420 THR Chi-restraints excluded: chain 6 residue 427 ILE Chi-restraints excluded: chain 6 residue 431 GLU Chi-restraints excluded: chain 6 residue 468 LEU Chi-restraints excluded: chain 6 residue 483 ILE Chi-restraints excluded: chain 6 residue 528 PHE Chi-restraints excluded: chain 6 residue 542 ASP Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 6 residue 588 VAL Chi-restraints excluded: chain 6 residue 633 GLU Chi-restraints excluded: chain 6 residue 648 ASP Chi-restraints excluded: chain 6 residue 666 VAL Chi-restraints excluded: chain 6 residue 686 GLU Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 221 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 21 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain M residue 53 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain Q residue 29 LEU Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 42 TRP Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 81 TYR Chi-restraints excluded: chain S residue 114 HIS Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 35 VAL Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain z residue 56 SER Chi-restraints excluded: chain z residue 78 ASP Chi-restraints excluded: chain z residue 92 ASP Chi-restraints excluded: chain z residue 111 PHE Chi-restraints excluded: chain z residue 128 VAL Chi-restraints excluded: chain z residue 169 ILE Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 208 SER Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 228 TYR Chi-restraints excluded: chain z residue 246 THR Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 87 MET Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 194 optimal weight: 5.9990 chunk 521 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 339 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 579 optimal weight: 10.0000 chunk 481 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 191 optimal weight: 5.9990 chunk 304 optimal weight: 50.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 457 GLN ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN D 85 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 HIS ** F 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 57976 Z= 0.206 Angle : 0.619 11.302 83527 Z= 0.326 Chirality : 0.039 0.255 10634 Planarity : 0.004 0.072 7205 Dihedral : 22.516 178.357 20344 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 3.80 % Allowed : 17.63 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.12), residues: 5072 helix: 1.12 (0.10), residues: 2654 sheet: -1.22 (0.22), residues: 517 loop : -1.45 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 6 326 HIS 0.007 0.001 HIS e 88 PHE 0.017 0.002 PHE D 112 TYR 0.026 0.002 TYR 5 311 ARG 0.010 0.001 ARG M 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 160 time to evaluate : 4.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 264 PHE cc_start: 0.4203 (t80) cc_final: 0.3899 (t80) REVERT: 5 274 MET cc_start: 0.2756 (OUTLIER) cc_final: 0.2485 (ptt) REVERT: 5 557 PHE cc_start: 0.7203 (m-80) cc_final: 0.6935 (m-80) REVERT: 5 631 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6707 (tp) REVERT: 5 688 LEU cc_start: 0.8288 (tp) cc_final: 0.7898 (tp) REVERT: 6 211 ASN cc_start: 0.7779 (m-40) cc_final: 0.7080 (t0) REVERT: 6 237 MET cc_start: 0.7455 (ppp) cc_final: 0.7094 (ppp) REVERT: 6 240 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7492 (tptp) REVERT: 6 353 MET cc_start: 0.6309 (pmm) cc_final: 0.4979 (ttp) REVERT: 6 366 ILE cc_start: 0.8211 (mp) cc_final: 0.7936 (mt) REVERT: 6 547 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7217 (mm) REVERT: C 36 HIS cc_start: 0.5954 (t-90) cc_final: 0.4911 (m170) REVERT: C 290 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6803 (tt) REVERT: D 119 MET cc_start: 0.7987 (tpp) cc_final: 0.7565 (tpt) REVERT: E 92 SER cc_start: 0.8235 (t) cc_final: 0.7937 (p) REVERT: E 94 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7915 (pm20) REVERT: E 102 ASN cc_start: 0.6412 (t0) cc_final: 0.4907 (p0) REVERT: M 107 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7405 (mt-10) REVERT: S 27 MET cc_start: 0.6825 (mmt) cc_final: 0.5626 (mtm) REVERT: S 52 LYS cc_start: 0.8749 (ptpp) cc_final: 0.8399 (ptmt) REVERT: S 53 LYS cc_start: 0.6651 (mttt) cc_final: 0.6419 (mttm) REVERT: S 114 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.6986 (t70) REVERT: e 81 ASP cc_start: 0.7491 (t0) cc_final: 0.7037 (t0) REVERT: f 5 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6817 (p-80) REVERT: f 67 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6168 (tmm) REVERT: z 92 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: z 242 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6505 (mt) REVERT: O 100 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6897 (pm20) outliers start: 95 outliers final: 54 residues processed: 240 average time/residue: 0.6074 time to fit residues: 256.6370 Evaluate side-chains 205 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 139 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 213 ILE Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 554 SER Chi-restraints excluded: chain 5 residue 589 THR Chi-restraints excluded: chain 5 residue 631 LEU Chi-restraints excluded: chain 5 residue 634 SER Chi-restraints excluded: chain 5 residue 661 PHE Chi-restraints excluded: chain 5 residue 685 LEU Chi-restraints excluded: chain 5 residue 746 ILE Chi-restraints excluded: chain 5 residue 846 ILE Chi-restraints excluded: chain 6 residue 191 HIS Chi-restraints excluded: chain 6 residue 225 ILE Chi-restraints excluded: chain 6 residue 240 LYS Chi-restraints excluded: chain 6 residue 260 THR Chi-restraints excluded: chain 6 residue 321 SER Chi-restraints excluded: chain 6 residue 323 VAL Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 427 ILE Chi-restraints excluded: chain 6 residue 468 LEU Chi-restraints excluded: chain 6 residue 528 PHE Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 6 residue 588 VAL Chi-restraints excluded: chain 6 residue 648 ASP Chi-restraints excluded: chain 6 residue 666 VAL Chi-restraints excluded: chain 6 residue 674 MET Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 43 TYR Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 114 HIS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 67 MET Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain z residue 19 VAL Chi-restraints excluded: chain z residue 78 ASP Chi-restraints excluded: chain z residue 92 ASP Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 242 LEU Chi-restraints excluded: chain z residue 246 THR Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 558 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 330 optimal weight: 6.9990 chunk 423 optimal weight: 8.9990 chunk 327 optimal weight: 0.9990 chunk 487 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 chunk 577 optimal weight: 10.0000 chunk 361 optimal weight: 0.3980 chunk 351 optimal weight: 10.0000 chunk 266 optimal weight: 7.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 270 GLN ** 5 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 747 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 57976 Z= 0.307 Angle : 0.681 10.965 83527 Z= 0.356 Chirality : 0.041 0.251 10634 Planarity : 0.005 0.073 7205 Dihedral : 22.470 179.825 20344 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.49 % Favored : 93.43 % Rotamer: Outliers : 4.20 % Allowed : 18.39 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5072 helix: 1.04 (0.10), residues: 2666 sheet: -1.27 (0.22), residues: 504 loop : -1.51 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP z 181 HIS 0.033 0.002 HIS F 194 PHE 0.027 0.002 PHE F 195 TYR 0.027 0.002 TYR Q 33 ARG 0.011 0.001 ARG M 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 140 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 315 LYS cc_start: 0.8748 (tptp) cc_final: 0.8299 (tmtt) REVERT: 5 445 MET cc_start: 0.5863 (ptp) cc_final: 0.5610 (ptp) REVERT: 5 631 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6733 (tp) REVERT: 6 178 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7796 (mm) REVERT: 6 196 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7706 (tp) REVERT: 6 211 ASN cc_start: 0.7635 (m-40) cc_final: 0.6891 (t0) REVERT: 6 237 MET cc_start: 0.7675 (ppp) cc_final: 0.7248 (ppp) REVERT: 6 240 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7512 (tptp) REVERT: 6 353 MET cc_start: 0.6314 (pmm) cc_final: 0.4993 (ttp) REVERT: 6 547 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7163 (mm) REVERT: C 3 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6682 (ttm170) REVERT: C 36 HIS cc_start: 0.6000 (t-90) cc_final: 0.5003 (m170) REVERT: C 290 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6821 (tt) REVERT: C 343 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8164 (mttp) REVERT: C 345 GLU cc_start: 0.7753 (mp0) cc_final: 0.7345 (mm-30) REVERT: D 119 MET cc_start: 0.8009 (tpp) cc_final: 0.7634 (tpt) REVERT: E 92 SER cc_start: 0.8378 (t) cc_final: 0.7773 (p) REVERT: F 138 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7117 (m-10) REVERT: M 107 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7286 (mt-10) REVERT: S 52 LYS cc_start: 0.8728 (ptpp) cc_final: 0.8374 (ptmt) REVERT: S 53 LYS cc_start: 0.6723 (mttt) cc_final: 0.6515 (mttm) REVERT: S 114 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.7053 (t70) REVERT: e 81 ASP cc_start: 0.7516 (t0) cc_final: 0.7094 (t0) REVERT: f 5 HIS cc_start: 0.7131 (OUTLIER) cc_final: 0.6760 (p-80) REVERT: f 67 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6278 (tmm) REVERT: z 29 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8121 (mp) REVERT: z 73 HIS cc_start: 0.8315 (OUTLIER) cc_final: 0.7689 (t-90) REVERT: O 19 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6902 (tt) REVERT: O 100 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.6954 (pm20) outliers start: 105 outliers final: 67 residues processed: 230 average time/residue: 0.6189 time to fit residues: 253.1872 Evaluate side-chains 212 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 128 time to evaluate : 4.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 215 TYR Chi-restraints excluded: chain 5 residue 291 THR Chi-restraints excluded: chain 5 residue 497 LEU Chi-restraints excluded: chain 5 residue 554 SER Chi-restraints excluded: chain 5 residue 589 THR Chi-restraints excluded: chain 5 residue 631 LEU Chi-restraints excluded: chain 5 residue 634 SER Chi-restraints excluded: chain 5 residue 641 LEU Chi-restraints excluded: chain 5 residue 661 PHE Chi-restraints excluded: chain 5 residue 685 LEU Chi-restraints excluded: chain 5 residue 746 ILE Chi-restraints excluded: chain 5 residue 846 ILE Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 191 HIS Chi-restraints excluded: chain 6 residue 196 LEU Chi-restraints excluded: chain 6 residue 240 LYS Chi-restraints excluded: chain 6 residue 260 THR Chi-restraints excluded: chain 6 residue 321 SER Chi-restraints excluded: chain 6 residue 323 VAL Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 427 ILE Chi-restraints excluded: chain 6 residue 468 LEU Chi-restraints excluded: chain 6 residue 528 PHE Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 6 residue 588 VAL Chi-restraints excluded: chain 6 residue 646 LEU Chi-restraints excluded: chain 6 residue 648 ASP Chi-restraints excluded: chain 6 residue 666 VAL Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 8 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain F residue 138 TYR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 194 HIS Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 43 TYR Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 78 TRP Chi-restraints excluded: chain S residue 114 HIS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 67 MET Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain z residue 19 VAL Chi-restraints excluded: chain z residue 29 LEU Chi-restraints excluded: chain z residue 73 HIS Chi-restraints excluded: chain z residue 128 VAL Chi-restraints excluded: chain z residue 174 VAL Chi-restraints excluded: chain z residue 208 SER Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 228 TYR Chi-restraints excluded: chain z residue 242 LEU Chi-restraints excluded: chain z residue 246 THR Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 357 optimal weight: 10.0000 chunk 230 optimal weight: 40.0000 chunk 344 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 367 optimal weight: 0.4980 chunk 393 optimal weight: 6.9990 chunk 285 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 453 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 747 ASN ** 6 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN ** D 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 57976 Z= 0.182 Angle : 0.578 12.094 83527 Z= 0.302 Chirality : 0.037 0.252 10634 Planarity : 0.004 0.063 7205 Dihedral : 22.320 179.259 20344 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 3.28 % Allowed : 19.23 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.31 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.12), residues: 5072 helix: 1.56 (0.10), residues: 2684 sheet: -1.18 (0.22), residues: 514 loop : -1.39 (0.14), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP z 181 HIS 0.005 0.001 HIS 5 465 PHE 0.018 0.002 PHE 6 339 TYR 0.025 0.002 TYR Q 33 ARG 0.008 0.001 ARG z 139 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10144 Ramachandran restraints generated. 5072 Oldfield, 0 Emsley, 5072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 150 time to evaluate : 4.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 274 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.3341 (ttt) REVERT: 5 367 TYR cc_start: 0.6071 (t80) cc_final: 0.5799 (t80) REVERT: 5 445 MET cc_start: 0.5732 (ptp) cc_final: 0.5507 (ptp) REVERT: 5 557 PHE cc_start: 0.7090 (m-80) cc_final: 0.6799 (m-80) REVERT: 5 631 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6547 (tp) REVERT: 5 688 LEU cc_start: 0.8300 (tp) cc_final: 0.7957 (tp) REVERT: 6 178 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7833 (mm) REVERT: 6 196 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7696 (tp) REVERT: 6 211 ASN cc_start: 0.7606 (m-40) cc_final: 0.6950 (t0) REVERT: 6 237 MET cc_start: 0.7464 (ppp) cc_final: 0.7019 (ppp) REVERT: 6 240 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7506 (tptp) REVERT: 6 282 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7305 (pp) REVERT: 6 547 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7768 (tp) REVERT: C 36 HIS cc_start: 0.5818 (t-90) cc_final: 0.4868 (m170) REVERT: C 345 GLU cc_start: 0.7825 (mp0) cc_final: 0.7486 (mm-30) REVERT: E 92 SER cc_start: 0.8474 (t) cc_final: 0.8147 (p) REVERT: E 94 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7972 (pm20) REVERT: M 107 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7385 (mt-10) REVERT: S 27 MET cc_start: 0.6754 (mmt) cc_final: 0.5556 (mtm) REVERT: S 52 LYS cc_start: 0.8626 (ptpp) cc_final: 0.8203 (ptmm) REVERT: S 114 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6875 (t70) REVERT: e 81 ASP cc_start: 0.7316 (t0) cc_final: 0.7014 (t0) REVERT: f 5 HIS cc_start: 0.7123 (OUTLIER) cc_final: 0.6747 (p-80) REVERT: f 67 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6174 (tmm) REVERT: z 73 HIS cc_start: 0.8332 (OUTLIER) cc_final: 0.7796 (t-90) REVERT: z 169 ILE cc_start: 0.4929 (OUTLIER) cc_final: 0.4529 (mp) REVERT: O 19 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6777 (tt) REVERT: O 100 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6885 (pm20) outliers start: 82 outliers final: 51 residues processed: 213 average time/residue: 0.6043 time to fit residues: 228.9678 Evaluate side-chains 202 residues out of total 4550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 136 time to evaluate : 4.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 215 TYR Chi-restraints excluded: chain 5 residue 274 MET Chi-restraints excluded: chain 5 residue 291 THR Chi-restraints excluded: chain 5 residue 554 SER Chi-restraints excluded: chain 5 residue 589 THR Chi-restraints excluded: chain 5 residue 631 LEU Chi-restraints excluded: chain 5 residue 634 SER Chi-restraints excluded: chain 5 residue 661 PHE Chi-restraints excluded: chain 5 residue 685 LEU Chi-restraints excluded: chain 5 residue 700 THR Chi-restraints excluded: chain 6 residue 178 LEU Chi-restraints excluded: chain 6 residue 191 HIS Chi-restraints excluded: chain 6 residue 196 LEU Chi-restraints excluded: chain 6 residue 225 ILE Chi-restraints excluded: chain 6 residue 240 LYS Chi-restraints excluded: chain 6 residue 260 THR Chi-restraints excluded: chain 6 residue 282 LEU Chi-restraints excluded: chain 6 residue 321 SER Chi-restraints excluded: chain 6 residue 345 THR Chi-restraints excluded: chain 6 residue 354 LEU Chi-restraints excluded: chain 6 residue 427 ILE Chi-restraints excluded: chain 6 residue 547 ILE Chi-restraints excluded: chain 6 residue 582 ILE Chi-restraints excluded: chain 6 residue 588 VAL Chi-restraints excluded: chain 6 residue 648 ASP Chi-restraints excluded: chain 6 residue 666 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 TYR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 101 PHE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain M residue 64 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 78 THR Chi-restraints excluded: chain M residue 107 GLU Chi-restraints excluded: chain Q residue 126 GLN Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 43 TYR Chi-restraints excluded: chain S residue 62 ASN Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 114 HIS Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain e residue 76 VAL Chi-restraints excluded: chain e residue 91 THR Chi-restraints excluded: chain f residue 5 HIS Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain f residue 67 MET Chi-restraints excluded: chain f residue 106 ASN Chi-restraints excluded: chain z residue 19 VAL Chi-restraints excluded: chain z residue 73 HIS Chi-restraints excluded: chain z residue 169 ILE Chi-restraints excluded: chain z residue 220 ILE Chi-restraints excluded: chain z residue 246 THR Chi-restraints excluded: chain O residue 9 ILE Chi-restraints excluded: chain O residue 19 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 120 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 599 random chunks: chunk 525 optimal weight: 10.0000 chunk 553 optimal weight: 10.0000 chunk 504 optimal weight: 10.0000 chunk 538 optimal weight: 9.9990 chunk 552 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 chunk 234 optimal weight: 0.0030 chunk 422 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 486 optimal weight: 3.9990 chunk 508 optimal weight: 10.0000 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: