Starting phenix.real_space_refine on Thu Mar 5 19:07:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j9e_9785/03_2026/6j9e_9785.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j9e_9785/03_2026/6j9e_9785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6j9e_9785/03_2026/6j9e_9785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j9e_9785/03_2026/6j9e_9785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6j9e_9785/03_2026/6j9e_9785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j9e_9785/03_2026/6j9e_9785.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 61 5.49 5 Mg 1 5.21 5 S 74 5.16 5 C 15172 2.51 5 N 4344 2.21 5 O 4773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 193 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24427 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1543 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 6, 'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 62 Chain: "B" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1449 Classifications: {'peptide': 208} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 9, 'ASP:plan': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 9355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1288, 9355 Classifications: {'peptide': 1288} Incomplete info: {'truncation_to_alanine': 198} Link IDs: {'PTRANS': 51, 'TRANS': 1236} Chain breaks: 9 Unresolved non-hydrogen bonds: 803 Unresolved non-hydrogen angles: 966 Unresolved non-hydrogen dihedrals: 656 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ARG:plan': 32, 'GLU:plan': 52, 'ASP:plan': 16, 'GLN:plan1': 14, 'HIS:plan': 5, 'PHE:plan': 3, 'ASN:plan1': 5} Unresolved non-hydrogen planarities: 530 Chain: "D" Number of atoms: 8733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1200, 8733 Classifications: {'peptide': 1200} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 45, 'TRANS': 1154} Chain breaks: 8 Unresolved non-hydrogen bonds: 686 Unresolved non-hydrogen angles: 824 Unresolved non-hydrogen dihedrals: 578 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 12, 'ARG:plan': 26, 'GLU:plan': 32, 'TYR:plan': 3, 'ASP:plan': 17, 'PHE:plan': 4, 'HIS:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 435 Chain: "E" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 467 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "G" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 582 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "H" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 450 Classifications: {'DNA': 22} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 21} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "I" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 266 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 10} Chain: "J" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 488 Classifications: {'peptide': 66} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 64} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1091 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 297 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 10, 'GLN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 161 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12897 SG CYS D 72 109.827 59.692 50.244 1.00 95.66 S ATOM 12987 SG CYS D 85 112.589 59.900 52.648 1.00 93.10 S ATOM 18397 SG CYS D 815 84.743 75.812 115.744 1.00 55.06 S ATOM 18833 SG CYS D 890 84.722 77.733 111.566 1.00 62.92 S ATOM 18898 SG CYS D 900 81.466 76.712 114.314 1.00 45.45 S Time building chain proxies: 5.19, per 1000 atoms: 0.21 Number of scatterers: 24427 At special positions: 0 Unit cell: (138.918, 165.282, 150.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 74 16.00 P 61 15.00 Mg 1 11.99 O 4773 8.00 N 4344 7.00 C 15172 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 900 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 890 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 815 " 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5946 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 45 sheets defined 38.8% alpha, 14.7% beta 24 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.594A pdb=" N LEU A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 removed outlier: 3.541A pdb=" N VAL A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 removed outlier: 3.852A pdb=" N VAL A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.894A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.930A pdb=" N PHE B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.790A pdb=" N ARG C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 41 removed outlier: 3.848A pdb=" N VAL C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.635A pdb=" N ALA C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 94 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.502A pdb=" N GLY C 219 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.511A pdb=" N ARG C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 254 " --> pdb=" O ARG C 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 254' Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 324 through 335 Processing helix chain 'C' and resid 351 through 360 removed outlier: 3.604A pdb=" N ASN C 355 " --> pdb=" O PRO C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 377 Processing helix chain 'C' and resid 383 through 396 removed outlier: 4.076A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 Processing helix chain 'C' and resid 437 through 448 removed outlier: 3.867A pdb=" N LYS C 441 " --> pdb=" O ASP C 437 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR C 448 " --> pdb=" O VAL C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 466 Processing helix chain 'C' and resid 483 through 507 removed outlier: 3.621A pdb=" N MET C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU C 505 " --> pdb=" O ARG C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 520 removed outlier: 3.679A pdb=" N GLU C 519 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 removed outlier: 4.768A pdb=" N VAL C 526 " --> pdb=" O ASN C 522 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 536 " --> pdb=" O GLU C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 556 Processing helix chain 'C' and resid 572 through 577 removed outlier: 3.834A pdb=" N ASP C 577 " --> pdb=" O PHE C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.634A pdb=" N TYR C 583 " --> pdb=" O PRO C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 688 removed outlier: 4.264A pdb=" N THR C 688 " --> pdb=" O PRO C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 702 removed outlier: 3.514A pdb=" N HIS C 701 " --> pdb=" O PHE C 698 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 702 " --> pdb=" O LEU C 699 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 698 through 702' Processing helix chain 'C' and resid 703 through 714 removed outlier: 3.587A pdb=" N ASN C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 715 through 717 No H-bonds generated for 'chain 'C' and resid 715 through 717' Processing helix chain 'C' and resid 732 through 741 removed outlier: 4.369A pdb=" N GLY C 741 " --> pdb=" O ALA C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 854 removed outlier: 3.870A pdb=" N GLU C 854 " --> pdb=" O ARG C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 926 through 935 Processing helix chain 'C' and resid 971 through 1008 Processing helix chain 'C' and resid 1053 through 1078 Processing helix chain 'C' and resid 1122 through 1126 Processing helix chain 'C' and resid 1142 through 1148 removed outlier: 4.031A pdb=" N SER C1146 " --> pdb=" O LEU C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1150 through 1175 removed outlier: 3.666A pdb=" N LEU C1154 " --> pdb=" O ILE C1150 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1191 removed outlier: 3.754A pdb=" N LEU C1182 " --> pdb=" O ALA C1178 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN C1191 " --> pdb=" O ASP C1187 " (cutoff:3.500A) Processing helix chain 'C' and resid 1208 through 1218 Processing helix chain 'C' and resid 1233 through 1244 removed outlier: 4.311A pdb=" N ALA C1244 " --> pdb=" O MET C1240 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1285 removed outlier: 3.979A pdb=" N LYS C1284 " --> pdb=" O LEU C1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 1304 through 1308 removed outlier: 4.002A pdb=" N PHE C1307 " --> pdb=" O LYS C1304 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY C1308 " --> pdb=" O ALA C1305 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1304 through 1308' Processing helix chain 'C' and resid 1313 through 1323 Processing helix chain 'C' and resid 1325 through 1334 removed outlier: 3.633A pdb=" N LEU C1333 " --> pdb=" O LEU C1329 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1353 removed outlier: 3.636A pdb=" N ARG C1343 " --> pdb=" O ASP C1339 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN C1344 " --> pdb=" O VAL C1340 " (cutoff:3.500A) Processing helix chain 'C' and resid 1362 through 1374 removed outlier: 3.679A pdb=" N ASN C1366 " --> pdb=" O PRO C1362 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 9 removed outlier: 3.705A pdb=" N PHE D 8 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN D 9 " --> pdb=" O ASN D 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 5 through 9' Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 99 removed outlier: 3.778A pdb=" N VAL D 97 " --> pdb=" O LEU D 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG D 98 " --> pdb=" O ALA D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.620A pdb=" N ILE D 135 " --> pdb=" O THR D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.700A pdb=" N VAL D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.605A pdb=" N ALA D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 230 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 285 removed outlier: 3.521A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 3.897A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 484 removed outlier: 3.552A pdb=" N MET D 484 " --> pdb=" O ALA D 480 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 515 removed outlier: 3.552A pdb=" N GLY D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 575 through 581 Processing helix chain 'D' and resid 598 through 613 Processing helix chain 'D' and resid 615 through 635 removed outlier: 3.646A pdb=" N ARG D 635 " --> pdb=" O ALA D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 671 removed outlier: 4.161A pdb=" N LYS D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 704 removed outlier: 3.524A pdb=" N ARG D 679 " --> pdb=" O THR D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 730 removed outlier: 4.237A pdb=" N GLY D 730 " --> pdb=" O MET D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 769 through 805 removed outlier: 3.619A pdb=" N ASN D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 867 through 878 Processing helix chain 'D' and resid 897 through 902 removed outlier: 3.543A pdb=" N TYR D 901 " --> pdb=" O CYS D 897 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY D 902 " --> pdb=" O ALA D 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 897 through 902' Processing helix chain 'D' and resid 918 through 926 Processing helix chain 'D' and resid 927 through 931 removed outlier: 4.213A pdb=" N THR D 930 " --> pdb=" O GLU D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1149 Processing helix chain 'D' and resid 1217 through 1225 removed outlier: 3.659A pdb=" N ILE D1221 " --> pdb=" O SER D1217 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D1225 " --> pdb=" O ILE D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1227 through 1246 Processing helix chain 'D' and resid 1250 through 1262 removed outlier: 4.490A pdb=" N ILE D1254 " --> pdb=" O ASN D1250 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1294 removed outlier: 4.538A pdb=" N VAL D1294 " --> pdb=" O ASN D1290 " (cutoff:3.500A) Processing helix chain 'D' and resid 1309 through 1314 removed outlier: 4.213A pdb=" N SER D1314 " --> pdb=" O ILE D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1328 through 1340 Processing helix chain 'D' and resid 1348 through 1355 Processing helix chain 'D' and resid 1363 through 1371 removed outlier: 3.528A pdb=" N ARG D1371 " --> pdb=" O HIS D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 13 removed outlier: 3.744A pdb=" N VAL E 13 " --> pdb=" O CYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 32 removed outlier: 3.668A pdb=" N LEU E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 61 through 76 Processing helix chain 'J' and resid 46 through 61 removed outlier: 3.665A pdb=" N PHE J 50 " --> pdb=" O SER J 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.664A pdb=" N LEU F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL F 8 " --> pdb=" O GLU F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 39 Processing helix chain 'F' and resid 107 through 136 Processing helix chain 'F' and resid 205 through 212 removed outlier: 3.529A pdb=" N MET F 209 " --> pdb=" O ALA F 205 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 removed outlier: 6.745A pdb=" N ASP A 198 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 183 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG A 181 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 61 removed outlier: 5.276A pdb=" N PHE A 54 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY A 148 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ILE A 56 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU A 146 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 58 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 104 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER A 101 " --> pdb=" O ARG A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.968A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.512A pdb=" N GLN A 152 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 174 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 17 removed outlier: 3.901A pdb=" N ARG B 181 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 61 removed outlier: 5.499A pdb=" N PHE B 54 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY B 148 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ILE B 56 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU B 146 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU B 58 " --> pdb=" O LYS B 144 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 144 " --> pdb=" O GLU B 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.882A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 151 through 152 removed outlier: 3.526A pdb=" N ALA B 174 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 14 through 15 removed outlier: 6.836A pdb=" N LYS C 14 " --> pdb=" O ALA C1225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 80 removed outlier: 3.788A pdb=" N ALA C 72 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL C 76 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N THR C 104 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR C 78 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ARG C 102 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU C 80 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA C 99 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU C 131 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 101 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL C 105 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N GLN C 125 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU C 107 " --> pdb=" O LYS C 123 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS C 123 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE C 109 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR C 121 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.686A pdb=" N PHE C 141 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 149 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN C 541 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 479 through 482 removed outlier: 6.025A pdb=" N SER C 152 " --> pdb=" O SER C 559 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 159 through 165 removed outlier: 4.048A pdb=" N LEU C 176 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG C 202 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 235 through 236 Processing sheet with id=AB7, first strand: chain 'C' and resid 307 through 308 removed outlier: 3.728A pdb=" N VAL C 307 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 317 " --> pdb=" O VAL C 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 586 through 587 removed outlier: 4.561A pdb=" N SER C 602 " --> pdb=" O CYS C 587 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 608 through 609 removed outlier: 5.328A pdb=" N ASP C 630 " --> pdb=" O LYS C 621 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 608 through 609 removed outlier: 3.740A pdb=" N LYS C 673 " --> pdb=" O VAL C 662 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 744 through 745 removed outlier: 7.122A pdb=" N VAL C 744 " --> pdb=" O LEU C 812 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 750 through 755 removed outlier: 5.988A pdb=" N ILE C 752 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS C 763 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN C 754 " --> pdb=" O VAL C 761 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 786 through 787 removed outlier: 4.028A pdb=" N THR C 786 " --> pdb=" O ILE C 794 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 794 " --> pdb=" O THR C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 1137 through 1139 removed outlier: 8.835A pdb=" N ILE C1137 " --> pdb=" O ASN C 828 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU C 830 " --> pdb=" O ILE C1137 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU C1139 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA C 832 " --> pdb=" O LEU C1139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET C 829 " --> pdb=" O MET C1272 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C1270 " --> pdb=" O ILE C 831 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE C 833 " --> pdb=" O THR C1268 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N THR C1268 " --> pdb=" O PHE C 833 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 844 through 847 removed outlier: 7.930A pdb=" N ILE C 845 " --> pdb=" O SER C1118 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C1120 " --> pdb=" O ILE C 845 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU C 847 " --> pdb=" O VAL C1120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 859 through 870 removed outlier: 3.932A pdb=" N LYS C1089 " --> pdb=" O ALA C 869 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 959 " --> pdb=" O PHE C1094 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C1096 " --> pdb=" O VAL C 957 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL C 957 " --> pdb=" O ALA C1096 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 911 through 913 removed outlier: 3.839A pdb=" N VAL C 913 " --> pdb=" O LEU C 947 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 916 through 917 Processing sheet with id=AD1, first strand: chain 'C' and resid 1286 through 1288 removed outlier: 3.662A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1286 through 1288 removed outlier: 8.019A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1310 through 1312 Processing sheet with id=AD4, first strand: chain 'C' and resid 1377 through 1381 Processing sheet with id=AD5, first strand: chain 'D' and resid 104 through 112 removed outlier: 10.404A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.905A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.626A pdb=" N LEU D 160 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 547 through 556 Processing sheet with id=AD8, first strand: chain 'D' and resid 707 through 710 Processing sheet with id=AD9, first strand: chain 'D' and resid 821 through 823 removed outlier: 4.034A pdb=" N VAL D 882 " --> pdb=" O MET D 823 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 826 through 827 removed outlier: 7.029A pdb=" N ILE D 826 " --> pdb=" O VAL D 833 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 952 through 953 removed outlier: 3.945A pdb=" N ALA D1020 " --> pdb=" O ILE D 952 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 959 through 960 removed outlier: 3.827A pdb=" N GLY D 982 " --> pdb=" O LEU D 999 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1187 through 1192 removed outlier: 4.026A pdb=" N HIS D1187 " --> pdb=" O ILE D1179 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D1179 " --> pdb=" O HIS D1187 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D1177 " --> pdb=" O GLU D1189 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1278 through 1280 Processing sheet with id=AE6, first strand: chain 'J' and resid 14 through 17 removed outlier: 6.519A pdb=" N LEU J 22 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP J 38 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL J 24 " --> pdb=" O GLU J 36 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLU J 36 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL J 26 " --> pdb=" O LEU J 34 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 48 through 49 removed outlier: 4.203A pdb=" N GLU F 58 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG F 61 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN F 100 " --> pdb=" O ARG F 61 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 145 through 150 removed outlier: 6.588A pdb=" N PHE F 155 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA F 149 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASN F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 190 through 191 removed outlier: 4.629A pdb=" N ARG F 191 " --> pdb=" O GLN F 198 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN F 198 " --> pdb=" O ARG F 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 985 hydrogen bonds defined for protein. 2808 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7110 1.33 - 1.45: 3742 1.45 - 1.57: 13804 1.57 - 1.69: 120 1.69 - 1.81: 129 Bond restraints: 24905 Sorted by residual: bond pdb=" C GLU D 927 " pdb=" N PRO D 928 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.85e+00 bond pdb=" C3' DA H 14 " pdb=" O3' DA H 14 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" C3' DG G 12 " pdb=" O3' DG G 12 " ideal model delta sigma weight residual 1.422 1.469 -0.047 3.00e-02 1.11e+03 2.43e+00 bond pdb=" C ASP J 47 " pdb=" N PRO J 48 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.25e-02 6.40e+03 2.28e+00 bond pdb=" C PHE C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.10e+00 ... (remaining 24900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 33638 2.16 - 4.32: 470 4.32 - 6.47: 40 6.47 - 8.63: 18 8.63 - 10.79: 4 Bond angle restraints: 34170 Sorted by residual: angle pdb=" C VAL C 61 " pdb=" N PHE C 62 " pdb=" CA PHE C 62 " ideal model delta sigma weight residual 120.06 124.82 -4.76 1.19e+00 7.06e-01 1.60e+01 angle pdb=" C GLY C 69 " pdb=" N ASN C 70 " pdb=" CA ASN C 70 " ideal model delta sigma weight residual 122.07 127.33 -5.26 1.43e+00 4.89e-01 1.35e+01 angle pdb=" N PHE C 62 " pdb=" CA PHE C 62 " pdb=" C PHE C 62 " ideal model delta sigma weight residual 113.57 118.22 -4.65 1.38e+00 5.25e-01 1.14e+01 angle pdb=" C PHE D 377 " pdb=" N LYS D 378 " pdb=" CA LYS D 378 " ideal model delta sigma weight residual 120.09 124.22 -4.13 1.25e+00 6.40e-01 1.09e+01 angle pdb=" C ALA C1305 " pdb=" N GLN C1306 " pdb=" CA GLN C1306 " ideal model delta sigma weight residual 122.61 127.71 -5.10 1.56e+00 4.11e-01 1.07e+01 ... (remaining 34165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.94: 14174 27.94 - 55.88: 589 55.88 - 83.82: 78 83.82 - 111.75: 4 111.75 - 139.69: 2 Dihedral angle restraints: 14847 sinusoidal: 5648 harmonic: 9199 Sorted by residual: dihedral pdb=" CA ALA D 426 " pdb=" C ALA D 426 " pdb=" N PRO D 427 " pdb=" CA PRO D 427 " ideal model delta harmonic sigma weight residual 180.00 154.64 25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA GLY C1324 " pdb=" C GLY C1324 " pdb=" N ALA C1325 " pdb=" CA ALA C1325 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LEU D 120 " pdb=" C LEU D 120 " pdb=" N PRO D 121 " pdb=" CA PRO D 121 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 14844 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3171 0.045 - 0.091: 659 0.091 - 0.136: 263 0.136 - 0.181: 28 0.181 - 0.226: 2 Chirality restraints: 4123 Sorted by residual: chirality pdb=" CB ILE C 752 " pdb=" CA ILE C 752 " pdb=" CG1 ILE C 752 " pdb=" CG2 ILE C 752 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE C 820 " pdb=" CA ILE C 820 " pdb=" CG1 ILE C 820 " pdb=" CG2 ILE C 820 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE C 323 " pdb=" CA ILE C 323 " pdb=" CG1 ILE C 323 " pdb=" CG2 ILE C 323 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.75e-01 ... (remaining 4120 not shown) Planarity restraints: 4249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 62 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO C 63 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 426 " 0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO D 427 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 427 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 427 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D1140 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO D1141 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO D1141 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D1141 " -0.030 5.00e-02 4.00e+02 ... (remaining 4246 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1465 2.74 - 3.28: 21756 3.28 - 3.82: 38485 3.82 - 4.36: 42934 4.36 - 4.90: 75567 Nonbonded interactions: 180207 Sorted by model distance: nonbonded pdb=" O3' A I 20 " pdb="MG MG D1501 " model vdw 2.198 2.170 nonbonded pdb=" O SER J 20 " pdb=" OG SER J 20 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR C1323 " pdb=" O ILE D 434 " model vdw 2.314 3.040 nonbonded pdb=" OG SER D1217 " pdb=" OD1 ASP D1220 " model vdw 2.324 3.040 nonbonded pdb=" OD1 ASP D 464 " pdb=" O2' A I 20 " model vdw 2.325 3.040 ... (remaining 180202 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 19 or (resid 20 through 21 and (name N or name \ CA or name C or name O or name CB )) or resid 22 through 28 or (resid 29 and (na \ me N or name CA or name C or name O or name CB )) or resid 30 through 61 or (res \ id 62 and (name N or name CA or name C or name O or name CB )) or resid 63 or (r \ esid 64 through 72 and (name N or name CA or name C or name O or name CB )) or r \ esid 73 or (resid 74 through 76 and (name N or name CA or name C or name O or na \ me CB )) or resid 77 through 81 or (resid 82 and (name N or name CA or name C or \ name O or name CB )) or resid 83 through 86 or (resid 87 and (name N or name CA \ or name C or name O or name CB )) or resid 88 through 91 or (resid 92 and (name \ N or name CA or name C or name O or name CB )) or resid 93 through 100 or (resi \ d 101 and (name N or name CA or name C or name O or name CB )) or resid 102 thro \ ugh 103 or (resid 104 through 105 and (name N or name CA or name C or name O or \ name CB )) or resid 106 through 135 or (resid 136 and (name N or name CA or name \ C or name O or name CB )) or resid 137 through 138 or (resid 139 through 141 an \ d (name N or name CA or name C or name O or name CB )) or resid 142 through 155 \ or resid 170 through 204 or (resid 205 and (name N or name CA or name C or name \ O or name CB )) or resid 206 through 212 or (resid 213 through 215 and (name N o \ r name CA or name C or name O or name CB )) or resid 216 through 230)) selection = (chain 'B' and (resid 11 through 20 or (resid 21 and (name N or name CA or name \ C or name O or name CB )) or resid 22 through 113 or (resid 114 and (name N or n \ ame CA or name C or name O or name CB )) or resid 115 or (resid 116 and (name N \ or name CA or name C or name O or name CB )) or resid 117 through 145 or (resid \ 146 and (name N or name CA or name C or name O or name CB )) or resid 147 throug \ h 194 or (resid 195 through 196 and (name N or name CA or name C or name O or na \ me CB )) or resid 197 through 230)) } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.005 0.432 24910 Z= 0.199 Angle : 0.613 10.790 34170 Z= 0.340 Chirality : 0.044 0.226 4123 Planarity : 0.005 0.065 4249 Dihedral : 14.743 139.692 8901 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.05 % Allowed : 6.55 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.74 (0.11), residues: 3143 helix: -2.73 (0.10), residues: 1136 sheet: -0.77 (0.26), residues: 363 loop : -2.73 (0.12), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1283 TYR 0.008 0.001 TYR C1347 PHE 0.009 0.001 PHE A 149 TRP 0.010 0.001 TRP C1160 HIS 0.006 0.000 HIS C 155 Details of bonding type rmsd covalent geometry : bond 0.00275 (24905) covalent geometry : angle 0.61313 (34170) hydrogen bonds : bond 0.18081 ( 1041) hydrogen bonds : angle 6.93374 ( 2932) metal coordination : bond 0.29006 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 532 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6033 (t0) cc_final: 0.5730 (t0) REVERT: A 122 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7381 (mt-10) REVERT: A 203 ASP cc_start: 0.8386 (p0) cc_final: 0.8183 (p0) REVERT: A 221 ASP cc_start: 0.7359 (t0) cc_final: 0.7155 (t0) REVERT: B 146 GLU cc_start: 0.7012 (mt-10) cc_final: 0.6417 (mt-10) REVERT: B 181 ARG cc_start: 0.7912 (ptm160) cc_final: 0.7697 (ptm160) REVERT: C 216 ARG cc_start: 0.8677 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: C 222 ASN cc_start: 0.7104 (p0) cc_final: 0.6775 (m110) REVERT: C 458 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7691 (mtpt) REVERT: C 763 LYS cc_start: 0.8314 (tttt) cc_final: 0.7427 (mptt) REVERT: C 845 ILE cc_start: 0.8772 (mm) cc_final: 0.8552 (mt) REVERT: C 1380 GLU cc_start: 0.7296 (tt0) cc_final: 0.6791 (tt0) REVERT: D 134 ASP cc_start: 0.8017 (m-30) cc_final: 0.7776 (m-30) REVERT: D 375 GLU cc_start: 0.8076 (tp30) cc_final: 0.7730 (mm-30) REVERT: D 384 LYS cc_start: 0.8586 (tppt) cc_final: 0.8196 (tppt) REVERT: D 400 LEU cc_start: 0.8525 (tp) cc_final: 0.8296 (tt) REVERT: D 534 LYS cc_start: 0.8771 (tptm) cc_final: 0.8482 (tppt) REVERT: D 627 TYR cc_start: 0.8091 (m-10) cc_final: 0.7865 (m-80) REVERT: D 1284 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7653 (tm-30) REVERT: J 25 LYS cc_start: 0.8842 (pttt) cc_final: 0.8516 (pttp) outliers start: 1 outliers final: 1 residues processed: 533 average time/residue: 0.2100 time to fit residues: 160.3664 Evaluate side-chains 368 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 367 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 818 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN B 37 HIS C 389 ASN C 393 ASN C 490 ASN C 579 HIS C 992 GLN C1111 HIS C1205 GLN C1310 GLN C1344 ASN C1349 ASN D 170 GLN D 340 GLN D 458 ASN D 666 GLN D 880 GLN D1260 GLN D1367 HIS J 17 GLN F 103 ASN F 128 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116517 restraints weight = 36673.580| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.51 r_work: 0.3227 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 24910 Z= 0.240 Angle : 0.604 8.818 34170 Z= 0.320 Chirality : 0.043 0.157 4123 Planarity : 0.005 0.050 4249 Dihedral : 13.439 137.517 4143 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.44 % Allowed : 14.18 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 3143 helix: -0.28 (0.14), residues: 1138 sheet: -0.47 (0.27), residues: 358 loop : -2.17 (0.13), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 133 TYR 0.012 0.001 TYR C1190 PHE 0.025 0.002 PHE D1326 TRP 0.009 0.002 TRP D 687 HIS 0.006 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00561 (24905) covalent geometry : angle 0.60441 (34170) hydrogen bonds : bond 0.04655 ( 1041) hydrogen bonds : angle 4.36993 ( 2932) metal coordination : bond 0.03695 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 376 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6690 (t0) cc_final: 0.6275 (t0) REVERT: A 203 ASP cc_start: 0.8751 (p0) cc_final: 0.8459 (p0) REVERT: A 221 ASP cc_start: 0.8236 (t0) cc_final: 0.8031 (t0) REVERT: B 146 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7424 (mt-10) REVERT: C 79 LYS cc_start: 0.8948 (mptt) cc_final: 0.8712 (mmtp) REVERT: C 141 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7515 (p90) REVERT: C 305 HIS cc_start: 0.7813 (p-80) cc_final: 0.7541 (p90) REVERT: C 458 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8341 (mtpt) REVERT: C 568 ARG cc_start: 0.8508 (ptp90) cc_final: 0.8307 (ptp90) REVERT: C 763 LYS cc_start: 0.8808 (tttt) cc_final: 0.7586 (mptt) REVERT: C 893 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7958 (mtm-85) REVERT: C 1274 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.8062 (m-80) REVERT: C 1371 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8042 (mt-10) REVERT: D 37 GLU cc_start: 0.7564 (tt0) cc_final: 0.7236 (tt0) REVERT: D 330 MET cc_start: 0.8926 (ttp) cc_final: 0.8439 (ttp) REVERT: D 375 GLU cc_start: 0.8892 (tp30) cc_final: 0.8536 (mm-30) REVERT: D 400 LEU cc_start: 0.8489 (tp) cc_final: 0.8108 (tt) REVERT: D 497 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7879 (mm-30) REVERT: D 534 LYS cc_start: 0.8983 (tptm) cc_final: 0.8675 (tppt) REVERT: D 880 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8019 (tt0) REVERT: D 905 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8479 (mm) REVERT: D 1284 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8303 (tm-30) REVERT: J 25 LYS cc_start: 0.8969 (pttt) cc_final: 0.8647 (pttp) REVERT: F 61 ARG cc_start: 0.6739 (ttt180) cc_final: 0.6353 (tmt170) REVERT: F 123 ARG cc_start: 0.7612 (tpt-90) cc_final: 0.6526 (tpt170) REVERT: F 124 GLU cc_start: 0.7764 (tp30) cc_final: 0.7476 (tp30) outliers start: 54 outliers final: 35 residues processed: 413 average time/residue: 0.1785 time to fit residues: 112.2949 Evaluate side-chains 376 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 338 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 631 VAL Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 982 ILE Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1090 MET Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 612 LEU Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1341 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 141 LEU Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 281 optimal weight: 0.0000 chunk 101 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 309 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 275 optimal weight: 0.9990 chunk 316 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 4.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS C 478 ASN C1060 GLN C1079 GLN C1149 ASN D 435 GLN D 458 ASN D 489 ASN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116288 restraints weight = 36418.027| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.44 r_work: 0.3214 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24910 Z= 0.146 Angle : 0.509 8.995 34170 Z= 0.266 Chirality : 0.041 0.174 4123 Planarity : 0.004 0.044 4249 Dihedral : 13.429 141.020 4143 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.02 % Allowed : 16.93 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.14), residues: 3143 helix: 0.78 (0.15), residues: 1138 sheet: -0.28 (0.27), residues: 359 loop : -1.89 (0.13), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 133 TYR 0.017 0.001 TYR A 184 PHE 0.016 0.001 PHE C 16 TRP 0.010 0.001 TRP C1160 HIS 0.006 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00342 (24905) covalent geometry : angle 0.50874 (34170) hydrogen bonds : bond 0.03891 ( 1041) hydrogen bonds : angle 3.99591 ( 2932) metal coordination : bond 0.00349 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 360 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASP cc_start: 0.6913 (t0) cc_final: 0.6553 (t0) REVERT: A 203 ASP cc_start: 0.8606 (p0) cc_final: 0.8336 (p0) REVERT: B 114 ASP cc_start: 0.7438 (m-30) cc_final: 0.6824 (m-30) REVERT: B 146 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6996 (mt-10) REVERT: C 141 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7586 (p90) REVERT: C 305 HIS cc_start: 0.7825 (p-80) cc_final: 0.7491 (p90) REVERT: C 458 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8208 (mtpt) REVERT: C 661 PHE cc_start: 0.8254 (m-80) cc_final: 0.7876 (m-10) REVERT: C 801 ASN cc_start: 0.8229 (t0) cc_final: 0.7998 (m-40) REVERT: C 1110 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8630 (ttp-170) REVERT: C 1265 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7790 (mtt-85) REVERT: C 1274 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: C 1307 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7475 (m-80) REVERT: D 37 GLU cc_start: 0.7258 (tt0) cc_final: 0.6770 (tt0) REVERT: D 106 ASP cc_start: 0.7513 (m-30) cc_final: 0.7139 (m-30) REVERT: D 375 GLU cc_start: 0.8640 (tp30) cc_final: 0.8294 (mm-30) REVERT: D 400 LEU cc_start: 0.8516 (tp) cc_final: 0.8240 (tt) REVERT: D 497 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7698 (mm-30) REVERT: D 534 LYS cc_start: 0.8885 (tptm) cc_final: 0.8601 (tppt) REVERT: D 1284 GLN cc_start: 0.8543 (tm-30) cc_final: 0.8112 (tm-30) REVERT: J 25 LYS cc_start: 0.8939 (pttt) cc_final: 0.8656 (pttp) REVERT: F 123 ARG cc_start: 0.7647 (tpt-90) cc_final: 0.6394 (tpt170) REVERT: F 124 GLU cc_start: 0.7875 (tp30) cc_final: 0.7485 (tp30) outliers start: 67 outliers final: 43 residues processed: 408 average time/residue: 0.1780 time to fit residues: 111.6996 Evaluate side-chains 383 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 335 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 181 ARG Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 1079 GLN Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1110 ARG Chi-restraints excluded: chain C residue 1192 HIS Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1265 ARG Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain D residue 1339 ARG Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 82 optimal weight: 0.0020 chunk 287 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS C 478 ASN C 660 GLN D 266 ASN D 458 ASN D 880 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114976 restraints weight = 36368.461| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.20 r_work: 0.3198 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24910 Z= 0.144 Angle : 0.509 9.149 34170 Z= 0.264 Chirality : 0.040 0.171 4123 Planarity : 0.004 0.040 4249 Dihedral : 13.407 140.945 4143 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.06 % Allowed : 17.38 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 3143 helix: 1.29 (0.16), residues: 1138 sheet: -0.08 (0.26), residues: 384 loop : -1.73 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 413 TYR 0.010 0.001 TYR B 184 PHE 0.015 0.001 PHE D1326 TRP 0.011 0.001 TRP C1160 HIS 0.005 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00337 (24905) covalent geometry : angle 0.50853 (34170) hydrogen bonds : bond 0.03759 ( 1041) hydrogen bonds : angle 3.81470 ( 2932) metal coordination : bond 0.00389 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 335 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.7963 (pt) cc_final: 0.7546 (mt) REVERT: A 118 ASP cc_start: 0.7100 (t0) cc_final: 0.6613 (t0) REVERT: A 203 ASP cc_start: 0.8634 (p0) cc_final: 0.8277 (p0) REVERT: B 90 ILE cc_start: 0.8881 (tt) cc_final: 0.8585 (pt) REVERT: B 114 ASP cc_start: 0.7512 (m-30) cc_final: 0.6909 (m-30) REVERT: B 146 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6880 (mt-10) REVERT: C 141 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7631 (p90) REVERT: C 305 HIS cc_start: 0.7946 (p-80) cc_final: 0.7549 (p90) REVERT: C 458 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8076 (mtmt) REVERT: C 801 ASN cc_start: 0.8205 (t0) cc_final: 0.7949 (m-40) REVERT: C 893 ARG cc_start: 0.7799 (ptp90) cc_final: 0.7440 (ptp-110) REVERT: C 959 ASP cc_start: 0.7892 (t0) cc_final: 0.7569 (m-30) REVERT: C 1110 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8658 (ttp-170) REVERT: C 1243 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8493 (tp) REVERT: C 1265 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7749 (mtt-85) REVERT: C 1274 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: C 1307 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: D 330 MET cc_start: 0.8794 (ttp) cc_final: 0.8563 (ttp) REVERT: D 375 GLU cc_start: 0.8670 (tp30) cc_final: 0.8310 (mm-30) REVERT: D 400 LEU cc_start: 0.8499 (tp) cc_final: 0.8225 (tt) REVERT: D 497 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7819 (mm-30) REVERT: D 534 LYS cc_start: 0.8832 (tptm) cc_final: 0.8551 (tppt) REVERT: D 756 ILE cc_start: 0.8844 (mt) cc_final: 0.8644 (mp) REVERT: D 834 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7138 (mm-30) REVERT: D 838 GLU cc_start: 0.8568 (tp30) cc_final: 0.8050 (tm-30) REVERT: D 1284 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8182 (tm-30) REVERT: E 10 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8156 (mm) REVERT: J 25 LYS cc_start: 0.8911 (pttt) cc_final: 0.8649 (pttp) REVERT: F 123 ARG cc_start: 0.7701 (tpt-90) cc_final: 0.6458 (tpt170) REVERT: F 124 GLU cc_start: 0.7840 (tp30) cc_final: 0.7424 (tp30) outliers start: 90 outliers final: 59 residues processed: 404 average time/residue: 0.1671 time to fit residues: 104.0900 Evaluate side-chains 383 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 317 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 575 VAL Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 793 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 1079 GLN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1110 ARG Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1265 ARG Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1286 HIS Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1312 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 574 THR Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 884 VAL Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain D residue 1314 SER Chi-restraints excluded: chain D residue 1339 ARG Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 201 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 48 optimal weight: 0.0970 chunk 102 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 207 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 259 optimal weight: 0.0870 chunk 182 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1079 GLN D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116481 restraints weight = 36282.814| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.45 r_work: 0.3236 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24910 Z= 0.109 Angle : 0.478 9.103 34170 Z= 0.248 Chirality : 0.040 0.165 4123 Planarity : 0.003 0.038 4249 Dihedral : 13.376 143.451 4143 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.84 % Allowed : 18.01 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3143 helix: 1.66 (0.16), residues: 1138 sheet: 0.02 (0.26), residues: 395 loop : -1.55 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1283 TYR 0.009 0.001 TYR B 184 PHE 0.012 0.001 PHE C 993 TRP 0.011 0.001 TRP C1160 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00249 (24905) covalent geometry : angle 0.47769 (34170) hydrogen bonds : bond 0.03381 ( 1041) hydrogen bonds : angle 3.67292 ( 2932) metal coordination : bond 0.00249 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 342 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.7899 (pt) cc_final: 0.7687 (mt) REVERT: A 118 ASP cc_start: 0.7220 (t0) cc_final: 0.6686 (t0) REVERT: A 200 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8720 (pt) REVERT: A 203 ASP cc_start: 0.8818 (p0) cc_final: 0.8453 (p0) REVERT: B 90 ILE cc_start: 0.8941 (tt) cc_final: 0.8658 (pt) REVERT: B 114 ASP cc_start: 0.7456 (m-30) cc_final: 0.6788 (m-30) REVERT: B 146 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7255 (mt-10) REVERT: C 141 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7817 (p90) REVERT: C 458 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8255 (mtmt) REVERT: C 541 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8766 (pt0) REVERT: C 801 ASN cc_start: 0.8327 (t0) cc_final: 0.8025 (m-40) REVERT: C 819 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7787 (t0) REVERT: C 893 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7587 (ptp-110) REVERT: C 959 ASP cc_start: 0.8109 (t0) cc_final: 0.7788 (m-30) REVERT: C 1079 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7280 (pp30) REVERT: C 1110 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8665 (ttp-170) REVERT: C 1202 ASP cc_start: 0.7208 (p0) cc_final: 0.6996 (p0) REVERT: C 1274 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: C 1307 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7429 (m-80) REVERT: D 330 MET cc_start: 0.9041 (ttp) cc_final: 0.8713 (ttp) REVERT: D 375 GLU cc_start: 0.8877 (tp30) cc_final: 0.8516 (mm-30) REVERT: D 386 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8653 (mt0) REVERT: D 400 LEU cc_start: 0.8423 (tp) cc_final: 0.8083 (tt) REVERT: D 497 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8041 (mm-30) REVERT: D 534 LYS cc_start: 0.8935 (tptm) cc_final: 0.8657 (tppt) REVERT: D 756 ILE cc_start: 0.8909 (mt) cc_final: 0.8684 (mp) REVERT: D 834 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7257 (mm-30) REVERT: D 838 GLU cc_start: 0.8671 (tp30) cc_final: 0.8065 (tm-30) REVERT: D 905 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8475 (mm) REVERT: D 1284 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8365 (tm-30) REVERT: E 10 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8125 (mm) REVERT: J 25 LYS cc_start: 0.8965 (pttt) cc_final: 0.8712 (pttp) REVERT: F 4 GLU cc_start: 0.7436 (mp0) cc_final: 0.7162 (mp0) REVERT: F 123 ARG cc_start: 0.7661 (tpt-90) cc_final: 0.6418 (tpt170) REVERT: F 124 GLU cc_start: 0.7810 (tp30) cc_final: 0.7366 (tp30) outliers start: 85 outliers final: 56 residues processed: 404 average time/residue: 0.1673 time to fit residues: 105.7610 Evaluate side-chains 393 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 326 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 541 GLN Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 793 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 819 ASP Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1079 GLN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1110 ARG Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1286 HIS Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 386 GLN Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain D residue 1339 ARG Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain F residue 109 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 170 optimal weight: 0.2980 chunk 200 optimal weight: 0.6980 chunk 165 optimal weight: 4.9990 chunk 267 optimal weight: 0.0670 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 291 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS C 660 GLN C1079 GLN D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116946 restraints weight = 35950.075| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.25 r_work: 0.3242 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24910 Z= 0.100 Angle : 0.471 9.312 34170 Z= 0.245 Chirality : 0.039 0.157 4123 Planarity : 0.003 0.040 4249 Dihedral : 13.350 144.384 4143 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.88 % Allowed : 18.65 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3143 helix: 1.89 (0.16), residues: 1138 sheet: 0.05 (0.26), residues: 395 loop : -1.46 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 413 TYR 0.009 0.001 TYR B 184 PHE 0.014 0.001 PHE C 993 TRP 0.011 0.001 TRP C1160 HIS 0.003 0.000 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00226 (24905) covalent geometry : angle 0.47098 (34170) hydrogen bonds : bond 0.03219 ( 1041) hydrogen bonds : angle 3.58421 ( 2932) metal coordination : bond 0.00198 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 340 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.7886 (pt) cc_final: 0.7622 (mt) REVERT: A 118 ASP cc_start: 0.7205 (t0) cc_final: 0.6678 (t0) REVERT: A 200 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8709 (pt) REVERT: A 203 ASP cc_start: 0.8814 (p0) cc_final: 0.8453 (p0) REVERT: B 90 ILE cc_start: 0.8891 (tt) cc_final: 0.8651 (pt) REVERT: B 114 ASP cc_start: 0.7485 (m-30) cc_final: 0.6846 (m-30) REVERT: B 146 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7133 (mt-10) REVERT: C 141 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.7836 (p90) REVERT: C 413 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.8351 (ttm170) REVERT: C 458 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8265 (mtmt) REVERT: C 801 ASN cc_start: 0.8320 (t0) cc_final: 0.8045 (m-40) REVERT: C 893 ARG cc_start: 0.7928 (ptp90) cc_final: 0.7599 (ptp-110) REVERT: C 959 ASP cc_start: 0.8120 (t0) cc_final: 0.7774 (m-30) REVERT: C 1265 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7804 (mtt-85) REVERT: C 1274 TYR cc_start: 0.8571 (OUTLIER) cc_final: 0.8144 (m-80) REVERT: C 1307 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7367 (m-80) REVERT: D 304 ASP cc_start: 0.8060 (t0) cc_final: 0.7842 (t0) REVERT: D 375 GLU cc_start: 0.8886 (tp30) cc_final: 0.8522 (mm-30) REVERT: D 386 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8519 (mt0) REVERT: D 400 LEU cc_start: 0.8409 (tp) cc_final: 0.8085 (tt) REVERT: D 484 MET cc_start: 0.9046 (mtt) cc_final: 0.8651 (mtt) REVERT: D 497 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8030 (mm-30) REVERT: D 534 LYS cc_start: 0.8926 (tptm) cc_final: 0.8651 (tppt) REVERT: D 756 ILE cc_start: 0.8895 (mt) cc_final: 0.8678 (mp) REVERT: D 834 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7150 (mm-30) REVERT: D 838 GLU cc_start: 0.8656 (tp30) cc_final: 0.8143 (tm-30) REVERT: D 905 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8438 (mm) REVERT: D 1284 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8345 (tm-30) REVERT: J 25 LYS cc_start: 0.8954 (pttt) cc_final: 0.8722 (pttp) REVERT: F 4 GLU cc_start: 0.7470 (mp0) cc_final: 0.7228 (mp0) REVERT: F 123 ARG cc_start: 0.7647 (tpt-90) cc_final: 0.6437 (tpt170) REVERT: F 124 GLU cc_start: 0.7869 (tp30) cc_final: 0.7465 (tp30) outliers start: 86 outliers final: 56 residues processed: 404 average time/residue: 0.1680 time to fit residues: 105.1181 Evaluate side-chains 388 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 325 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 793 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1265 ARG Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1286 HIS Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 386 GLN Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 150 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 115 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 279 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.146560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113275 restraints weight = 36347.327| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.43 r_work: 0.3193 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24910 Z= 0.164 Angle : 0.528 10.252 34170 Z= 0.273 Chirality : 0.041 0.168 4123 Planarity : 0.004 0.043 4249 Dihedral : 13.424 142.501 4143 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.11 % Allowed : 19.19 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3143 helix: 1.73 (0.16), residues: 1149 sheet: 0.08 (0.26), residues: 390 loop : -1.43 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1150 TYR 0.009 0.001 TYR C 36 PHE 0.016 0.001 PHE C 993 TRP 0.010 0.001 TRP C1160 HIS 0.003 0.001 HIS C 582 Details of bonding type rmsd covalent geometry : bond 0.00387 (24905) covalent geometry : angle 0.52765 (34170) hydrogen bonds : bond 0.03925 ( 1041) hydrogen bonds : angle 3.68558 ( 2932) metal coordination : bond 0.00475 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 323 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 ILE cc_start: 0.8036 (pt) cc_final: 0.7700 (mt) REVERT: A 118 ASP cc_start: 0.7303 (t0) cc_final: 0.6790 (t0) REVERT: A 200 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8757 (pt) REVERT: A 203 ASP cc_start: 0.8810 (p0) cc_final: 0.8450 (p0) REVERT: B 50 SER cc_start: 0.8841 (p) cc_final: 0.8637 (p) REVERT: B 90 ILE cc_start: 0.8974 (tt) cc_final: 0.8711 (pt) REVERT: B 114 ASP cc_start: 0.7534 (m-30) cc_final: 0.6920 (m-30) REVERT: B 146 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 141 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.7701 (p90) REVERT: C 413 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.8293 (ttm110) REVERT: C 458 LYS cc_start: 0.8729 (ttmt) cc_final: 0.8270 (mtmt) REVERT: C 568 ARG cc_start: 0.8506 (ptp90) cc_final: 0.8119 (ptp-110) REVERT: C 893 ARG cc_start: 0.7933 (ptp90) cc_final: 0.7608 (ptp-110) REVERT: C 959 ASP cc_start: 0.8181 (t0) cc_final: 0.7846 (m-30) REVERT: C 1265 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7769 (mtt-85) REVERT: C 1274 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: C 1307 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: D 304 ASP cc_start: 0.8157 (t0) cc_final: 0.7950 (t0) REVERT: D 330 MET cc_start: 0.8923 (ttp) cc_final: 0.8617 (ttp) REVERT: D 375 GLU cc_start: 0.8897 (tp30) cc_final: 0.8514 (mm-30) REVERT: D 392 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8096 (p) REVERT: D 497 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8054 (mm-30) REVERT: D 534 LYS cc_start: 0.8934 (tptm) cc_final: 0.8670 (tppt) REVERT: D 699 MET cc_start: 0.8151 (tpp) cc_final: 0.7673 (tpp) REVERT: D 756 ILE cc_start: 0.8901 (mt) cc_final: 0.8689 (mp) REVERT: D 838 GLU cc_start: 0.8698 (tp30) cc_final: 0.8326 (tm-30) REVERT: D 905 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8581 (mm) REVERT: D 1284 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8374 (tm-30) REVERT: D 1290 ASN cc_start: 0.7619 (t0) cc_final: 0.7102 (t0) REVERT: E 10 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8186 (mm) REVERT: J 25 LYS cc_start: 0.8977 (pttt) cc_final: 0.8722 (pttp) REVERT: F 4 GLU cc_start: 0.7434 (mp0) cc_final: 0.7214 (mp0) REVERT: F 123 ARG cc_start: 0.7665 (tpt-90) cc_final: 0.6411 (tpt170) REVERT: F 124 GLU cc_start: 0.7848 (tp30) cc_final: 0.7638 (tp30) outliers start: 91 outliers final: 67 residues processed: 393 average time/residue: 0.1625 time to fit residues: 100.0264 Evaluate side-chains 390 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 315 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 505 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 793 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1265 ARG Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1286 HIS Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1312 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain D residue 1341 THR Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain F residue 109 ILE Chi-restraints excluded: chain F residue 141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 217 optimal weight: 0.0470 chunk 210 optimal weight: 0.6980 chunk 224 optimal weight: 0.6980 chunk 270 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 124 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.148330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.115342 restraints weight = 36062.201| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.44 r_work: 0.3223 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24910 Z= 0.106 Angle : 0.491 10.074 34170 Z= 0.254 Chirality : 0.039 0.164 4123 Planarity : 0.003 0.039 4249 Dihedral : 13.407 145.414 4143 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.66 % Allowed : 19.73 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3143 helix: 1.96 (0.16), residues: 1145 sheet: 0.11 (0.26), residues: 388 loop : -1.34 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1283 TYR 0.010 0.001 TYR C 128 PHE 0.017 0.001 PHE C 993 TRP 0.011 0.001 TRP C1160 HIS 0.003 0.001 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00240 (24905) covalent geometry : angle 0.49083 (34170) hydrogen bonds : bond 0.03356 ( 1041) hydrogen bonds : angle 3.58925 ( 2932) metal coordination : bond 0.00238 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 324 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: A 115 ILE cc_start: 0.7969 (pt) cc_final: 0.7551 (mt) REVERT: A 118 ASP cc_start: 0.7240 (t0) cc_final: 0.6703 (t0) REVERT: A 200 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8701 (pt) REVERT: A 203 ASP cc_start: 0.8799 (p0) cc_final: 0.8440 (p0) REVERT: B 90 ILE cc_start: 0.8889 (tt) cc_final: 0.8620 (pt) REVERT: B 114 ASP cc_start: 0.7497 (m-30) cc_final: 0.6874 (m-30) REVERT: B 146 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7214 (mt-10) REVERT: C 141 PHE cc_start: 0.8589 (OUTLIER) cc_final: 0.7876 (p90) REVERT: C 413 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8294 (ttm110) REVERT: C 458 LYS cc_start: 0.8712 (ttmt) cc_final: 0.8273 (mtmt) REVERT: C 568 ARG cc_start: 0.8473 (ptp90) cc_final: 0.8094 (ptp-110) REVERT: C 801 ASN cc_start: 0.8331 (t0) cc_final: 0.7912 (m-40) REVERT: C 893 ARG cc_start: 0.7909 (ptp90) cc_final: 0.7585 (ptp-110) REVERT: C 959 ASP cc_start: 0.8173 (t0) cc_final: 0.7833 (m-30) REVERT: C 1202 ASP cc_start: 0.7347 (p0) cc_final: 0.6948 (p0) REVERT: C 1265 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7764 (mtt-85) REVERT: C 1274 TYR cc_start: 0.8584 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: C 1307 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: D 127 MET cc_start: 0.8924 (tpp) cc_final: 0.8683 (mmm) REVERT: D 304 ASP cc_start: 0.8134 (t0) cc_final: 0.7899 (t0) REVERT: D 330 MET cc_start: 0.8918 (ttp) cc_final: 0.8610 (ttp) REVERT: D 392 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8008 (p) REVERT: D 400 LEU cc_start: 0.8445 (tp) cc_final: 0.8198 (tt) REVERT: D 484 MET cc_start: 0.9034 (mtt) cc_final: 0.8563 (mtt) REVERT: D 497 GLU cc_start: 0.8323 (mm-30) cc_final: 0.8103 (mm-30) REVERT: D 534 LYS cc_start: 0.8932 (tptm) cc_final: 0.8668 (tppt) REVERT: D 756 ILE cc_start: 0.8899 (mt) cc_final: 0.8686 (mp) REVERT: D 838 GLU cc_start: 0.8653 (tp30) cc_final: 0.8392 (tm-30) REVERT: D 841 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9141 (tt) REVERT: D 905 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8480 (mm) REVERT: D 1284 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8381 (tm-30) REVERT: D 1290 ASN cc_start: 0.7633 (t0) cc_final: 0.7145 (t0) REVERT: E 10 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8193 (mm) REVERT: J 25 LYS cc_start: 0.8962 (pttt) cc_final: 0.8736 (pttp) REVERT: F 4 GLU cc_start: 0.7411 (mp0) cc_final: 0.7207 (mp0) REVERT: F 123 ARG cc_start: 0.7684 (tpt-90) cc_final: 0.6489 (tpt170) REVERT: F 124 GLU cc_start: 0.7807 (tp30) cc_final: 0.7574 (tp30) outliers start: 81 outliers final: 61 residues processed: 392 average time/residue: 0.1600 time to fit residues: 98.3080 Evaluate side-chains 386 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 316 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 793 CYS Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1265 ARG Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1286 HIS Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 109 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 264 optimal weight: 0.0170 chunk 42 optimal weight: 0.7980 chunk 314 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1079 GLN D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111810 restraints weight = 36311.574| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.25 r_work: 0.3175 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24910 Z= 0.183 Angle : 0.555 11.634 34170 Z= 0.287 Chirality : 0.042 0.176 4123 Planarity : 0.004 0.043 4249 Dihedral : 13.520 141.908 4143 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.61 % Allowed : 20.09 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3143 helix: 1.72 (0.16), residues: 1154 sheet: -0.07 (0.26), residues: 384 loop : -1.37 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1283 TYR 0.009 0.001 TYR D 773 PHE 0.017 0.002 PHE C 993 TRP 0.010 0.001 TRP C1160 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00434 (24905) covalent geometry : angle 0.55519 (34170) hydrogen bonds : bond 0.04191 ( 1041) hydrogen bonds : angle 3.77003 ( 2932) metal coordination : bond 0.00561 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 324 time to evaluate : 0.908 Fit side-chains REVERT: A 118 ASP cc_start: 0.7351 (t0) cc_final: 0.6826 (t0) REVERT: A 200 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8716 (pt) REVERT: A 203 ASP cc_start: 0.8794 (p0) cc_final: 0.8454 (p0) REVERT: B 90 ILE cc_start: 0.8958 (tt) cc_final: 0.8692 (pt) REVERT: B 142 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.6873 (mpp80) REVERT: B 146 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 141 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.7602 (p90) REVERT: C 413 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8348 (ttm110) REVERT: C 458 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8523 (mtpp) REVERT: C 568 ARG cc_start: 0.8546 (ptp90) cc_final: 0.8163 (ptp-110) REVERT: C 573 PHE cc_start: 0.7491 (t80) cc_final: 0.7229 (t80) REVERT: C 801 ASN cc_start: 0.8287 (t0) cc_final: 0.7884 (m-40) REVERT: C 893 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7616 (ptp-110) REVERT: C 959 ASP cc_start: 0.8106 (t0) cc_final: 0.7782 (m-30) REVERT: C 993 PHE cc_start: 0.7085 (t80) cc_final: 0.6795 (t80) REVERT: C 1202 ASP cc_start: 0.7444 (p0) cc_final: 0.7019 (p0) REVERT: C 1265 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7788 (mtt-85) REVERT: C 1274 TYR cc_start: 0.8636 (OUTLIER) cc_final: 0.8196 (m-80) REVERT: C 1307 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7539 (m-10) REVERT: D 304 ASP cc_start: 0.8195 (t0) cc_final: 0.7980 (t0) REVERT: D 330 MET cc_start: 0.8869 (ttp) cc_final: 0.8558 (ttp) REVERT: D 392 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8159 (p) REVERT: D 416 ILE cc_start: 0.9039 (tt) cc_final: 0.8828 (tt) REVERT: D 497 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8069 (mm-30) REVERT: D 534 LYS cc_start: 0.8926 (tptm) cc_final: 0.8692 (tppt) REVERT: D 756 ILE cc_start: 0.8932 (mt) cc_final: 0.8731 (mp) REVERT: D 838 GLU cc_start: 0.8696 (tp30) cc_final: 0.8457 (tm-30) REVERT: D 841 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9188 (tt) REVERT: D 905 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8607 (mm) REVERT: D 1284 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8447 (tm-30) REVERT: D 1290 ASN cc_start: 0.7709 (t0) cc_final: 0.7278 (t0) REVERT: D 1326 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.8056 (p90) REVERT: E 10 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8159 (mm) REVERT: J 25 LYS cc_start: 0.8981 (pttt) cc_final: 0.8720 (pttp) REVERT: F 4 GLU cc_start: 0.7494 (mp0) cc_final: 0.7271 (mp0) REVERT: F 123 ARG cc_start: 0.7674 (tpt-90) cc_final: 0.6456 (tpt170) REVERT: F 124 GLU cc_start: 0.7826 (tp30) cc_final: 0.7590 (tp30) outliers start: 80 outliers final: 62 residues processed: 389 average time/residue: 0.1650 time to fit residues: 100.7277 Evaluate side-chains 392 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 319 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 793 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 1079 GLN Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1150 ILE Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1265 ARG Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1286 HIS Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 386 GLN Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 841 LEU Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain D residue 1326 PHE Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain J residue 55 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 109 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 101 optimal weight: 0.8980 chunk 197 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 15 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 173 optimal weight: 0.0370 overall best weight: 0.4868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1079 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112585 restraints weight = 36310.778| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.33 r_work: 0.3191 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24910 Z= 0.104 Angle : 0.511 10.780 34170 Z= 0.265 Chirality : 0.040 0.171 4123 Planarity : 0.003 0.039 4249 Dihedral : 13.500 145.692 4143 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.16 % Allowed : 20.95 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3143 helix: 1.95 (0.16), residues: 1145 sheet: 0.17 (0.26), residues: 379 loop : -1.30 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 133 TYR 0.011 0.001 TYR C 128 PHE 0.018 0.001 PHE C 993 TRP 0.012 0.001 TRP C1160 HIS 0.003 0.001 HIS C 861 Details of bonding type rmsd covalent geometry : bond 0.00231 (24905) covalent geometry : angle 0.51123 (34170) hydrogen bonds : bond 0.03507 ( 1041) hydrogen bonds : angle 3.62691 ( 2932) metal coordination : bond 0.00270 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6286 Ramachandran restraints generated. 3143 Oldfield, 0 Emsley, 3143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 336 time to evaluate : 0.683 Fit side-chains REVERT: A 118 ASP cc_start: 0.7301 (t0) cc_final: 0.6738 (t0) REVERT: A 200 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8689 (pt) REVERT: A 203 ASP cc_start: 0.8829 (p0) cc_final: 0.8449 (p0) REVERT: B 90 ILE cc_start: 0.8909 (tt) cc_final: 0.8661 (pt) REVERT: B 114 ASP cc_start: 0.7549 (m-30) cc_final: 0.6941 (m-30) REVERT: B 122 GLU cc_start: 0.7953 (mp0) cc_final: 0.7680 (mp0) REVERT: B 142 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6870 (mpp80) REVERT: B 146 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7290 (mt-10) REVERT: B 175 SER cc_start: 0.9059 (p) cc_final: 0.8857 (p) REVERT: C 141 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7923 (p90) REVERT: C 413 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8352 (ttm110) REVERT: C 458 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8427 (mtpp) REVERT: C 568 ARG cc_start: 0.8458 (ptp90) cc_final: 0.8064 (ptp-110) REVERT: C 573 PHE cc_start: 0.7321 (t80) cc_final: 0.7101 (t80) REVERT: C 801 ASN cc_start: 0.8283 (t0) cc_final: 0.7865 (m-40) REVERT: C 893 ARG cc_start: 0.7908 (ptp90) cc_final: 0.7563 (ptp-110) REVERT: C 959 ASP cc_start: 0.8125 (t0) cc_final: 0.7780 (m-30) REVERT: C 993 PHE cc_start: 0.6995 (t80) cc_final: 0.6749 (t80) REVERT: C 1202 ASP cc_start: 0.7275 (p0) cc_final: 0.6891 (p0) REVERT: C 1265 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7760 (mtt-85) REVERT: C 1274 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: C 1307 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.7341 (m-10) REVERT: D 127 MET cc_start: 0.8904 (tpp) cc_final: 0.8627 (mmm) REVERT: D 237 MET cc_start: 0.8970 (mtp) cc_final: 0.8682 (mtt) REVERT: D 304 ASP cc_start: 0.8222 (t0) cc_final: 0.7982 (t0) REVERT: D 330 MET cc_start: 0.8776 (ttp) cc_final: 0.8429 (ttp) REVERT: D 416 ILE cc_start: 0.8973 (tt) cc_final: 0.8751 (tt) REVERT: D 497 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8051 (mm-30) REVERT: D 534 LYS cc_start: 0.8887 (tptm) cc_final: 0.8621 (tppt) REVERT: D 756 ILE cc_start: 0.8960 (mt) cc_final: 0.8753 (mp) REVERT: D 838 GLU cc_start: 0.8659 (tp30) cc_final: 0.8387 (tm-30) REVERT: D 905 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8245 (mt) REVERT: D 1284 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8386 (tm-30) REVERT: D 1290 ASN cc_start: 0.7692 (t0) cc_final: 0.7261 (t0) REVERT: E 10 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8210 (mm) REVERT: J 25 LYS cc_start: 0.8938 (pttt) cc_final: 0.8681 (pttp) REVERT: F 4 GLU cc_start: 0.7432 (mp0) cc_final: 0.7221 (mp0) REVERT: F 123 ARG cc_start: 0.7664 (tpt-90) cc_final: 0.6483 (tpt170) REVERT: F 124 GLU cc_start: 0.7797 (tp30) cc_final: 0.7558 (tp30) outliers start: 70 outliers final: 55 residues processed: 390 average time/residue: 0.1653 time to fit residues: 100.7258 Evaluate side-chains 389 residues out of total 2707 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 326 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 ARG Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 141 PHE Chi-restraints excluded: chain C residue 193 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 793 CYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 THR Chi-restraints excluded: chain C residue 1087 VAL Chi-restraints excluded: chain C residue 1097 VAL Chi-restraints excluded: chain C residue 1219 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1265 ARG Chi-restraints excluded: chain C residue 1274 TYR Chi-restraints excluded: chain C residue 1275 LEU Chi-restraints excluded: chain C residue 1286 HIS Chi-restraints excluded: chain C residue 1307 PHE Chi-restraints excluded: chain C residue 1379 MET Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 96 LYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 483 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 555 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 674 VAL Chi-restraints excluded: chain D residue 701 THR Chi-restraints excluded: chain D residue 758 THR Chi-restraints excluded: chain D residue 794 SER Chi-restraints excluded: chain D residue 818 THR Chi-restraints excluded: chain D residue 905 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 1197 ILE Chi-restraints excluded: chain D residue 1294 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 109 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 103 optimal weight: 6.9990 chunk 193 optimal weight: 0.3980 chunk 153 optimal weight: 0.0670 chunk 150 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 300 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 113 optimal weight: 4.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 386 GLN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113294 restraints weight = 36266.324| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.32 r_work: 0.3192 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24910 Z= 0.107 Angle : 0.506 11.239 34170 Z= 0.259 Chirality : 0.040 0.165 4123 Planarity : 0.003 0.040 4249 Dihedral : 13.460 145.872 4143 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.21 % Allowed : 21.08 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.15), residues: 3143 helix: 2.02 (0.16), residues: 1145 sheet: 0.16 (0.26), residues: 379 loop : -1.26 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1283 TYR 0.009 0.001 TYR C 67 PHE 0.018 0.001 PHE C 993 TRP 0.010 0.001 TRP C1160 HIS 0.003 0.000 HIS C 861 Details of bonding type rmsd covalent geometry : bond 0.00243 (24905) covalent geometry : angle 0.50573 (34170) hydrogen bonds : bond 0.03335 ( 1041) hydrogen bonds : angle 3.53980 ( 2932) metal coordination : bond 0.00242 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6455.47 seconds wall clock time: 110 minutes 24.49 seconds (6624.49 seconds total)