Starting phenix.real_space_refine on Tue Jan 21 17:54:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xks_38424/01_2025/8xks_38424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xks_38424/01_2025/8xks_38424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xks_38424/01_2025/8xks_38424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xks_38424/01_2025/8xks_38424.map" model { file = "/net/cci-nas-00/data/ceres_data/8xks_38424/01_2025/8xks_38424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xks_38424/01_2025/8xks_38424.cif" } resolution = 3.2 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1 5.49 5 S 276 5.16 5 C 43084 2.51 5 N 11817 2.21 5 O 12348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 67528 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 5557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5557 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 46, 'TRANS': 668} Chain breaks: 1 Chain: "B" Number of atoms: 4588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4588 Classifications: {'peptide': 603} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 564} Chain breaks: 4 Chain: "C" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3085 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 28, 'TRANS': 362} Chain breaks: 2 Chain: "D" Number of atoms: 7551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7551 Classifications: {'peptide': 971} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 913} Chain breaks: 2 Chain: "E" Number of atoms: 12035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1458, 12035 Classifications: {'peptide': 1458} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1409} Chain breaks: 27 Chain: "F" Number of atoms: 5216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5216 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 33, 'TRANS': 642} Chain breaks: 3 Chain: "G" Number of atoms: 5260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5260 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 35, 'TRANS': 638} Chain breaks: 5 Chain: "H" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3670 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 37, 'TRANS': 462} Chain breaks: 1 Chain: "I" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1619 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 13, 'TRANS': 190} Chain breaks: 1 Chain: "J" Number of atoms: 2101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2101 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain breaks: 1 Chain: "K" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2853 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 26, 'TRANS': 343} Chain: "L" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1541 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 17, 'TRANS': 167} Chain: "M" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1127 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "N" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1005 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 9, 'TRANS': 115} Chain: "O" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1517 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 192} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3245 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 379} Chain: "Q" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2880 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 1 Chain: "R" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 633 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "S" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 909 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain: "T" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 840 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'DGA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'DGD': 1, 'LMG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 Chain: "K" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'ACD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ACD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'DGD': 1, 'LMG': 1, 'SQD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10646 SG CYS C 58 83.793 143.556 152.841 1.00 32.84 S ATOM 10672 SG CYS C 61 86.230 143.509 155.883 1.00 33.92 S ATOM 12261 SG CYS C 306 82.461 144.225 156.490 1.00 24.06 S ATOM 12284 SG CYS C 309 83.587 141.093 154.546 1.00 29.23 S ATOM 10722 SG CYS C 69 80.736 148.477 169.727 1.00 49.25 S ATOM 10740 SG CYS C 72 81.714 150.819 172.719 1.00 39.22 S ATOM 10754 SG CYS C 113 78.378 149.057 172.901 1.00 39.49 S ATOM 10778 SG CYS C 116 81.252 146.799 172.445 1.00 35.47 S Time building chain proxies: 27.17, per 1000 atoms: 0.40 Number of scatterers: 67528 At special positions: 0 Unit cell: (170.56, 239.2, 227.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 276 16.00 P 1 15.00 O 12348 8.00 N 11817 7.00 C 43084 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS P 136 " - pdb=" SG CYS P 189 " distance=1.99 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.45 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 58 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 61 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 306 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 309 " pdb=" ZN C 502 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 116 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 69 " pdb="ZN ZN C 502 " - pdb=" SG CYS C 72 " Number of angles added : 12 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15924 Finding SS restraints... Secondary structure from input PDB file: 395 helices and 41 sheets defined 55.7% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.47 Creating SS restraints... Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 161 through 172 Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 244 through 256 removed outlier: 3.723A pdb=" N VAL A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 361 through 382 Proline residue: A 379 - end of helix Processing helix chain 'A' and resid 593 through 604 Processing helix chain 'A' and resid 614 through 621 Processing helix chain 'A' and resid 626 through 644 removed outlier: 5.125A pdb=" N ASN A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 663 removed outlier: 3.884A pdb=" N PHE A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 697 removed outlier: 3.573A pdb=" N LEU A 679 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLU A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 757 removed outlier: 4.285A pdb=" N GLY A 748 " --> pdb=" O LEU A 744 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLY A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 779 removed outlier: 4.437A pdb=" N ALA A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASP A 766 " --> pdb=" O PHE A 762 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 772 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 789 removed outlier: 4.093A pdb=" N ALA A 789 " --> pdb=" O ALA A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 804 removed outlier: 3.759A pdb=" N PHE A 803 " --> pdb=" O SER A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 4.225A pdb=" N PHE A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ALA A 823 " --> pdb=" O MET A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 833 removed outlier: 3.647A pdb=" N ARG A 833 " --> pdb=" O GLU A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 869 Processing helix chain 'A' and resid 869 through 884 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.988A pdb=" N LEU A 912 " --> pdb=" O ALA A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 940 Processing helix chain 'A' and resid 944 through 954 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 137 through 147 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 509 through 523 removed outlier: 4.366A pdb=" N GLU B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 547 through 560 removed outlier: 3.627A pdb=" N ALA B 552 " --> pdb=" O LYS B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 594 Processing helix chain 'B' and resid 603 through 606 removed outlier: 3.553A pdb=" N VAL B 606 " --> pdb=" O LEU B 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 603 through 606' Processing helix chain 'B' and resid 617 through 632 Processing helix chain 'B' and resid 673 through 680 Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 707 through 721 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 755 through 776 Processing helix chain 'B' and resid 803 through 810 Processing helix chain 'B' and resid 813 through 836 removed outlier: 4.275A pdb=" N GLY B 827 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 840 Processing helix chain 'B' and resid 841 through 843 No H-bonds generated for 'chain 'B' and resid 841 through 843' Processing helix chain 'B' and resid 844 through 861 removed outlier: 3.764A pdb=" N GLN B 849 " --> pdb=" O GLN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 930 removed outlier: 3.610A pdb=" N VAL B 906 " --> pdb=" O ARG B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 945 Processing helix chain 'B' and resid 949 through 960 Processing helix chain 'B' and resid 961 through 971 Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.677A pdb=" N PHE C 9 " --> pdb=" O SER C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 20 removed outlier: 4.408A pdb=" N SER C 20 " --> pdb=" O ASP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 50 Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.714A pdb=" N ASP C 123 " --> pdb=" O CYS C 120 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA C 124 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU C 125 " --> pdb=" O TRP C 122 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 126 " --> pdb=" O ASP C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 126' Processing helix chain 'C' and resid 127 through 143 removed outlier: 3.955A pdb=" N TYR C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR C 142 " --> pdb=" O ARG C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 159 Processing helix chain 'C' and resid 182 through 192 Processing helix chain 'C' and resid 192 through 204 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.598A pdb=" N ARG C 247 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR C 248 " --> pdb=" O PRO C 245 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N GLN C 249 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS C 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 289 removed outlier: 3.720A pdb=" N GLN C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 removed outlier: 3.688A pdb=" N GLY C 327 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 328 " --> pdb=" O MET C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 328' Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 398 through 408 Processing helix chain 'C' and resid 409 through 413 Processing helix chain 'C' and resid 427 through 442 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 131 through 137 removed outlier: 3.895A pdb=" N THR D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 153 through 167 Processing helix chain 'D' and resid 169 through 181 removed outlier: 3.924A pdb=" N LYS D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 230 through 233 Processing helix chain 'D' and resid 265 through 269 Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 291 through 296 removed outlier: 3.522A pdb=" N GLY D 296 " --> pdb=" O PHE D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 306 Processing helix chain 'D' and resid 340 through 344 Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 353 through 373 Processing helix chain 'D' and resid 416 through 426 Processing helix chain 'D' and resid 455 through 470 Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.718A pdb=" N VAL D 478 " --> pdb=" O TYR D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 508 removed outlier: 3.807A pdb=" N GLU D 508 " --> pdb=" O ALA D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 520 removed outlier: 3.760A pdb=" N VAL D 520 " --> pdb=" O SER D 517 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 517 through 520' Processing helix chain 'D' and resid 525 through 541 Processing helix chain 'D' and resid 551 through 556 Processing helix chain 'D' and resid 564 through 586 removed outlier: 3.866A pdb=" N ALA D 585 " --> pdb=" O MET D 581 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN D 586 " --> pdb=" O ASP D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'D' and resid 623 through 635 Processing helix chain 'D' and resid 643 through 654 removed outlier: 3.623A pdb=" N LEU D 647 " --> pdb=" O ASP D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 673 removed outlier: 3.587A pdb=" N ALA D 671 " --> pdb=" O MET D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 697 removed outlier: 3.924A pdb=" N ASN D 695 " --> pdb=" O VAL D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 725 Processing helix chain 'D' and resid 752 through 757 Processing helix chain 'D' and resid 764 through 769 Processing helix chain 'D' and resid 788 through 795 Processing helix chain 'D' and resid 796 through 811 removed outlier: 3.743A pdb=" N LEU D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 803 " --> pdb=" O PRO D 799 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG D 804 " --> pdb=" O LEU D 800 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 807 " --> pdb=" O GLY D 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 820 removed outlier: 3.721A pdb=" N THR D 820 " --> pdb=" O SER D 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 817 through 820' Processing helix chain 'D' and resid 821 through 836 removed outlier: 3.693A pdb=" N ALA D 825 " --> pdb=" O ALA D 821 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP D 826 " --> pdb=" O GLN D 822 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE D 828 " --> pdb=" O LEU D 824 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU D 829 " --> pdb=" O ALA D 825 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 877 Processing helix chain 'D' and resid 878 through 901 Processing helix chain 'D' and resid 901 through 914 Processing helix chain 'D' and resid 922 through 932 Processing helix chain 'D' and resid 947 through 952 Processing helix chain 'D' and resid 957 through 967 removed outlier: 4.189A pdb=" N LEU D 961 " --> pdb=" O GLU D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1031 Processing helix chain 'D' and resid 1036 through 1041 Processing helix chain 'D' and resid 1041 through 1057 Processing helix chain 'D' and resid 1058 through 1074 Processing helix chain 'D' and resid 1088 through 1093 Processing helix chain 'D' and resid 1107 through 1112 Processing helix chain 'D' and resid 1122 through 1128 removed outlier: 3.766A pdb=" N ILE D1126 " --> pdb=" O SER D1122 " (cutoff:3.500A) Processing helix chain 'D' and resid 1129 through 1136 Processing helix chain 'D' and resid 1144 through 1148 removed outlier: 3.717A pdb=" N ILE D1147 " --> pdb=" O GLU D1144 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 276 Processing helix chain 'E' and resid 331 through 334 Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.694A pdb=" N VAL E 339 " --> pdb=" O TRP E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 448 through 474 Processing helix chain 'E' and resid 548 through 557 Processing helix chain 'E' and resid 566 through 575 Processing helix chain 'E' and resid 618 through 622 removed outlier: 4.213A pdb=" N TYR E 622 " --> pdb=" O LEU E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 624 through 644 removed outlier: 3.900A pdb=" N ILE E 629 " --> pdb=" O ALA E 625 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN E 630 " --> pdb=" O LEU E 626 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 828 removed outlier: 3.813A pdb=" N TYR E 813 " --> pdb=" O ARG E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 890 through 897 Processing helix chain 'E' and resid 937 through 957 Processing helix chain 'E' and resid 973 through 989 removed outlier: 4.502A pdb=" N ARG E 979 " --> pdb=" O TRP E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 990 through 993 Processing helix chain 'E' and resid 1159 through 1172 Processing helix chain 'E' and resid 1181 through 1185 removed outlier: 4.079A pdb=" N LEU E1185 " --> pdb=" O TRP E1182 " (cutoff:3.500A) Processing helix chain 'E' and resid 1221 through 1236 Processing helix chain 'E' and resid 1249 through 1263 removed outlier: 3.535A pdb=" N TRP E1255 " --> pdb=" O ARG E1251 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR E1257 " --> pdb=" O ASN E1253 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN E1258 " --> pdb=" O LEU E1254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG E1261 " --> pdb=" O THR E1257 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN E1262 " --> pdb=" O GLN E1258 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLN E1263 " --> pdb=" O LYS E1259 " (cutoff:3.500A) Processing helix chain 'E' and resid 1291 through 1309 removed outlier: 4.209A pdb=" N ILE E1297 " --> pdb=" O SER E1293 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER E1298 " --> pdb=" O LYS E1294 " (cutoff:3.500A) Processing helix chain 'E' and resid 1335 through 1340 Processing helix chain 'E' and resid 1361 through 1375 removed outlier: 4.023A pdb=" N SER E1365 " --> pdb=" O GLU E1361 " (cutoff:3.500A) Processing helix chain 'E' and resid 1378 through 1382 Processing helix chain 'E' and resid 1387 through 1412 Processing helix chain 'E' and resid 1413 through 1445 Processing helix chain 'E' and resid 1676 through 1691 removed outlier: 3.907A pdb=" N ASP E1680 " --> pdb=" O PRO E1676 " (cutoff:3.500A) Processing helix chain 'E' and resid 1693 through 1703 Processing helix chain 'E' and resid 1732 through 1759 Processing helix chain 'E' and resid 1762 through 1777 removed outlier: 3.575A pdb=" N GLY E1772 " --> pdb=" O ARG E1768 " (cutoff:3.500A) Processing helix chain 'E' and resid 1778 through 1780 No H-bonds generated for 'chain 'E' and resid 1778 through 1780' Processing helix chain 'E' and resid 1781 through 1790 removed outlier: 4.122A pdb=" N THR E1785 " --> pdb=" O ASP E1781 " (cutoff:3.500A) Processing helix chain 'E' and resid 1793 through 1797 removed outlier: 3.553A pdb=" N LEU E1797 " --> pdb=" O VAL E1794 " (cutoff:3.500A) Processing helix chain 'E' and resid 1801 through 1813 removed outlier: 3.915A pdb=" N ASN E1805 " --> pdb=" O LYS E1801 " (cutoff:3.500A) Processing helix chain 'E' and resid 1980 through 1984 Processing helix chain 'E' and resid 1990 through 2007 removed outlier: 3.852A pdb=" N GLN E1994 " --> pdb=" O ASN E1990 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLN E1995 " --> pdb=" O SER E1991 " (cutoff:3.500A) Proline residue: E1996 - end of helix Processing helix chain 'E' and resid 2031 through 2045 Processing helix chain 'E' and resid 2054 through 2057 Processing helix chain 'E' and resid 2064 through 2077 removed outlier: 3.726A pdb=" N LYS E2068 " --> pdb=" O ALA E2064 " (cutoff:3.500A) Processing helix chain 'E' and resid 2078 through 2080 No H-bonds generated for 'chain 'E' and resid 2078 through 2080' Processing helix chain 'E' and resid 2115 through 2120 Processing helix chain 'E' and resid 2126 through 2143 removed outlier: 3.606A pdb=" N ASN E2131 " --> pdb=" O VAL E2127 " (cutoff:3.500A) Processing helix chain 'E' and resid 2157 through 2169 removed outlier: 3.616A pdb=" N LEU E2161 " --> pdb=" O ILE E2157 " (cutoff:3.500A) Processing helix chain 'E' and resid 2235 through 2243 Processing helix chain 'E' and resid 2260 through 2266 Processing helix chain 'E' and resid 2268 through 2272 Processing helix chain 'E' and resid 2274 through 2290 Processing helix chain 'E' and resid 2295 through 2305 removed outlier: 3.926A pdb=" N VAL E2301 " --> pdb=" O THR E2297 " (cutoff:3.500A) Processing helix chain 'E' and resid 2326 through 2330 Processing helix chain 'E' and resid 2347 through 2360 removed outlier: 5.141A pdb=" N LYS E2353 " --> pdb=" O LEU E2349 " (cutoff:3.500A) Processing helix chain 'E' and resid 2367 through 2375 removed outlier: 3.905A pdb=" N ILE E2372 " --> pdb=" O LYS E2369 " (cutoff:3.500A) Processing helix chain 'E' and resid 2411 through 2422 removed outlier: 3.820A pdb=" N TYR E2415 " --> pdb=" O ASN E2411 " (cutoff:3.500A) Processing helix chain 'E' and resid 2446 through 2460 removed outlier: 3.707A pdb=" N ILE E2450 " --> pdb=" O ASN E2446 " (cutoff:3.500A) Processing helix chain 'E' and resid 2504 through 2531 Processing helix chain 'E' and resid 2561 through 2571 Processing helix chain 'E' and resid 2573 through 2594 removed outlier: 3.695A pdb=" N GLN E2580 " --> pdb=" O LYS E2576 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLY E2587 " --> pdb=" O LEU E2583 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N LYS E2588 " --> pdb=" O ILE E2584 " (cutoff:3.500A) Processing helix chain 'E' and resid 2598 through 2603 Processing helix chain 'E' and resid 2631 through 2636 removed outlier: 4.414A pdb=" N ALA E2635 " --> pdb=" O LEU E2631 " (cutoff:3.500A) Processing helix chain 'E' and resid 2637 through 2640 removed outlier: 4.287A pdb=" N ALA E2640 " --> pdb=" O SER E2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2637 through 2640' Processing helix chain 'E' and resid 2652 through 2668 removed outlier: 3.534A pdb=" N LYS E2667 " --> pdb=" O SER E2663 " (cutoff:3.500A) Processing helix chain 'E' and resid 2673 through 2677 Processing helix chain 'E' and resid 2701 through 2717 removed outlier: 3.750A pdb=" N ASN E2709 " --> pdb=" O LYS E2705 " (cutoff:3.500A) Processing helix chain 'E' and resid 2731 through 2749 Processing helix chain 'E' and resid 2774 through 2779 removed outlier: 4.109A pdb=" N THR E2779 " --> pdb=" O SER E2776 " (cutoff:3.500A) Processing helix chain 'E' and resid 2788 through 2796 removed outlier: 3.569A pdb=" N TYR E2792 " --> pdb=" O ASN E2788 " (cutoff:3.500A) Processing helix chain 'E' and resid 2818 through 2824 Processing helix chain 'E' and resid 2895 through 2918 removed outlier: 3.902A pdb=" N THR E2904 " --> pdb=" O GLU E2900 " (cutoff:3.500A) Processing helix chain 'E' and resid 2920 through 2933 removed outlier: 3.808A pdb=" N THR E2933 " --> pdb=" O ASN E2929 " (cutoff:3.500A) Processing helix chain 'E' and resid 2958 through 2968 removed outlier: 3.573A pdb=" N LEU E2964 " --> pdb=" O LYS E2960 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 374 through 382 removed outlier: 4.789A pdb=" N SER F 380 " --> pdb=" O ASP F 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 421 removed outlier: 4.556A pdb=" N VAL F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) Proline residue: F 409 - end of helix Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.736A pdb=" N GLU F 443 " --> pdb=" O ARG F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 471 through 475 Processing helix chain 'F' and resid 481 through 494 Processing helix chain 'F' and resid 494 through 500 Processing helix chain 'F' and resid 518 through 531 Processing helix chain 'F' and resid 549 through 564 Processing helix chain 'F' and resid 588 through 601 Processing helix chain 'F' and resid 642 through 657 removed outlier: 4.009A pdb=" N ASN F 656 " --> pdb=" O VAL F 652 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS F 657 " --> pdb=" O HIS F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 672 Processing helix chain 'F' and resid 676 through 695 removed outlier: 3.663A pdb=" N VAL F 680 " --> pdb=" O THR F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 718 Processing helix chain 'F' and resid 742 through 762 Processing helix chain 'F' and resid 776 through 779 Processing helix chain 'F' and resid 789 through 794 removed outlier: 3.648A pdb=" N ASN F 793 " --> pdb=" O ASP F 789 " (cutoff:3.500A) Processing helix chain 'F' and resid 799 through 822 removed outlier: 4.140A pdb=" N GLY F 813 " --> pdb=" O VAL F 809 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ARG F 814 " --> pdb=" O HIS F 810 " (cutoff:3.500A) Processing helix chain 'F' and resid 827 through 829 No H-bonds generated for 'chain 'F' and resid 827 through 829' Processing helix chain 'F' and resid 830 through 847 Processing helix chain 'F' and resid 895 through 924 Processing helix chain 'F' and resid 924 through 939 Processing helix chain 'F' and resid 943 through 953 Processing helix chain 'F' and resid 1006 through 1011 Processing helix chain 'F' and resid 1029 through 1033 Processing helix chain 'G' and resid 143 through 160 Processing helix chain 'G' and resid 168 through 181 Processing helix chain 'G' and resid 186 through 192 Processing helix chain 'G' and resid 197 through 201 removed outlier: 3.622A pdb=" N VAL G 201 " --> pdb=" O PRO G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 218 Processing helix chain 'G' and resid 292 through 302 Processing helix chain 'G' and resid 323 through 333 Processing helix chain 'G' and resid 373 through 381 Processing helix chain 'G' and resid 393 through 398 Processing helix chain 'G' and resid 399 through 422 Proline residue: G 409 - end of helix removed outlier: 3.945A pdb=" N ILE G 420 " --> pdb=" O LEU G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 446 removed outlier: 4.365A pdb=" N ARG G 442 " --> pdb=" O ILE G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 475 Processing helix chain 'G' and resid 480 through 494 removed outlier: 4.282A pdb=" N GLU G 484 " --> pdb=" O GLU G 480 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G 488 " --> pdb=" O GLU G 484 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 531 Processing helix chain 'G' and resid 539 through 543 removed outlier: 4.089A pdb=" N TYR G 543 " --> pdb=" O GLY G 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 539 through 543' Processing helix chain 'G' and resid 548 through 564 removed outlier: 3.820A pdb=" N ARG G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 577 Processing helix chain 'G' and resid 587 through 603 removed outlier: 3.780A pdb=" N ALA G 591 " --> pdb=" O GLY G 587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY G 603 " --> pdb=" O VAL G 599 " (cutoff:3.500A) Processing helix chain 'G' and resid 618 through 622 Processing helix chain 'G' and resid 742 through 763 Processing helix chain 'G' and resid 799 through 822 removed outlier: 4.300A pdb=" N GLY G 813 " --> pdb=" O VAL G 809 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG G 814 " --> pdb=" O HIS G 810 " (cutoff:3.500A) Processing helix chain 'G' and resid 827 through 829 No H-bonds generated for 'chain 'G' and resid 827 through 829' Processing helix chain 'G' and resid 830 through 847 Processing helix chain 'G' and resid 895 through 923 Processing helix chain 'G' and resid 924 through 939 Processing helix chain 'G' and resid 943 through 954 Processing helix chain 'G' and resid 1046 through 1057 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 159 through 169 Processing helix chain 'H' and resid 170 through 178 removed outlier: 3.840A pdb=" N ALA H 174 " --> pdb=" O ASN H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 207 Processing helix chain 'H' and resid 208 through 210 No H-bonds generated for 'chain 'H' and resid 208 through 210' Processing helix chain 'H' and resid 218 through 223 Processing helix chain 'H' and resid 263 through 271 Processing helix chain 'H' and resid 278 through 285 Processing helix chain 'H' and resid 285 through 295 removed outlier: 3.820A pdb=" N ALA H 289 " --> pdb=" O ASP H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 300 Processing helix chain 'H' and resid 313 through 329 Processing helix chain 'H' and resid 354 through 360 Processing helix chain 'H' and resid 364 through 374 Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.604A pdb=" N GLY H 392 " --> pdb=" O VAL H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 397 through 406 Processing helix chain 'H' and resid 462 through 466 Processing helix chain 'H' and resid 477 through 490 Processing helix chain 'H' and resid 495 through 506 Processing helix chain 'H' and resid 506 through 511 Processing helix chain 'H' and resid 559 through 581 removed outlier: 3.511A pdb=" N ALA H 581 " --> pdb=" O LEU H 577 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 636 Processing helix chain 'H' and resid 637 through 650 Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 102 through 117 removed outlier: 3.580A pdb=" N ALA I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 124 removed outlier: 3.701A pdb=" N ALA I 121 " --> pdb=" O ASN I 117 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG I 122 " --> pdb=" O PRO I 118 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP I 123 " --> pdb=" O ARG I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 140 removed outlier: 3.848A pdb=" N THR I 140 " --> pdb=" O GLU I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 removed outlier: 3.691A pdb=" N THR I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 170 removed outlier: 3.635A pdb=" N ASP I 170 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 220 Processing helix chain 'I' and resid 292 through 301 removed outlier: 3.719A pdb=" N MET I 298 " --> pdb=" O VAL I 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 303 through 310 removed outlier: 3.769A pdb=" N ALA I 307 " --> pdb=" O GLY I 303 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 93 Processing helix chain 'J' and resid 96 through 125 Processing helix chain 'J' and resid 133 through 139 Processing helix chain 'J' and resid 142 through 157 removed outlier: 3.518A pdb=" N ILE J 157 " --> pdb=" O GLU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 238 Processing helix chain 'J' and resid 240 through 245 Processing helix chain 'J' and resid 246 through 260 removed outlier: 3.780A pdb=" N LEU J 252 " --> pdb=" O GLY J 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 289 Processing helix chain 'J' and resid 291 through 295 Processing helix chain 'J' and resid 298 through 303 removed outlier: 3.703A pdb=" N ALA J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 324 Processing helix chain 'J' and resid 345 through 356 Processing helix chain 'K' and resid 65 through 69 removed outlier: 3.807A pdb=" N TRP K 68 " --> pdb=" O ALA K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 90 removed outlier: 3.837A pdb=" N GLN K 88 " --> pdb=" O LEU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 123 Proline residue: K 109 - end of helix Processing helix chain 'K' and resid 128 through 155 Processing helix chain 'K' and resid 162 through 175 Processing helix chain 'K' and resid 176 through 178 No H-bonds generated for 'chain 'K' and resid 176 through 178' Processing helix chain 'K' and resid 180 through 194 Processing helix chain 'K' and resid 210 through 219 Processing helix chain 'K' and resid 225 through 235 removed outlier: 3.668A pdb=" N ALA K 231 " --> pdb=" O ALA K 227 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG K 232 " --> pdb=" O MET K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 242 Processing helix chain 'K' and resid 243 through 252 removed outlier: 3.756A pdb=" N TRP K 252 " --> pdb=" O TRP K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 260 removed outlier: 6.503A pdb=" N LEU K 257 " --> pdb=" O GLY K 254 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG K 258 " --> pdb=" O LEU K 255 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS K 259 " --> pdb=" O ASP K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 263 No H-bonds generated for 'chain 'K' and resid 261 through 263' Processing helix chain 'K' and resid 264 through 288 Proline residue: K 275 - end of helix removed outlier: 4.520A pdb=" N LEU K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) Proline residue: K 284 - end of helix Processing helix chain 'K' and resid 292 through 297 removed outlier: 3.653A pdb=" N SER K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 318 removed outlier: 3.886A pdb=" N HIS K 318 " --> pdb=" O SER K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 339 Processing helix chain 'K' and resid 348 through 355 Processing helix chain 'K' and resid 361 through 367 Processing helix chain 'K' and resid 371 through 373 No H-bonds generated for 'chain 'K' and resid 371 through 373' Processing helix chain 'K' and resid 374 through 386 Processing helix chain 'K' and resid 396 through 406 removed outlier: 3.664A pdb=" N LEU K 400 " --> pdb=" O SER K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 419 through 430 removed outlier: 3.561A pdb=" N VAL K 423 " --> pdb=" O PRO K 419 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU K 426 " --> pdb=" O GLU K 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 79 Processing helix chain 'L' and resid 87 through 92 removed outlier: 3.725A pdb=" N LYS L 91 " --> pdb=" O PHE L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 122 removed outlier: 3.951A pdb=" N LEU L 115 " --> pdb=" O THR L 111 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL L 116 " --> pdb=" O VAL L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 164 Processing helix chain 'L' and resid 174 through 183 Processing helix chain 'L' and resid 187 through 202 Processing helix chain 'M' and resid 129 through 144 removed outlier: 3.792A pdb=" N ALA M 136 " --> pdb=" O ALA M 132 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL M 137 " --> pdb=" O VAL M 133 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE M 144 " --> pdb=" O TRP M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 168 removed outlier: 3.812A pdb=" N GLU M 168 " --> pdb=" O ARG M 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 176 Processing helix chain 'M' and resid 182 through 196 removed outlier: 4.075A pdb=" N ILE M 186 " --> pdb=" O LEU M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 204 Processing helix chain 'M' and resid 204 through 216 Processing helix chain 'M' and resid 223 through 232 removed outlier: 3.647A pdb=" N TRP M 227 " --> pdb=" O THR M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 254 removed outlier: 4.873A pdb=" N VAL M 251 " --> pdb=" O GLN M 247 " (cutoff:3.500A) Proline residue: M 252 - end of helix Processing helix chain 'N' and resid 15 through 36 Proline residue: N 21 - end of helix Processing helix chain 'N' and resid 47 through 52 Processing helix chain 'N' and resid 65 through 73 removed outlier: 3.501A pdb=" N ALA N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 104 Processing helix chain 'N' and resid 109 through 114 Processing helix chain 'N' and resid 126 through 132 Processing helix chain 'O' and resid 111 through 113 No H-bonds generated for 'chain 'O' and resid 111 through 113' Processing helix chain 'O' and resid 114 through 127 Processing helix chain 'O' and resid 145 through 166 removed outlier: 3.649A pdb=" N GLN O 149 " --> pdb=" O CYS O 145 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN O 166 " --> pdb=" O ALA O 162 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 251 Processing helix chain 'O' and resid 281 through 301 removed outlier: 4.030A pdb=" N ALA O 287 " --> pdb=" O ARG O 283 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU O 290 " --> pdb=" O ALA O 286 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU O 291 " --> pdb=" O ALA O 287 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU O 292 " --> pdb=" O GLY O 288 " (cutoff:3.500A) Processing helix chain 'O' and resid 341 through 366 removed outlier: 4.037A pdb=" N TYR O 345 " --> pdb=" O ASN O 341 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU O 347 " --> pdb=" O THR O 343 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU O 348 " --> pdb=" O ILE O 344 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR O 364 " --> pdb=" O SER O 360 " (cutoff:3.500A) Processing helix chain 'O' and resid 376 through 397 Proline residue: O 382 - end of helix Processing helix chain 'O' and resid 401 through 429 removed outlier: 3.591A pdb=" N SER O 405 " --> pdb=" O PHE O 401 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL O 406 " --> pdb=" O ASP O 402 " (cutoff:3.500A) Processing helix chain 'O' and resid 431 through 436 Processing helix chain 'P' and resid 24 through 53 removed outlier: 5.097A pdb=" N GLN P 50 " --> pdb=" O GLN P 46 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE P 51 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 59 Processing helix chain 'P' and resid 60 through 69 Processing helix chain 'P' and resid 75 through 85 Processing helix chain 'P' and resid 93 through 102 Processing helix chain 'P' and resid 113 through 131 Processing helix chain 'P' and resid 139 through 144 removed outlier: 3.785A pdb=" N TRP P 143 " --> pdb=" O PRO P 139 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 168 Processing helix chain 'P' and resid 253 through 268 Processing helix chain 'P' and resid 281 through 285 removed outlier: 4.084A pdb=" N LYS P 284 " --> pdb=" O TRP P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 297 through 319 Processing helix chain 'P' and resid 332 through 354 Processing helix chain 'P' and resid 358 through 362 Processing helix chain 'P' and resid 368 through 376 Processing helix chain 'P' and resid 395 through 405 Processing helix chain 'P' and resid 409 through 427 Processing helix chain 'Q' and resid 108 through 127 removed outlier: 3.600A pdb=" N ALA Q 120 " --> pdb=" O CYS Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 131 removed outlier: 3.652A pdb=" N GLN Q 131 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 128 through 131' Processing helix chain 'Q' and resid 134 through 142 removed outlier: 3.614A pdb=" N ARG Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 182 Processing helix chain 'Q' and resid 185 through 196 Processing helix chain 'Q' and resid 224 through 236 Processing helix chain 'Q' and resid 242 through 248 removed outlier: 4.294A pdb=" N LEU Q 246 " --> pdb=" O LYS Q 242 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU Q 248 " --> pdb=" O PRO Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 251 through 258 Processing helix chain 'Q' and resid 259 through 261 No H-bonds generated for 'chain 'Q' and resid 259 through 261' Processing helix chain 'Q' and resid 265 through 269 Processing helix chain 'Q' and resid 276 through 281 removed outlier: 3.886A pdb=" N ARG Q 281 " --> pdb=" O GLY Q 277 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 289 Processing helix chain 'Q' and resid 294 through 305 Processing helix chain 'Q' and resid 311 through 331 Processing helix chain 'Q' and resid 340 through 352 Processing helix chain 'Q' and resid 355 through 368 removed outlier: 3.688A pdb=" N ASN Q 368 " --> pdb=" O LEU Q 364 " (cutoff:3.500A) Processing helix chain 'Q' and resid 377 through 383 removed outlier: 3.746A pdb=" N ALA Q 383 " --> pdb=" O ARG Q 379 " (cutoff:3.500A) Processing helix chain 'Q' and resid 384 through 398 Processing helix chain 'Q' and resid 399 through 402 Processing helix chain 'Q' and resid 405 through 419 Processing helix chain 'Q' and resid 423 through 434 Processing helix chain 'Q' and resid 437 through 453 Processing helix chain 'Q' and resid 459 through 468 Processing helix chain 'Q' and resid 473 through 489 Processing helix chain 'R' and resid 8 through 25 Processing helix chain 'R' and resid 36 through 41 Processing helix chain 'R' and resid 43 through 59 Processing helix chain 'R' and resid 66 through 70 removed outlier: 3.625A pdb=" N ILE R 70 " --> pdb=" O ALA R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 88 removed outlier: 4.006A pdb=" N GLY R 88 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 15 Processing helix chain 'S' and resid 31 through 46 Processing helix chain 'S' and resid 47 through 71 Processing helix chain 'S' and resid 85 through 90 Processing helix chain 'S' and resid 101 through 116 removed outlier: 4.058A pdb=" N ARG S 105 " --> pdb=" O ASP S 101 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 23 Processing helix chain 'T' and resid 28 through 37 Processing helix chain 'T' and resid 43 through 47 Processing helix chain 'T' and resid 50 through 56 removed outlier: 3.560A pdb=" N ALA T 56 " --> pdb=" O ALA T 52 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 83 removed outlier: 3.790A pdb=" N ALA T 67 " --> pdb=" O ALA T 63 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL T 71 " --> pdb=" O ALA T 67 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR T 75 " --> pdb=" O VAL T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 102 removed outlier: 3.740A pdb=" N ILE T 95 " --> pdb=" O GLU T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 84 Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 222 removed outlier: 6.700A pdb=" N LEU A 188 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N HIS A 299 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL A 190 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 259 through 260 Processing sheet with id=AA5, first strand: chain 'A' and resid 720 through 722 removed outlier: 3.617A pdb=" N ARG A 707 " --> pdb=" O MET A 721 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 132 removed outlier: 7.153A pdb=" N SER B 79 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N SER B 152 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL B 81 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'B' and resid 537 through 541 removed outlier: 6.497A pdb=" N VAL B 538 " --> pdb=" O GLY B 645 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N THR B 647 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU B 540 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE B 598 " --> pdb=" O MET B 644 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ALA B 646 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE B 600 " --> pdb=" O ALA B 646 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 797 through 800 Processing sheet with id=AB1, first strand: chain 'B' and resid 879 through 882 removed outlier: 8.783A pdb=" N GLN E2871 " --> pdb=" O PHE B 889 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN B 891 " --> pdb=" O GLN E2871 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N TYR E2873 " --> pdb=" O GLN B 891 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR B 893 " --> pdb=" O TYR E2873 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 55 through 57 Processing sheet with id=AB3, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AB4, first strand: chain 'D' and resid 281 through 287 Processing sheet with id=AB5, first strand: chain 'D' and resid 256 through 257 Processing sheet with id=AB6, first strand: chain 'D' and resid 311 through 312 removed outlier: 4.401A pdb=" N TYR D 319 " --> pdb=" O LEU G 185 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 430 through 432 removed outlier: 6.005A pdb=" N ILE D 546 " --> pdb=" O ILE D 594 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ALA D 596 " --> pdb=" O ILE D 546 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 548 " --> pdb=" O ALA D 596 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE D 486 " --> pdb=" O GLY D 595 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR D 597 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N PHE D 488 " --> pdb=" O THR D 597 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 747 through 750 Processing sheet with id=AB9, first strand: chain 'D' and resid 775 through 777 Processing sheet with id=AC1, first strand: chain 'D' and resid 1118 through 1119 Processing sheet with id=AC2, first strand: chain 'E' and resid 738 through 739 removed outlier: 5.247A pdb=" N LEU H 470 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA H 457 " --> pdb=" O LEU H 470 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS H 253 " --> pdb=" O TRP H 237 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TRP H 237 " --> pdb=" O LYS H 253 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TRP H 255 " --> pdb=" O ALA H 235 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ALA H 235 " --> pdb=" O TRP H 255 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU H 257 " --> pdb=" O ARG H 233 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG H 233 " --> pdb=" O LEU H 257 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA H 259 " --> pdb=" O VAL H 231 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS E 542 " --> pdb=" O GLN H 230 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR E 745 " --> pdb=" O SER E 545 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYS E 746 " --> pdb=" O ALA H 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 2047 through 2052 removed outlier: 7.073A pdb=" N LYS E2047 " --> pdb=" O ILE E2084 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU E2086 " --> pdb=" O LYS E2047 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE E2049 " --> pdb=" O LEU E2086 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLU E2088 " --> pdb=" O ILE E2049 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASP E2051 " --> pdb=" O GLU E2088 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS E2015 " --> pdb=" O VAL E2314 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA E2316 " --> pdb=" O LYS E2015 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E2017 " --> pdb=" O ALA E2316 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR E2318 " --> pdb=" O ILE E2017 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU E2019 " --> pdb=" O THR E2318 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE E2338 " --> pdb=" O ASN E2016 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU E2018 " --> pdb=" O ILE E2338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 2880 through 2882 Processing sheet with id=AC5, first strand: chain 'E' and resid 2936 through 2937 Processing sheet with id=AC6, first strand: chain 'F' and resid 363 through 367 removed outlier: 3.589A pdb=" N VAL F 384 " --> pdb=" O ALA F 337 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE F 341 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 509 through 513 Processing sheet with id=AC8, first strand: chain 'F' and resid 537 through 538 Processing sheet with id=AC9, first strand: chain 'F' and resid 782 through 787 removed outlier: 6.695A pdb=" N PHE F 783 " --> pdb=" O VAL F 772 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL F 772 " --> pdb=" O PHE F 783 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU F 785 " --> pdb=" O ALA F 770 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU F 768 " --> pdb=" O VAL F 787 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 967 through 968 removed outlier: 3.848A pdb=" N GLY F 967 " --> pdb=" O ARG F 975 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 363 through 367 removed outlier: 3.758A pdb=" N LYS G 348 " --> pdb=" O TYR G 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG G 340 " --> pdb=" O MET G 350 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ALA G 337 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP G 386 " --> pdb=" O ALA G 337 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL G 339 " --> pdb=" O ASP G 386 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 533 through 538 removed outlier: 3.823A pdb=" N PHE G 535 " --> pdb=" O ILE G 568 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA G 567 " --> pdb=" O VAL G 611 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU G 613 " --> pdb=" O ALA G 567 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU G 569 " --> pdb=" O LEU G 613 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA G 615 " --> pdb=" O LEU G 569 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE G 571 " --> pdb=" O ALA G 615 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY G 508 " --> pdb=" O ARG G 634 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE G 636 " --> pdb=" O GLY G 508 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU G 510 " --> pdb=" O ILE G 636 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET G 638 " --> pdb=" O LEU G 510 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA G 512 " --> pdb=" O MET G 638 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 782 through 786 removed outlier: 3.992A pdb=" N ARG G 771 " --> pdb=" O LEU G 785 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 860 through 864 Processing sheet with id=AD6, first strand: chain 'H' and resid 311 through 312 Processing sheet with id=AD7, first strand: chain 'H' and resid 536 through 537 removed outlier: 4.413A pdb=" N GLY H 536 " --> pdb=" O VAL I 312 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE I 314 " --> pdb=" O GLY H 536 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU I 189 " --> pdb=" O PRO I 200 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 74 through 79 Processing sheet with id=AD9, first strand: chain 'I' and resid 99 through 100 removed outlier: 6.512A pdb=" N PHE I 99 " --> pdb=" O MET I 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'I' and resid 182 through 185 Processing sheet with id=AE2, first strand: chain 'K' and resid 208 through 209 removed outlier: 6.053A pdb=" N LEU K 208 " --> pdb=" O TYR K 410 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 343 through 346 Processing sheet with id=AE4, first strand: chain 'P' and resid 136 through 137 Processing sheet with id=AE5, first strand: chain 'P' and resid 136 through 137 removed outlier: 3.661A pdb=" N LYS P 195 " --> pdb=" O TYR P 215 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU P 207 " --> pdb=" O ARG P 203 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL P 232 " --> pdb=" O VAL P 236 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VAL P 236 " --> pdb=" O VAL P 232 " (cutoff:3.500A) 3306 hydrogen bonds defined for protein. 9468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.52 Time building geometry restraints manager: 14.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.28: 11154 1.28 - 1.42: 17823 1.42 - 1.57: 39568 1.57 - 1.72: 48 1.72 - 1.86: 491 Bond restraints: 69084 Sorted by residual: bond pdb=" C1 ACD K 501 " pdb=" O1 ACD K 501 " ideal model delta sigma weight residual 1.246 1.490 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C8 ACD K 501 " pdb=" C9 ACD K 501 " ideal model delta sigma weight residual 1.332 1.572 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C11 ACD K 501 " pdb=" C12 ACD K 501 " ideal model delta sigma weight residual 1.332 1.570 -0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" C14 ACD K 501 " pdb=" C15 ACD K 501 " ideal model delta sigma weight residual 1.332 1.569 -0.237 2.00e-02 2.50e+03 1.41e+02 bond pdb=" C5 ACD K 501 " pdb=" C6 ACD K 501 " ideal model delta sigma weight residual 1.332 1.567 -0.235 2.00e-02 2.50e+03 1.39e+02 ... (remaining 69079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 92994 4.36 - 8.72: 686 8.72 - 13.09: 53 13.09 - 17.45: 25 17.45 - 21.81: 4 Bond angle restraints: 93762 Sorted by residual: angle pdb=" N PRO D1096 " pdb=" CD PRO D1096 " pdb=" CG PRO D1096 " ideal model delta sigma weight residual 103.20 83.23 19.97 1.50e+00 4.44e-01 1.77e+02 angle pdb=" CA PRO E1186 " pdb=" N PRO E1186 " pdb=" CD PRO E1186 " ideal model delta sigma weight residual 112.00 94.72 17.28 1.40e+00 5.10e-01 1.52e+02 angle pdb=" CA PRO A 262 " pdb=" N PRO A 262 " pdb=" CD PRO A 262 " ideal model delta sigma weight residual 112.00 96.22 15.78 1.40e+00 5.10e-01 1.27e+02 angle pdb=" CA PRO A 379 " pdb=" N PRO A 379 " pdb=" CD PRO A 379 " ideal model delta sigma weight residual 112.00 96.68 15.32 1.40e+00 5.10e-01 1.20e+02 angle pdb=" N PRO D1096 " pdb=" CA PRO D1096 " pdb=" CB PRO D1096 " ideal model delta sigma weight residual 103.25 94.65 8.60 1.05e+00 9.07e-01 6.70e+01 ... (remaining 93757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.77: 38544 27.77 - 55.54: 2613 55.54 - 83.31: 271 83.31 - 111.08: 48 111.08 - 138.85: 8 Dihedral angle restraints: 41484 sinusoidal: 16776 harmonic: 24708 Sorted by residual: dihedral pdb=" CA ALA G 565 " pdb=" C ALA G 565 " pdb=" N PRO G 566 " pdb=" CA PRO G 566 " ideal model delta harmonic sigma weight residual 180.00 116.34 63.66 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA PHE E 970 " pdb=" C PHE E 970 " pdb=" N PRO E 971 " pdb=" CA PRO E 971 " ideal model delta harmonic sigma weight residual 180.00 135.18 44.82 0 5.00e+00 4.00e-02 8.04e+01 dihedral pdb=" CA SER D1095 " pdb=" C SER D1095 " pdb=" N PRO D1096 " pdb=" CA PRO D1096 " ideal model delta harmonic sigma weight residual 180.00 143.28 36.72 0 5.00e+00 4.00e-02 5.39e+01 ... (remaining 41481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 10142 0.140 - 0.281: 134 0.281 - 0.421: 21 0.421 - 0.561: 5 0.561 - 0.701: 2 Chirality restraints: 10304 Sorted by residual: chirality pdb=" CB VAL O 242 " pdb=" CA VAL O 242 " pdb=" CG1 VAL O 242 " pdb=" CG2 VAL O 242 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CG LEU E1260 " pdb=" CB LEU E1260 " pdb=" CD1 LEU E1260 " pdb=" CD2 LEU E1260 " both_signs ideal model delta sigma weight residual False -2.59 -3.24 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CB ILE G 506 " pdb=" CA ILE G 506 " pdb=" CG1 ILE G 506 " pdb=" CG2 ILE G 506 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.77e+00 ... (remaining 10301 not shown) Planarity restraints: 12122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 ACD K 501 " 0.328 2.00e-02 2.50e+03 3.34e-01 1.12e+03 pdb=" C14 ACD K 501 " -0.315 2.00e-02 2.50e+03 pdb=" C15 ACD K 501 " -0.352 2.00e-02 2.50e+03 pdb=" C16 ACD K 501 " 0.339 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 ACD K 501 " 0.109 2.00e-02 2.50e+03 1.69e-01 2.85e+02 pdb=" C7 ACD K 501 " -0.110 2.00e-02 2.50e+03 pdb=" C8 ACD K 501 " 0.212 2.00e-02 2.50e+03 pdb=" C9 ACD K 501 " -0.212 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 ACD K 501 " -0.152 2.00e-02 2.50e+03 1.51e-01 2.29e+02 pdb=" C11 ACD K 501 " 0.156 2.00e-02 2.50e+03 pdb=" C12 ACD K 501 " 0.146 2.00e-02 2.50e+03 pdb=" C13 ACD K 501 " -0.150 2.00e-02 2.50e+03 ... (remaining 12119 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1874 2.70 - 3.25: 64220 3.25 - 3.80: 112394 3.80 - 4.35: 144716 4.35 - 4.90: 240340 Nonbonded interactions: 563544 Sorted by model distance: nonbonded pdb=" NH1 ARG K 72 " pdb=" O LEU K 390 " model vdw 2.150 3.120 nonbonded pdb=" NH2 ARG K 72 " pdb=" O GLY K 387 " model vdw 2.155 3.120 nonbonded pdb=" OH TYR I 135 " pdb=" OG1 THR I 299 " model vdw 2.178 3.040 nonbonded pdb=" O ARG K 232 " pdb=" OG1 THR K 236 " model vdw 2.180 3.040 nonbonded pdb=" O LEU A 228 " pdb=" NZ LYS C 342 " model vdw 2.186 3.120 ... (remaining 563539 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 individual isotropic 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.040 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 125.720 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.007 0.373 69084 Z= 0.450 Angle : 0.955 21.811 93762 Z= 0.507 Chirality : 0.053 0.701 10304 Planarity : 0.009 0.334 12122 Dihedral : 17.834 138.848 25557 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.79 % Allowed : 7.95 % Favored : 91.26 % Rotamer: Outliers : 0.53 % Allowed : 22.74 % Favored : 76.73 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.02 % 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: -1.35 (0.09), residues: 8429 helix: -0.09 (0.07), residues: 4368 sheet: -0.74 (0.24), residues: 472 loop : -1.90 (0.10), residues: 3589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP J 63 HIS 0.037 0.001 HIS G 168 PHE 0.054 0.002 PHE G 604 TYR 0.036 0.002 TYR T 27 ARG 0.061 0.001 ARG G 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 648 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 484 LYS cc_start: 0.5142 (OUTLIER) cc_final: 0.4742 (mmtm) REVERT: E 1343 ASP cc_start: 0.6136 (OUTLIER) cc_final: 0.5602 (t70) REVERT: F 768 GLU cc_start: 0.7163 (pp20) cc_final: 0.6666 (pp20) REVERT: I 206 GLU cc_start: 0.6794 (tp30) cc_final: 0.6536 (tp30) REVERT: J 360 GLN cc_start: 0.7790 (pm20) cc_final: 0.7544 (pm20) REVERT: O 419 GLU cc_start: 0.7735 (mp0) cc_final: 0.7418 (mp0) REVERT: T 123 ARG cc_start: 0.6730 (ttp-170) cc_final: 0.6300 (ptt90) outliers start: 37 outliers final: 16 residues processed: 671 average time/residue: 0.7339 time to fit residues: 842.3162 Evaluate side-chains 629 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 611 time to evaluate : 5.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain E residue 615 ASN Chi-restraints excluded: chain E residue 1343 ASP Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 2246 LYS Chi-restraints excluded: chain E residue 2749 ASN Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain J residue 94 ASP Chi-restraints excluded: chain J residue 354 GLN Chi-restraints excluded: chain K residue 70 PHE Chi-restraints excluded: chain L residue 93 MET Chi-restraints excluded: chain N residue 72 TYR Chi-restraints excluded: chain S residue 99 ASN Chi-restraints excluded: chain S residue 108 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 716 optimal weight: 4.9990 chunk 643 optimal weight: 3.9990 chunk 357 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 434 optimal weight: 5.9990 chunk 343 optimal weight: 0.9990 chunk 665 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 404 optimal weight: 2.9990 chunk 495 optimal weight: 0.7980 chunk 770 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN A 293 HIS B 173 GLN B 507 ASN B 890 GLN D 900 GLN E 570 GLN E 621 HIS ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 946 HIS E1372 ASN E1392 GLN E1678 ASN E1990 ASN ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2892 ASN F 617 ASN F 664 ASN G 160 HIS G 171 HIS H 407 GLN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 HIS J 127 GLN J 354 GLN K 259 HIS K 432 GLN ** M 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN P 355 ASN S 104 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.112462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.091726 restraints weight = 130763.029| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.67 r_work: 0.3220 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 69084 Z= 0.326 Angle : 0.642 11.694 93762 Z= 0.327 Chirality : 0.043 0.221 10304 Planarity : 0.006 0.121 12122 Dihedral : 7.810 131.026 9753 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.65 % Allowed : 8.30 % Favored : 91.04 % Rotamer: Outliers : 2.93 % Allowed : 21.10 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % 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: -0.73 (0.09), residues: 8429 helix: 0.57 (0.08), residues: 4388 sheet: -0.88 (0.24), residues: 477 loop : -1.78 (0.11), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 353 HIS 0.009 0.001 HIS G 421 PHE 0.026 0.002 PHE E2891 TYR 0.023 0.002 TYR I 216 ARG 0.008 0.001 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 649 time to evaluate : 5.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.6460 (p90) REVERT: B 105 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: C 72 CYS cc_start: 0.5046 (OUTLIER) cc_final: 0.4613 (p) REVERT: C 150 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8222 (mtp) REVERT: D 484 LYS cc_start: 0.5009 (OUTLIER) cc_final: 0.4552 (mmtm) REVERT: D 769 MET cc_start: 0.8495 (mmt) cc_final: 0.8224 (mmt) REVERT: D 925 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8361 (tp) REVERT: D 953 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6159 (tt0) REVERT: D 1150 LEU cc_start: 0.6729 (mt) cc_final: 0.6500 (mt) REVERT: E 557 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8642 (mp) REVERT: E 1448 ASN cc_start: 0.3796 (OUTLIER) cc_final: 0.2993 (m110) REVERT: E 2443 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.7036 (mttt) REVERT: F 768 GLU cc_start: 0.7942 (pp20) cc_final: 0.7600 (pp20) REVERT: G 434 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.4803 (mtm180) REVERT: G 607 ASN cc_start: 0.6608 (p0) cc_final: 0.6323 (p0) REVERT: H 210 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8338 (mp) REVERT: H 615 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5354 (tm-30) REVERT: I 206 GLU cc_start: 0.7126 (tp30) cc_final: 0.6704 (tp30) REVERT: J 360 GLN cc_start: 0.8061 (pm20) cc_final: 0.7619 (pm20) REVERT: N 83 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8175 (tp) REVERT: Q 306 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: R 36 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7633 (mtpp) REVERT: S 93 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7317 (mtp-110) REVERT: S 108 MET cc_start: 0.8122 (mmt) cc_final: 0.7742 (mmt) outliers start: 204 outliers final: 102 residues processed: 804 average time/residue: 0.6685 time to fit residues: 908.8020 Evaluate side-chains 725 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 607 time to evaluate : 5.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 661 PHE Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 953 GLU Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 1430 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1661 TYR Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1778 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 1974 ASP Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2443 LYS Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2955 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 963 THR Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 355 LYS Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 391 LEU Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 405 ASN Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 306 GLU Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 93 ARG Chi-restraints excluded: chain S residue 104 GLN Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain T residue 50 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 187 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 318 optimal weight: 0.0000 chunk 789 optimal weight: 4.9990 chunk 283 optimal weight: 0.8980 chunk 598 optimal weight: 0.0070 chunk 431 optimal weight: 9.9990 chunk 178 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 114 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 507 ASN B 899 ASN E2344 HIS E2416 ASN G 171 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 HIS J 127 GLN J 354 GLN ** M 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.114546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.093742 restraints weight = 130270.059| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.64 r_work: 0.3269 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 69084 Z= 0.165 Angle : 0.553 11.095 93762 Z= 0.283 Chirality : 0.039 0.236 10304 Planarity : 0.005 0.114 12122 Dihedral : 6.643 138.735 9723 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.46 % Favored : 91.96 % Rotamer: Outliers : 2.52 % Allowed : 21.72 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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: -0.24 (0.09), residues: 8429 helix: 1.03 (0.08), residues: 4385 sheet: -0.76 (0.24), residues: 448 loop : -1.62 (0.11), residues: 3596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 353 HIS 0.008 0.001 HIS G 421 PHE 0.016 0.001 PHE D 359 TYR 0.018 0.001 TYR E1789 ARG 0.005 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 663 time to evaluate : 5.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 950 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6917 (mm-30) REVERT: C 72 CYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4867 (p) REVERT: C 158 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7511 (mp) REVERT: D 484 LYS cc_start: 0.5039 (OUTLIER) cc_final: 0.4601 (mmtm) REVERT: D 769 MET cc_start: 0.8478 (mmt) cc_final: 0.8261 (mmt) REVERT: D 968 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6368 (mp10) REVERT: D 1150 LEU cc_start: 0.6794 (mt) cc_final: 0.6520 (mt) REVERT: E 1448 ASN cc_start: 0.3871 (OUTLIER) cc_final: 0.3054 (m110) REVERT: F 317 GLU cc_start: 0.6053 (tp30) cc_final: 0.5848 (mt-10) REVERT: F 321 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6655 (mm-30) REVERT: F 568 ILE cc_start: 0.5978 (OUTLIER) cc_final: 0.5668 (mm) REVERT: G 628 ARG cc_start: 0.6341 (ttt90) cc_final: 0.6048 (tpt-90) REVERT: H 168 ASP cc_start: 0.7310 (m-30) cc_final: 0.7016 (m-30) REVERT: H 245 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.4640 (tt) REVERT: H 285 ASP cc_start: 0.7207 (t0) cc_final: 0.7006 (t0) REVERT: H 431 ASP cc_start: 0.7909 (p0) cc_final: 0.7649 (p0) REVERT: H 615 GLU cc_start: 0.6112 (OUTLIER) cc_final: 0.5415 (tm-30) REVERT: I 148 GLN cc_start: 0.4202 (pm20) cc_final: 0.3916 (pm20) REVERT: J 360 GLN cc_start: 0.8060 (pm20) cc_final: 0.7708 (pm20) REVERT: K 217 MET cc_start: 0.5630 (tpt) cc_final: 0.5250 (tpt) REVERT: N 83 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8160 (tp) REVERT: P 253 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6839 (mt0) REVERT: Q 223 TYR cc_start: 0.8262 (m-80) cc_final: 0.7664 (m-80) REVERT: Q 306 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7100 (pt0) REVERT: Q 452 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6996 (tt) REVERT: R 36 LYS cc_start: 0.8045 (mmtp) cc_final: 0.7686 (mtpp) REVERT: S 108 MET cc_start: 0.8042 (mmt) cc_final: 0.7675 (mmt) REVERT: T 33 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7809 (tm-30) outliers start: 175 outliers final: 98 residues processed: 793 average time/residue: 0.6763 time to fit residues: 913.1354 Evaluate side-chains 723 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 612 time to evaluate : 5.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 873 ARG Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain D residue 1128 MET Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 753 THR Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 1974 ASP Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2013 ILE Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2320 ILE Chi-restraints excluded: chain E residue 2461 VAL Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2955 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 136 GLU Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 84 THR Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 354 GLN Chi-restraints excluded: chain J residue 355 LYS Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 196 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 253 GLN Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 405 ASN Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 306 GLU Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 452 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 104 GLN Chi-restraints excluded: chain S residue 115 GLU Chi-restraints excluded: chain T residue 50 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 245 optimal weight: 3.9990 chunk 737 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 647 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 630 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 386 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 899 ASN C 289 GLN E1227 GLN E1678 ASN F 381 ASN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.111620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.091018 restraints weight = 131146.711| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.68 r_work: 0.3204 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 69084 Z= 0.338 Angle : 0.618 12.395 93762 Z= 0.315 Chirality : 0.043 0.278 10304 Planarity : 0.005 0.114 12122 Dihedral : 6.631 126.640 9720 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.28 % Favored : 91.13 % Rotamer: Outliers : 3.75 % Allowed : 21.05 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.02 % 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: -0.36 (0.09), residues: 8429 helix: 0.93 (0.08), residues: 4397 sheet: -0.88 (0.24), residues: 468 loop : -1.66 (0.11), residues: 3564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 353 HIS 0.009 0.001 HIS G 421 PHE 0.028 0.002 PHE E2891 TYR 0.023 0.002 TYR T 34 ARG 0.013 0.000 ARG D 711 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 261 poor density : 627 time to evaluate : 5.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.6849 (p90) REVERT: B 105 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: B 174 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6406 (mp0) REVERT: B 599 PHE cc_start: 0.6452 (t80) cc_final: 0.6072 (t80) REVERT: B 703 MET cc_start: 0.6558 (OUTLIER) cc_final: 0.5510 (ppp) REVERT: B 765 MET cc_start: 0.8659 (ttm) cc_final: 0.8357 (mtp) REVERT: C 72 CYS cc_start: 0.5595 (OUTLIER) cc_final: 0.5051 (p) REVERT: C 158 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7533 (mp) REVERT: D 484 LYS cc_start: 0.5057 (OUTLIER) cc_final: 0.4500 (mmtm) REVERT: D 673 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5786 (tt) REVERT: D 769 MET cc_start: 0.8550 (mmt) cc_final: 0.8332 (mmt) REVERT: D 925 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8430 (tp) REVERT: D 968 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: D 1031 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7084 (tpt) REVERT: D 1150 LEU cc_start: 0.6834 (mt) cc_final: 0.6574 (mt) REVERT: E 557 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8694 (mp) REVERT: E 1448 ASN cc_start: 0.3906 (OUTLIER) cc_final: 0.3126 (m110) REVERT: E 2117 GLU cc_start: 0.7607 (tp30) cc_final: 0.7383 (tp30) REVERT: E 2250 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8216 (mt) REVERT: E 2717 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8305 (t) REVERT: F 568 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5475 (mm) REVERT: G 434 ARG cc_start: 0.5970 (OUTLIER) cc_final: 0.4644 (mtm180) REVERT: G 602 ASP cc_start: 0.6362 (OUTLIER) cc_final: 0.5414 (t0) REVERT: G 1054 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: H 152 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7777 (pp) REVERT: H 245 LEU cc_start: 0.5500 (OUTLIER) cc_final: 0.4749 (tt) REVERT: H 546 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7407 (p) REVERT: I 148 GLN cc_start: 0.4156 (pm20) cc_final: 0.3824 (pm20) REVERT: I 206 GLU cc_start: 0.7068 (tp30) cc_final: 0.6640 (tp30) REVERT: J 360 GLN cc_start: 0.8041 (pm20) cc_final: 0.7574 (pm20) REVERT: K 217 MET cc_start: 0.5967 (tpt) cc_final: 0.5570 (tpt) REVERT: N 83 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8212 (tp) REVERT: P 333 ARG cc_start: 0.6707 (ptt-90) cc_final: 0.6116 (ttp80) REVERT: Q 223 TYR cc_start: 0.8348 (m-80) cc_final: 0.7852 (m-80) REVERT: Q 452 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7077 (tt) REVERT: R 36 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7636 (mtpp) REVERT: S 49 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7602 (mm-30) REVERT: S 108 MET cc_start: 0.8065 (mmt) cc_final: 0.7663 (mmt) outliers start: 261 outliers final: 166 residues processed: 828 average time/residue: 0.6705 time to fit residues: 951.0849 Evaluate side-chains 788 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 597 time to evaluate : 5.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 835 ASP Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 873 ARG Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 942 LEU Chi-restraints excluded: chain D residue 965 VAL Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 627 LYS Chi-restraints excluded: chain E residue 753 THR Chi-restraints excluded: chain E residue 786 SER Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1430 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1778 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 1974 ASP Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2250 ILE Chi-restraints excluded: chain E residue 2405 GLU Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2714 PHE Chi-restraints excluded: chain E residue 2717 THR Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2955 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 650 MET Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain F residue 1041 VAL Chi-restraints excluded: chain G residue 168 HIS Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 543 TYR Chi-restraints excluded: chain G residue 602 ASP Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 797 ILE Chi-restraints excluded: chain G residue 862 VAL Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 963 THR Chi-restraints excluded: chain G residue 1041 VAL Chi-restraints excluded: chain G residue 1054 GLU Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 383 MET Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 546 THR Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 208 LEU Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 384 TYR Chi-restraints excluded: chain O residue 391 LEU Chi-restraints excluded: chain O residue 407 VAL Chi-restraints excluded: chain O residue 415 CYS Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 452 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 85 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 126 optimal weight: 0.9990 chunk 329 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 439 optimal weight: 7.9990 chunk 673 optimal weight: 1.9990 chunk 590 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 685 optimal weight: 0.8980 chunk 378 optimal weight: 9.9990 chunk 396 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS B 507 ASN B 626 GLN B 899 ASN E1959 HIS ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN K 318 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.093039 restraints weight = 130537.073| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.62 r_work: 0.3249 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 69084 Z= 0.184 Angle : 0.549 12.034 93762 Z= 0.281 Chirality : 0.040 0.280 10304 Planarity : 0.005 0.112 12122 Dihedral : 6.366 129.738 9720 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.37 % Favored : 92.05 % Rotamer: Outliers : 3.20 % Allowed : 21.60 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.00 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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: -0.11 (0.10), residues: 8429 helix: 1.14 (0.08), residues: 4403 sheet: -0.78 (0.24), residues: 448 loop : -1.55 (0.11), residues: 3578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 353 HIS 0.008 0.001 HIS G 421 PHE 0.018 0.001 PHE E2891 TYR 0.018 0.001 TYR K 143 ARG 0.005 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 632 time to evaluate : 5.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.6768 (p90) REVERT: A 207 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8425 (mtt-85) REVERT: B 105 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: B 174 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: B 599 PHE cc_start: 0.6494 (t80) cc_final: 0.6160 (t80) REVERT: B 703 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.5462 (ppp) REVERT: B 753 PHE cc_start: 0.5125 (OUTLIER) cc_final: 0.3871 (t80) REVERT: B 765 MET cc_start: 0.8603 (ttm) cc_final: 0.8350 (mtp) REVERT: B 859 MET cc_start: 0.9220 (mmm) cc_final: 0.8977 (mmm) REVERT: B 950 GLU cc_start: 0.7195 (mm-30) cc_final: 0.6901 (mm-30) REVERT: B 967 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7964 (ttm170) REVERT: C 72 CYS cc_start: 0.5528 (OUTLIER) cc_final: 0.5010 (p) REVERT: C 158 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7556 (mp) REVERT: D 484 LYS cc_start: 0.5022 (OUTLIER) cc_final: 0.4538 (mmtm) REVERT: D 673 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5797 (tt) REVERT: D 769 MET cc_start: 0.8492 (mmt) cc_final: 0.8271 (mmt) REVERT: D 968 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6243 (mp10) REVERT: D 1031 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7062 (tpt) REVERT: D 1150 LEU cc_start: 0.6706 (mt) cc_final: 0.6481 (mt) REVERT: E 557 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8740 (mp) REVERT: E 1448 ASN cc_start: 0.3766 (OUTLIER) cc_final: 0.3092 (m110) REVERT: E 2040 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8742 (tp) REVERT: E 2250 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8140 (mt) REVERT: E 2330 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7408 (mmm-85) REVERT: E 2717 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.8186 (t) REVERT: F 321 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6708 (mm-30) REVERT: F 568 ILE cc_start: 0.5940 (OUTLIER) cc_final: 0.5555 (mm) REVERT: F 597 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7295 (tt) REVERT: G 434 ARG cc_start: 0.5869 (OUTLIER) cc_final: 0.4600 (mtp180) REVERT: G 604 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.5712 (m-80) REVERT: G 628 ARG cc_start: 0.6143 (ttt90) cc_final: 0.5838 (tpt-90) REVERT: H 245 LEU cc_start: 0.5382 (OUTLIER) cc_final: 0.4621 (tt) REVERT: H 431 ASP cc_start: 0.7999 (p0) cc_final: 0.7772 (p0) REVERT: H 432 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: H 546 THR cc_start: 0.7808 (OUTLIER) cc_final: 0.7375 (p) REVERT: H 615 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5458 (tm-30) REVERT: I 148 GLN cc_start: 0.4171 (pm20) cc_final: 0.3832 (pm20) REVERT: I 169 LYS cc_start: 0.7635 (tppt) cc_final: 0.7096 (ttmt) REVERT: J 198 TRP cc_start: 0.6576 (m-90) cc_final: 0.6351 (m-90) REVERT: J 360 GLN cc_start: 0.8038 (pm20) cc_final: 0.7792 (pm20) REVERT: L 78 TYR cc_start: 0.8776 (m-80) cc_final: 0.8447 (m-80) REVERT: M 154 MET cc_start: 0.8428 (mmm) cc_final: 0.8160 (mtp) REVERT: N 83 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8178 (tp) REVERT: P 253 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.6869 (mt0) REVERT: P 333 ARG cc_start: 0.6673 (ptt-90) cc_final: 0.6466 (ptt-90) REVERT: Q 223 TYR cc_start: 0.8312 (m-80) cc_final: 0.7876 (m-80) REVERT: Q 452 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6999 (tt) REVERT: R 36 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7747 (mtpp) REVERT: S 49 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: S 108 MET cc_start: 0.8025 (mmt) cc_final: 0.7636 (mmt) REVERT: T 33 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7843 (tm-30) outliers start: 223 outliers final: 140 residues processed: 811 average time/residue: 0.6865 time to fit residues: 950.2118 Evaluate side-chains 778 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 607 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 873 ARG Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 942 LEU Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 786 SER Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1438 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1773 THR Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 1974 ASP Chi-restraints excluded: chain E residue 1980 THR Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2040 LEU Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2179 THR Chi-restraints excluded: chain E residue 2250 ILE Chi-restraints excluded: chain E residue 2405 GLU Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2714 PHE Chi-restraints excluded: chain E residue 2717 THR Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2955 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 650 MET Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain F residue 1041 VAL Chi-restraints excluded: chain G residue 168 HIS Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 543 TYR Chi-restraints excluded: chain G residue 602 ASP Chi-restraints excluded: chain G residue 604 PHE Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 797 ILE Chi-restraints excluded: chain G residue 862 VAL Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain G residue 942 THR Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain H residue 152 LEU Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 546 THR Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 40 ASP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 369 TRP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 384 TYR Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 253 GLN Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 452 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 85 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 795 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 817 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 649 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS E1678 ASN ** E1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN P 182 GLN S 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090570 restraints weight = 130818.519| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.63 r_work: 0.3198 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 69084 Z= 0.346 Angle : 0.622 12.157 93762 Z= 0.316 Chirality : 0.043 0.310 10304 Planarity : 0.005 0.113 12122 Dihedral : 6.497 120.011 9720 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.27 % Favored : 91.15 % Rotamer: Outliers : 4.02 % Allowed : 21.14 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.01 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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 (0.09), residues: 8429 helix: 0.96 (0.08), residues: 4406 sheet: -0.99 (0.23), residues: 470 loop : -1.59 (0.11), residues: 3553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 244 HIS 0.009 0.001 HIS G 421 PHE 0.028 0.002 PHE E2891 TYR 0.023 0.002 TYR K 143 ARG 0.005 0.000 ARG K 418 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 630 time to evaluate : 5.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.6869 (p90) REVERT: A 155 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7661 (ptt180) REVERT: A 207 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8240 (mtt180) REVERT: A 776 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8797 (ttpt) REVERT: B 105 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: B 174 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: B 599 PHE cc_start: 0.6566 (t80) cc_final: 0.6268 (t80) REVERT: B 703 MET cc_start: 0.6706 (OUTLIER) cc_final: 0.5575 (ppp) REVERT: B 753 PHE cc_start: 0.5642 (OUTLIER) cc_final: 0.4404 (t80) REVERT: B 859 MET cc_start: 0.9242 (mmm) cc_final: 0.8978 (mmm) REVERT: B 950 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6890 (mm-30) REVERT: B 967 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.8064 (ttm170) REVERT: C 72 CYS cc_start: 0.5644 (OUTLIER) cc_final: 0.5167 (p) REVERT: C 150 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8112 (mtp) REVERT: C 158 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7596 (mp) REVERT: D 484 LYS cc_start: 0.5273 (OUTLIER) cc_final: 0.4861 (mmtm) REVERT: D 673 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5842 (tt) REVERT: D 769 MET cc_start: 0.8544 (mmt) cc_final: 0.8330 (mmt) REVERT: D 925 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8437 (tp) REVERT: D 968 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6034 (mp10) REVERT: D 1031 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7073 (tpt) REVERT: D 1150 LEU cc_start: 0.6857 (mt) cc_final: 0.6630 (mt) REVERT: E 557 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8763 (mp) REVERT: E 1448 ASN cc_start: 0.3763 (OUTLIER) cc_final: 0.2990 (m110) REVERT: E 1972 PHE cc_start: 0.8662 (m-80) cc_final: 0.8458 (m-80) REVERT: E 2250 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8161 (mt) REVERT: E 2330 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7575 (mmm-85) REVERT: E 2717 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8212 (t) REVERT: F 321 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6806 (mm-30) REVERT: F 568 ILE cc_start: 0.5923 (OUTLIER) cc_final: 0.5471 (mm) REVERT: F 597 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7293 (tt) REVERT: F 681 MET cc_start: 0.7721 (mmm) cc_final: 0.7487 (mmt) REVERT: F 768 GLU cc_start: 0.7934 (pp20) cc_final: 0.7648 (pp20) REVERT: F 887 PHE cc_start: 0.8042 (t80) cc_final: 0.7701 (t80) REVERT: G 286 MET cc_start: 0.7852 (mmp) cc_final: 0.7568 (mmp) REVERT: G 434 ARG cc_start: 0.6070 (OUTLIER) cc_final: 0.4830 (mtm180) REVERT: G 446 HIS cc_start: 0.7337 (m-70) cc_final: 0.7029 (m170) REVERT: G 602 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.5704 (t70) REVERT: H 245 LEU cc_start: 0.5534 (OUTLIER) cc_final: 0.4792 (tt) REVERT: H 431 ASP cc_start: 0.8078 (p0) cc_final: 0.7823 (p0) REVERT: H 432 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: H 615 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5354 (tm-30) REVERT: I 148 GLN cc_start: 0.4285 (pm20) cc_final: 0.3918 (pm20) REVERT: I 155 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.6705 (tpt) REVERT: I 292 GLU cc_start: 0.7930 (mp0) cc_final: 0.7562 (mt-10) REVERT: J 360 GLN cc_start: 0.8041 (pm20) cc_final: 0.7627 (pm20) REVERT: N 53 LEU cc_start: 0.7568 (mp) cc_final: 0.7296 (mp) REVERT: N 83 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8248 (tp) REVERT: P 333 ARG cc_start: 0.6701 (ptt-90) cc_final: 0.6479 (ptt-90) REVERT: P 362 LEU cc_start: 0.8393 (mt) cc_final: 0.8109 (mt) REVERT: Q 223 TYR cc_start: 0.8333 (m-80) cc_final: 0.7921 (m-80) REVERT: Q 452 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6905 (tt) REVERT: Q 473 GLU cc_start: 0.5301 (OUTLIER) cc_final: 0.4934 (mp0) REVERT: S 49 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7616 (mm-30) REVERT: S 108 MET cc_start: 0.7982 (mmt) cc_final: 0.7582 (mmt) REVERT: T 33 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7866 (tm-30) outliers start: 280 outliers final: 182 residues processed: 853 average time/residue: 0.6661 time to fit residues: 968.5321 Evaluate side-chains 825 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 609 time to evaluate : 5.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 776 LYS Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 873 ARG Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 484 LYS Chi-restraints excluded: chain D residue 503 ILE Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 942 LEU Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 753 THR Chi-restraints excluded: chain E residue 786 SER Chi-restraints excluded: chain E residue 787 VAL Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1430 LEU Chi-restraints excluded: chain E residue 1438 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1773 THR Chi-restraints excluded: chain E residue 1778 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2250 ILE Chi-restraints excluded: chain E residue 2405 GLU Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2714 PHE Chi-restraints excluded: chain E residue 2717 THR Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2955 GLU Chi-restraints excluded: chain E residue 2964 LEU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 650 MET Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 825 GLN Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain F residue 1041 VAL Chi-restraints excluded: chain G residue 168 HIS Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 543 TYR Chi-restraints excluded: chain G residue 602 ASP Chi-restraints excluded: chain G residue 797 ILE Chi-restraints excluded: chain G residue 862 VAL Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain G residue 942 THR Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 963 THR Chi-restraints excluded: chain G residue 1041 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 546 THR Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 369 TRP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 384 TYR Chi-restraints excluded: chain O residue 391 LEU Chi-restraints excluded: chain O residue 415 CYS Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 275 ASP Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 452 LEU Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 104 GLN Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 85 TYR Chi-restraints excluded: chain T residue 123 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 399 optimal weight: 0.9980 chunk 101 optimal weight: 0.0170 chunk 577 optimal weight: 0.7980 chunk 592 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 601 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 351 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 560 optimal weight: 5.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 ASN B 899 ASN ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.112342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.091927 restraints weight = 130393.377| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.62 r_work: 0.3226 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 69084 Z= 0.226 Angle : 0.573 12.259 93762 Z= 0.292 Chirality : 0.041 0.271 10304 Planarity : 0.005 0.111 12122 Dihedral : 6.316 124.679 9720 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.57 % Favored : 91.91 % Rotamer: Outliers : 3.58 % Allowed : 21.77 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.01 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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: -0.14 (0.10), residues: 8429 helix: 1.11 (0.08), residues: 4393 sheet: -0.97 (0.24), residues: 460 loop : -1.53 (0.11), residues: 3576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 244 HIS 0.008 0.001 HIS G 421 PHE 0.021 0.001 PHE E1419 TYR 0.019 0.001 TYR K 143 ARG 0.007 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 629 time to evaluate : 5.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.6846 (p90) REVERT: A 155 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7633 (ptt180) REVERT: A 207 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8320 (mtt-85) REVERT: B 105 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: B 174 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: B 599 PHE cc_start: 0.6644 (t80) cc_final: 0.6334 (t80) REVERT: B 703 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.5567 (ppp) REVERT: B 753 PHE cc_start: 0.5643 (OUTLIER) cc_final: 0.4428 (t80) REVERT: B 859 MET cc_start: 0.9241 (mmm) cc_final: 0.8963 (mmm) REVERT: B 950 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6885 (mm-30) REVERT: B 967 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7982 (ttm170) REVERT: B 975 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: C 72 CYS cc_start: 0.5525 (OUTLIER) cc_final: 0.5020 (p) REVERT: C 158 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7571 (mp) REVERT: D 673 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.6053 (tt) REVERT: D 925 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8303 (tp) REVERT: D 968 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6044 (mp10) REVERT: D 1031 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7026 (tpt) REVERT: D 1150 LEU cc_start: 0.6768 (mt) cc_final: 0.6541 (mt) REVERT: E 557 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8756 (mp) REVERT: E 1448 ASN cc_start: 0.3732 (OUTLIER) cc_final: 0.2981 (m110) REVERT: E 1765 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8611 (mm) REVERT: E 2040 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8755 (tp) REVERT: E 2068 LYS cc_start: 0.7729 (ttpt) cc_final: 0.7419 (tttp) REVERT: E 2250 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8094 (mt) REVERT: E 2330 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7653 (mmm-85) REVERT: E 2404 ARG cc_start: 0.5248 (mtt90) cc_final: 0.4957 (ptp-170) REVERT: E 2717 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8191 (t) REVERT: F 321 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6714 (mm-30) REVERT: F 368 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5710 (mt) REVERT: F 568 ILE cc_start: 0.5914 (OUTLIER) cc_final: 0.5501 (mm) REVERT: F 597 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7345 (tt) REVERT: F 768 GLU cc_start: 0.7860 (pp20) cc_final: 0.7643 (pp20) REVERT: F 887 PHE cc_start: 0.7928 (t80) cc_final: 0.7509 (t80) REVERT: G 434 ARG cc_start: 0.6003 (OUTLIER) cc_final: 0.4817 (mtp180) REVERT: G 446 HIS cc_start: 0.7355 (m-70) cc_final: 0.7061 (m170) REVERT: H 245 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.4704 (tt) REVERT: H 432 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: H 546 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7487 (p) REVERT: H 615 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5377 (tm-30) REVERT: I 148 GLN cc_start: 0.4226 (pm20) cc_final: 0.3855 (pm20) REVERT: I 155 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.6568 (tpt) REVERT: I 169 LYS cc_start: 0.7548 (tppt) cc_final: 0.6938 (ttpt) REVERT: I 292 GLU cc_start: 0.7907 (mp0) cc_final: 0.7543 (mt-10) REVERT: J 360 GLN cc_start: 0.8056 (pm20) cc_final: 0.7774 (pm20) REVERT: M 128 LEU cc_start: 0.3719 (OUTLIER) cc_final: 0.3454 (mp) REVERT: N 53 LEU cc_start: 0.7583 (mp) cc_final: 0.7333 (mp) REVERT: N 83 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8195 (tp) REVERT: P 253 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.6922 (mt0) REVERT: P 362 LEU cc_start: 0.8480 (mt) cc_final: 0.8204 (mt) REVERT: Q 223 TYR cc_start: 0.8313 (m-80) cc_final: 0.7928 (m-80) REVERT: Q 415 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8270 (tt) REVERT: Q 452 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6989 (tt) REVERT: S 49 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7583 (mm-30) REVERT: T 33 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7831 (tm-30) outliers start: 249 outliers final: 173 residues processed: 836 average time/residue: 0.6631 time to fit residues: 943.2623 Evaluate side-chains 808 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 598 time to evaluate : 5.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 967 ARG Chi-restraints excluded: chain B residue 975 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 615 VAL Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 942 LEU Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 753 THR Chi-restraints excluded: chain E residue 786 SER Chi-restraints excluded: chain E residue 787 VAL Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1430 LEU Chi-restraints excluded: chain E residue 1438 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1765 LEU Chi-restraints excluded: chain E residue 1773 THR Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1778 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 1974 ASP Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2040 LEU Chi-restraints excluded: chain E residue 2048 ILE Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2250 ILE Chi-restraints excluded: chain E residue 2405 GLU Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2717 THR Chi-restraints excluded: chain E residue 2744 SER Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 650 MET Chi-restraints excluded: chain F residue 825 GLN Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain F residue 1041 VAL Chi-restraints excluded: chain G residue 168 HIS Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 543 TYR Chi-restraints excluded: chain G residue 602 ASP Chi-restraints excluded: chain G residue 635 ILE Chi-restraints excluded: chain G residue 797 ILE Chi-restraints excluded: chain G residue 862 VAL Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain G residue 942 THR Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 963 THR Chi-restraints excluded: chain G residue 1041 VAL Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 546 THR Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 145 THR Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 171 ARG Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 369 TRP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 384 TYR Chi-restraints excluded: chain O residue 391 LEU Chi-restraints excluded: chain O residue 415 CYS Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 253 GLN Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 452 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 85 TYR Chi-restraints excluded: chain T residue 123 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 828 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 172 optimal weight: 3.9990 chunk 146 optimal weight: 0.6980 chunk 739 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 804 optimal weight: 7.9990 chunk 794 optimal weight: 6.9990 chunk 126 optimal weight: 0.7980 chunk 226 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS C 408 HIS ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1439 ASN ** E1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 HIS ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090569 restraints weight = 130652.599| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.61 r_work: 0.3203 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 69084 Z= 0.316 Angle : 0.616 12.884 93762 Z= 0.313 Chirality : 0.043 0.334 10304 Planarity : 0.005 0.112 12122 Dihedral : 6.353 120.955 9716 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.45 % Favored : 91.03 % Rotamer: Outliers : 3.82 % Allowed : 21.53 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.01 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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: -0.27 (0.09), residues: 8429 helix: 1.00 (0.08), residues: 4393 sheet: -1.01 (0.23), residues: 477 loop : -1.59 (0.11), residues: 3559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 244 HIS 0.009 0.001 HIS G 421 PHE 0.025 0.002 PHE E2891 TYR 0.022 0.002 TYR T 34 ARG 0.007 0.000 ARG L 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 613 time to evaluate : 5.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8451 (OUTLIER) cc_final: 0.6912 (p90) REVERT: A 155 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.7633 (ptt180) REVERT: A 207 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8262 (mtt-85) REVERT: A 616 LEU cc_start: 0.7134 (tp) cc_final: 0.6859 (tp) REVERT: B 105 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: B 174 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: B 599 PHE cc_start: 0.6704 (t80) cc_final: 0.6387 (t80) REVERT: B 631 MET cc_start: 0.7286 (mmm) cc_final: 0.6947 (tpt) REVERT: B 703 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.5689 (ppp) REVERT: B 753 PHE cc_start: 0.5669 (OUTLIER) cc_final: 0.4518 (t80) REVERT: B 859 MET cc_start: 0.9271 (mmm) cc_final: 0.8985 (mmm) REVERT: B 950 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6916 (mm-30) REVERT: B 975 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: C 72 CYS cc_start: 0.5543 (OUTLIER) cc_final: 0.5093 (p) REVERT: C 150 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8166 (mtp) REVERT: C 158 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7630 (mp) REVERT: D 673 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.6038 (tt) REVERT: D 925 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8346 (tp) REVERT: D 968 GLN cc_start: 0.6797 (OUTLIER) cc_final: 0.5986 (mp10) REVERT: D 1031 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7067 (tpt) REVERT: D 1150 LEU cc_start: 0.6903 (mt) cc_final: 0.6696 (mt) REVERT: E 276 LYS cc_start: 0.6706 (mptt) cc_final: 0.6452 (mptt) REVERT: E 557 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8825 (mp) REVERT: E 1448 ASN cc_start: 0.3710 (OUTLIER) cc_final: 0.2968 (m110) REVERT: E 1765 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8712 (mm) REVERT: E 2040 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8789 (tp) REVERT: E 2068 LYS cc_start: 0.7760 (ttpt) cc_final: 0.7442 (tttp) REVERT: E 2250 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8124 (mt) REVERT: E 2404 ARG cc_start: 0.5101 (mtt90) cc_final: 0.4887 (ptp-170) REVERT: E 2717 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8203 (t) REVERT: F 321 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6692 (mm-30) REVERT: F 368 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5749 (mt) REVERT: F 568 ILE cc_start: 0.5990 (OUTLIER) cc_final: 0.5524 (mm) REVERT: F 597 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7251 (tt) REVERT: F 666 TYR cc_start: 0.7171 (t80) cc_final: 0.6884 (t80) REVERT: F 667 GLU cc_start: 0.7399 (tt0) cc_final: 0.7104 (tt0) REVERT: F 887 PHE cc_start: 0.8047 (t80) cc_final: 0.7647 (t80) REVERT: G 286 MET cc_start: 0.7785 (mmp) cc_final: 0.7319 (mmp) REVERT: G 434 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.4836 (mtp180) REVERT: G 602 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.5686 (t70) REVERT: H 245 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.4788 (tt) REVERT: H 432 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7473 (tt0) REVERT: H 546 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7539 (p) REVERT: H 615 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5335 (tm-30) REVERT: I 148 GLN cc_start: 0.3934 (pm20) cc_final: 0.3549 (pm20) REVERT: I 155 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.6634 (tpt) REVERT: I 292 GLU cc_start: 0.7890 (mp0) cc_final: 0.7520 (mt-10) REVERT: J 360 GLN cc_start: 0.8073 (pm20) cc_final: 0.7787 (pm20) REVERT: M 154 MET cc_start: 0.8418 (mmm) cc_final: 0.8216 (mtp) REVERT: N 53 LEU cc_start: 0.7573 (mp) cc_final: 0.7327 (mp) REVERT: N 83 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8215 (tp) REVERT: P 362 LEU cc_start: 0.8439 (mt) cc_final: 0.8165 (mt) REVERT: Q 223 TYR cc_start: 0.8342 (m-80) cc_final: 0.7960 (m-80) REVERT: Q 415 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8279 (tt) REVERT: Q 473 GLU cc_start: 0.5228 (OUTLIER) cc_final: 0.4852 (mp0) REVERT: R 36 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7706 (mtpp) REVERT: S 49 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: T 33 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7800 (tm-30) outliers start: 266 outliers final: 190 residues processed: 828 average time/residue: 0.6709 time to fit residues: 951.3855 Evaluate side-chains 825 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 226 poor density : 599 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 975 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 942 LEU Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 753 THR Chi-restraints excluded: chain E residue 786 SER Chi-restraints excluded: chain E residue 787 VAL Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1430 LEU Chi-restraints excluded: chain E residue 1438 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1765 LEU Chi-restraints excluded: chain E residue 1773 THR Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1778 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2040 LEU Chi-restraints excluded: chain E residue 2048 ILE Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2179 THR Chi-restraints excluded: chain E residue 2250 ILE Chi-restraints excluded: chain E residue 2405 GLU Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2717 THR Chi-restraints excluded: chain E residue 2744 SER Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2904 THR Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 443 GLU Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 601 MET Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 650 MET Chi-restraints excluded: chain F residue 825 GLN Chi-restraints excluded: chain F residue 974 LEU Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain F residue 1041 VAL Chi-restraints excluded: chain G residue 168 HIS Chi-restraints excluded: chain G residue 172 VAL Chi-restraints excluded: chain G residue 219 ASP Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 543 TYR Chi-restraints excluded: chain G residue 602 ASP Chi-restraints excluded: chain G residue 797 ILE Chi-restraints excluded: chain G residue 862 VAL Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain G residue 942 THR Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 963 THR Chi-restraints excluded: chain G residue 1041 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 413 LEU Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 546 THR Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 366 VAL Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 171 ARG Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 234 LEU Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 362 PHE Chi-restraints excluded: chain O residue 369 TRP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 384 TYR Chi-restraints excluded: chain O residue 391 LEU Chi-restraints excluded: chain O residue 415 CYS Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain P residue 359 ARG Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 85 TYR Chi-restraints excluded: chain T residue 123 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 399 optimal weight: 1.9990 chunk 796 optimal weight: 20.0000 chunk 724 optimal weight: 4.9990 chunk 698 optimal weight: 1.9990 chunk 757 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 746 optimal weight: 0.0870 chunk 440 optimal weight: 0.0970 chunk 695 optimal weight: 0.6980 chunk 439 optimal weight: 2.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2132 GLN ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.112542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.091872 restraints weight = 131123.426| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.66 r_work: 0.3226 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 69084 Z= 0.205 Angle : 0.571 12.661 93762 Z= 0.291 Chirality : 0.040 0.304 10304 Planarity : 0.005 0.111 12122 Dihedral : 6.147 125.836 9716 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.53 % Favored : 91.97 % Rotamer: Outliers : 3.56 % Allowed : 21.85 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.01 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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: -0.09 (0.10), residues: 8429 helix: 1.16 (0.08), residues: 4390 sheet: -0.95 (0.24), residues: 467 loop : -1.51 (0.11), residues: 3572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 244 HIS 0.008 0.001 HIS G 421 PHE 0.020 0.001 PHE E1419 TYR 0.019 0.001 TYR E1789 ARG 0.007 0.000 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 619 time to evaluate : 5.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.6899 (p90) REVERT: A 155 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7597 (ptt180) REVERT: A 207 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8320 (mtt-85) REVERT: A 616 LEU cc_start: 0.7150 (tp) cc_final: 0.6905 (tp) REVERT: B 105 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: B 174 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: B 631 MET cc_start: 0.7285 (mmm) cc_final: 0.6978 (tpt) REVERT: B 703 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.5609 (ppp) REVERT: B 706 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5881 (pmm) REVERT: B 753 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.4450 (t80) REVERT: B 950 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6888 (mm-30) REVERT: B 975 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: C 72 CYS cc_start: 0.5576 (OUTLIER) cc_final: 0.5189 (p) REVERT: C 158 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7613 (mp) REVERT: D 673 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6132 (tt) REVERT: D 925 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8289 (tp) REVERT: D 968 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6138 (mp10) REVERT: D 1031 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7030 (tpt) REVERT: D 1150 LEU cc_start: 0.6759 (mt) cc_final: 0.6539 (mt) REVERT: E 276 LYS cc_start: 0.6755 (mptt) cc_final: 0.6479 (mptt) REVERT: E 557 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8816 (mp) REVERT: E 941 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7446 (mp) REVERT: E 1448 ASN cc_start: 0.3775 (OUTLIER) cc_final: 0.3071 (m110) REVERT: E 1765 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8708 (mm) REVERT: E 2040 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8732 (tp) REVERT: E 2068 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7449 (tttp) REVERT: E 2250 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8089 (mt) REVERT: F 321 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6712 (mm-30) REVERT: F 368 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5733 (mt) REVERT: F 568 ILE cc_start: 0.6068 (OUTLIER) cc_final: 0.5684 (mm) REVERT: F 597 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7350 (tt) REVERT: F 667 GLU cc_start: 0.7354 (tt0) cc_final: 0.7120 (tt0) REVERT: F 887 PHE cc_start: 0.7927 (t80) cc_final: 0.7435 (t80) REVERT: G 434 ARG cc_start: 0.6023 (OUTLIER) cc_final: 0.4812 (mtp180) REVERT: G 451 LEU cc_start: 0.7173 (pp) cc_final: 0.6903 (pp) REVERT: H 245 LEU cc_start: 0.5356 (OUTLIER) cc_final: 0.4659 (tt) REVERT: H 432 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: H 546 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7506 (p) REVERT: H 615 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5339 (tm-30) REVERT: I 148 GLN cc_start: 0.3802 (pm20) cc_final: 0.3423 (pm20) REVERT: I 155 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6647 (tpt) REVERT: I 169 LYS cc_start: 0.7595 (tppt) cc_final: 0.6877 (ttpt) REVERT: J 360 GLN cc_start: 0.8075 (pm20) cc_final: 0.7815 (pm20) REVERT: M 128 LEU cc_start: 0.3843 (OUTLIER) cc_final: 0.3562 (mp) REVERT: N 53 LEU cc_start: 0.7581 (mp) cc_final: 0.7356 (mp) REVERT: N 83 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8173 (tp) REVERT: P 253 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: P 362 LEU cc_start: 0.8475 (mt) cc_final: 0.8194 (mt) REVERT: P 377 GLN cc_start: 0.7066 (mp10) cc_final: 0.6774 (mp10) REVERT: Q 223 TYR cc_start: 0.8293 (m-80) cc_final: 0.7938 (m-80) REVERT: Q 415 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8212 (tt) REVERT: Q 473 GLU cc_start: 0.5208 (OUTLIER) cc_final: 0.4845 (mp0) REVERT: R 36 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7682 (mtpp) REVERT: S 49 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7578 (mm-30) outliers start: 248 outliers final: 175 residues processed: 822 average time/residue: 0.6994 time to fit residues: 989.2899 Evaluate side-chains 816 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 604 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 975 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 351 ASP Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 942 LEU Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 753 THR Chi-restraints excluded: chain E residue 786 SER Chi-restraints excluded: chain E residue 787 VAL Chi-restraints excluded: chain E residue 941 LEU Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1430 LEU Chi-restraints excluded: chain E residue 1438 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1765 LEU Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1778 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2040 LEU Chi-restraints excluded: chain E residue 2048 ILE Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2179 THR Chi-restraints excluded: chain E residue 2250 ILE Chi-restraints excluded: chain E residue 2405 GLU Chi-restraints excluded: chain E residue 2524 LEU Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2744 SER Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2955 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 386 ASP Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 825 GLN Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain F residue 1041 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 543 TYR Chi-restraints excluded: chain G residue 602 ASP Chi-restraints excluded: chain G residue 797 ILE Chi-restraints excluded: chain G residue 862 VAL Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain G residue 942 THR Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 963 THR Chi-restraints excluded: chain G residue 964 THR Chi-restraints excluded: chain G residue 1041 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 450 GLU Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 546 THR Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 171 ARG Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 369 TRP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 384 TYR Chi-restraints excluded: chain O residue 391 LEU Chi-restraints excluded: chain O residue 415 CYS Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 50 GLN Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 253 GLN Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 85 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 238 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 538 optimal weight: 2.9990 chunk 396 optimal weight: 0.0030 chunk 687 optimal weight: 0.6980 chunk 331 optimal weight: 8.9990 chunk 636 optimal weight: 5.9990 chunk 437 optimal weight: 8.9990 chunk 347 optimal weight: 4.9990 overall best weight: 1.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.111782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.091268 restraints weight = 130689.209| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.61 r_work: 0.3215 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 69084 Z= 0.267 Angle : 0.595 13.128 93762 Z= 0.302 Chirality : 0.042 0.308 10304 Planarity : 0.005 0.111 12122 Dihedral : 6.176 123.332 9716 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.17 % Favored : 91.35 % Rotamer: Outliers : 3.42 % Allowed : 22.02 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.01 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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: -0.14 (0.10), residues: 8429 helix: 1.11 (0.08), residues: 4388 sheet: -0.97 (0.24), residues: 465 loop : -1.52 (0.11), residues: 3576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP K 119 HIS 0.008 0.001 HIS G 421 PHE 0.021 0.001 PHE E2891 TYR 0.020 0.002 TYR T 34 ARG 0.005 0.000 ARG K 418 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16858 Ramachandran restraints generated. 8429 Oldfield, 0 Emsley, 8429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 615 time to evaluate : 5.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.6914 (p90) REVERT: A 155 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.7618 (ptt180) REVERT: A 207 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8330 (mtt-85) REVERT: A 616 LEU cc_start: 0.7163 (tp) cc_final: 0.6890 (tp) REVERT: B 105 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: B 174 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: B 631 MET cc_start: 0.7343 (mmm) cc_final: 0.7050 (tpt) REVERT: B 703 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.5685 (ppp) REVERT: B 706 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5898 (pmm) REVERT: B 753 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.4550 (t80) REVERT: B 859 MET cc_start: 0.9258 (mmm) cc_final: 0.8958 (mmm) REVERT: B 950 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6910 (mm-30) REVERT: B 975 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: C 72 CYS cc_start: 0.5583 (OUTLIER) cc_final: 0.5127 (p) REVERT: C 150 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8175 (mtp) REVERT: C 158 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7597 (mp) REVERT: D 673 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6186 (tt) REVERT: D 925 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8311 (tp) REVERT: D 968 GLN cc_start: 0.6879 (OUTLIER) cc_final: 0.6084 (mp10) REVERT: D 1031 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7012 (tpt) REVERT: D 1150 LEU cc_start: 0.6793 (mt) cc_final: 0.6570 (mt) REVERT: E 276 LYS cc_start: 0.6644 (mptt) cc_final: 0.6379 (mptt) REVERT: E 557 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8730 (mp) REVERT: E 1448 ASN cc_start: 0.3975 (OUTLIER) cc_final: 0.3249 (m110) REVERT: E 2032 TYR cc_start: 0.7843 (OUTLIER) cc_final: 0.7106 (t80) REVERT: E 2040 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8783 (tp) REVERT: E 2068 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7430 (tttp) REVERT: E 2250 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8115 (mt) REVERT: F 321 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6758 (mm-30) REVERT: F 368 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5806 (mt) REVERT: F 568 ILE cc_start: 0.6038 (OUTLIER) cc_final: 0.5613 (mm) REVERT: F 597 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7274 (tt) REVERT: F 667 GLU cc_start: 0.7452 (tt0) cc_final: 0.7076 (tt0) REVERT: F 887 PHE cc_start: 0.8019 (t80) cc_final: 0.7612 (t80) REVERT: G 434 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.4843 (mtm110) REVERT: H 194 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7720 (mmm160) REVERT: H 245 LEU cc_start: 0.5440 (OUTLIER) cc_final: 0.4739 (tt) REVERT: H 373 GLU cc_start: 0.6448 (pp20) cc_final: 0.6208 (pp20) REVERT: H 432 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: H 546 THR cc_start: 0.8032 (OUTLIER) cc_final: 0.7525 (p) REVERT: H 615 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5361 (tm-30) REVERT: I 148 GLN cc_start: 0.3841 (pm20) cc_final: 0.3440 (pm20) REVERT: I 155 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6677 (tpt) REVERT: I 169 LYS cc_start: 0.7595 (tppt) cc_final: 0.6886 (ttpt) REVERT: J 360 GLN cc_start: 0.8077 (pm20) cc_final: 0.7825 (pm20) REVERT: L 59 ILE cc_start: 0.8806 (tt) cc_final: 0.8590 (tt) REVERT: M 154 MET cc_start: 0.8478 (mmm) cc_final: 0.8232 (mtp) REVERT: N 53 LEU cc_start: 0.7618 (mp) cc_final: 0.7391 (mp) REVERT: N 83 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8237 (tp) REVERT: P 253 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: P 362 LEU cc_start: 0.8457 (mt) cc_final: 0.8181 (mt) REVERT: P 377 GLN cc_start: 0.7102 (mp10) cc_final: 0.6806 (mp10) REVERT: Q 223 TYR cc_start: 0.8318 (m-80) cc_final: 0.7974 (m-80) REVERT: Q 415 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8254 (tt) REVERT: Q 473 GLU cc_start: 0.5272 (OUTLIER) cc_final: 0.4888 (mp0) REVERT: R 36 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7710 (mtpp) REVERT: S 49 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7608 (mm-30) outliers start: 238 outliers final: 184 residues processed: 811 average time/residue: 0.6601 time to fit residues: 912.8882 Evaluate side-chains 819 residues out of total 6959 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 599 time to evaluate : 5.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 710 ILE Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 887 LEU Chi-restraints excluded: chain B residue 105 GLN Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 600 ILE Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 703 MET Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 753 PHE Chi-restraints excluded: chain B residue 813 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 975 GLU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 309 CYS Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 197 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain D residue 548 ILE Chi-restraints excluded: chain D residue 560 THR Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 690 LEU Chi-restraints excluded: chain D residue 761 MET Chi-restraints excluded: chain D residue 777 THR Chi-restraints excluded: chain D residue 877 LEU Chi-restraints excluded: chain D residue 925 LEU Chi-restraints excluded: chain D residue 942 LEU Chi-restraints excluded: chain D residue 968 GLN Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1109 ASP Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 561 THR Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 566 LEU Chi-restraints excluded: chain E residue 753 THR Chi-restraints excluded: chain E residue 786 SER Chi-restraints excluded: chain E residue 787 VAL Chi-restraints excluded: chain E residue 1237 LEU Chi-restraints excluded: chain E residue 1402 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1418 CYS Chi-restraints excluded: chain E residue 1430 LEU Chi-restraints excluded: chain E residue 1438 LEU Chi-restraints excluded: chain E residue 1448 ASN Chi-restraints excluded: chain E residue 1671 PHE Chi-restraints excluded: chain E residue 1675 ILE Chi-restraints excluded: chain E residue 1763 THR Chi-restraints excluded: chain E residue 1773 THR Chi-restraints excluded: chain E residue 1774 LEU Chi-restraints excluded: chain E residue 1778 ILE Chi-restraints excluded: chain E residue 1961 HIS Chi-restraints excluded: chain E residue 2012 GLN Chi-restraints excluded: chain E residue 2032 TYR Chi-restraints excluded: chain E residue 2040 LEU Chi-restraints excluded: chain E residue 2048 ILE Chi-restraints excluded: chain E residue 2133 VAL Chi-restraints excluded: chain E residue 2159 THR Chi-restraints excluded: chain E residue 2179 THR Chi-restraints excluded: chain E residue 2250 ILE Chi-restraints excluded: chain E residue 2405 GLU Chi-restraints excluded: chain E residue 2524 LEU Chi-restraints excluded: chain E residue 2560 LEU Chi-restraints excluded: chain E residue 2744 SER Chi-restraints excluded: chain E residue 2862 VAL Chi-restraints excluded: chain E residue 2904 THR Chi-restraints excluded: chain E residue 2955 GLU Chi-restraints excluded: chain F residue 319 LEU Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 411 MET Chi-restraints excluded: chain F residue 475 ILE Chi-restraints excluded: chain F residue 478 ILE Chi-restraints excluded: chain F residue 492 LEU Chi-restraints excluded: chain F residue 506 ILE Chi-restraints excluded: chain F residue 517 THR Chi-restraints excluded: chain F residue 549 VAL Chi-restraints excluded: chain F residue 568 ILE Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 610 ILE Chi-restraints excluded: chain F residue 729 VAL Chi-restraints excluded: chain F residue 825 GLN Chi-restraints excluded: chain F residue 982 THR Chi-restraints excluded: chain F residue 1002 THR Chi-restraints excluded: chain F residue 1041 VAL Chi-restraints excluded: chain G residue 293 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain G residue 303 PHE Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 339 VAL Chi-restraints excluded: chain G residue 387 THR Chi-restraints excluded: chain G residue 434 ARG Chi-restraints excluded: chain G residue 447 VAL Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 506 ILE Chi-restraints excluded: chain G residue 543 TYR Chi-restraints excluded: chain G residue 602 ASP Chi-restraints excluded: chain G residue 797 ILE Chi-restraints excluded: chain G residue 862 VAL Chi-restraints excluded: chain G residue 894 MET Chi-restraints excluded: chain G residue 942 THR Chi-restraints excluded: chain G residue 955 VAL Chi-restraints excluded: chain G residue 963 THR Chi-restraints excluded: chain G residue 964 THR Chi-restraints excluded: chain G residue 1041 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 173 LEU Chi-restraints excluded: chain H residue 185 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 293 LEU Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 311 LEU Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain H residue 389 VAL Chi-restraints excluded: chain H residue 432 GLU Chi-restraints excluded: chain H residue 463 VAL Chi-restraints excluded: chain H residue 480 LEU Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 546 THR Chi-restraints excluded: chain H residue 615 GLU Chi-restraints excluded: chain H residue 629 MET Chi-restraints excluded: chain I residue 88 VAL Chi-restraints excluded: chain I residue 110 ILE Chi-restraints excluded: chain I residue 127 LEU Chi-restraints excluded: chain I residue 129 VAL Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 190 THR Chi-restraints excluded: chain I residue 203 LEU Chi-restraints excluded: chain I residue 204 CYS Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 288 VAL Chi-restraints excluded: chain I residue 312 VAL Chi-restraints excluded: chain I residue 321 ARG Chi-restraints excluded: chain J residue 157 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 326 SER Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain K residue 162 MET Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 237 THR Chi-restraints excluded: chain K residue 339 VAL Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain L residue 55 THR Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 187 SER Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 128 LEU Chi-restraints excluded: chain M residue 130 PHE Chi-restraints excluded: chain M residue 171 ARG Chi-restraints excluded: chain M residue 238 VAL Chi-restraints excluded: chain N residue 42 VAL Chi-restraints excluded: chain N residue 49 ASP Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 114 SER Chi-restraints excluded: chain O residue 165 THR Chi-restraints excluded: chain O residue 302 ASP Chi-restraints excluded: chain O residue 362 PHE Chi-restraints excluded: chain O residue 369 TRP Chi-restraints excluded: chain O residue 371 VAL Chi-restraints excluded: chain O residue 374 ASN Chi-restraints excluded: chain O residue 384 TYR Chi-restraints excluded: chain O residue 391 LEU Chi-restraints excluded: chain O residue 415 CYS Chi-restraints excluded: chain O residue 419 GLU Chi-restraints excluded: chain P residue 189 CYS Chi-restraints excluded: chain P residue 192 VAL Chi-restraints excluded: chain P residue 253 GLN Chi-restraints excluded: chain P residue 358 THR Chi-restraints excluded: chain Q residue 190 LEU Chi-restraints excluded: chain Q residue 229 LEU Chi-restraints excluded: chain Q residue 275 ASP Chi-restraints excluded: chain Q residue 276 LEU Chi-restraints excluded: chain Q residue 290 ARG Chi-restraints excluded: chain Q residue 305 LEU Chi-restraints excluded: chain Q residue 311 THR Chi-restraints excluded: chain Q residue 337 VAL Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain S residue 49 GLU Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 50 ASP Chi-restraints excluded: chain T residue 85 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 849 random chunks: chunk 847 optimal weight: 6.9990 chunk 246 optimal weight: 0.4980 chunk 34 optimal weight: 0.0570 chunk 210 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 768 optimal weight: 8.9990 chunk 403 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 330 optimal weight: 10.0000 overall best weight: 1.0502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 HIS ** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 744 GLN ** H 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 127 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092194 restraints weight = 130488.816| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.61 r_work: 0.3231 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 69084 Z= 0.214 Angle : 0.574 13.017 93762 Z= 0.292 Chirality : 0.041 0.298 10304 Planarity : 0.005 0.111 12122 Dihedral : 6.081 125.600 9716 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.68 % Favored : 91.85 % Rotamer: Outliers : 3.38 % Allowed : 22.19 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.84 % Cis-general : 0.01 % Twisted Proline : 0.42 % Twisted General : 0.01 % 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: -0.06 (0.10), residues: 8429 helix: 1.19 (0.08), residues: 4386 sheet: -0.93 (0.24), residues: 466 loop : -1.49 (0.11), residues: 3577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP K 119 HIS 0.008 0.001 HIS G 421 PHE 0.020 0.001 PHE E1419 TYR 0.020 0.001 TYR E1434 ARG 0.010 0.000 ARG K 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32352.00 seconds wall clock time: 555 minutes 46.91 seconds (33346.91 seconds total)