Starting phenix.real_space_refine on Sat Aug 8 05:55:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypa_33997/08_2026/7ypa_33997.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 83 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 16044 2.51 5 N 4596 2.21 5 O 5191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 156 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26022 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1663 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1655 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 10060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10060 Classifications: {'peptide': 1285} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1231} Chain breaks: 3 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'GLU:plan': 8, 'TYR:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 64 Chain: "D" Number of atoms: 10269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1333, 10269 Classifications: {'peptide': 1333} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 1277} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 1, 'ARG:plan': 5, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 591 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 2, 'TRANS': 71} Chain: "F" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 577 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "G" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "H" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 416 Classifications: {'RNAv2': 20} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 13} Link IDs: {'rna2p': 1, 'rna3p': 18} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'RNAv2': 10} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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 13795 SG CYS D 72 112.384 48.935 61.085 1.00 68.58 S ATOM 13892 SG CYS D 85 115.189 49.139 63.467 1.00 72.91 S ATOM 13912 SG CYS D 88 112.079 51.998 63.043 1.00 76.43 S ATOM 19579 SG CYS D 814 87.667 67.919 125.063 1.00 37.98 S ATOM 20144 SG CYS D 888 86.105 68.261 121.576 1.00 29.67 S ATOM 20195 SG CYS D 895 84.867 65.130 123.142 1.00 23.03 S ATOM 20216 SG CYS D 898 83.072 68.255 123.998 1.00 21.40 S Time building chain proxies: 5.32, per 1000 atoms: 0.20 Number of scatterers: 26022 At special positions: 0 Unit cell: (135.928, 160.761, 164.682, 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 105 16.00 P 83 15.00 Mg 1 11.99 O 5191 8.00 N 4596 7.00 C 16044 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " Number of angles added : 6 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5776 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 45 sheets defined 36.2% alpha, 17.4% beta 36 base pairs and 65 stacking pairs defined. Time for finding SS restraints: 3.18 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.865A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.889A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 234 removed outlier: 4.643A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.769A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.748A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 227 removed outlier: 3.773A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.744A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.952A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.560A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.186A pdb=" N SER C 166 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 163 through 167' Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.553A pdb=" N ASP C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 295 removed outlier: 3.624A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.654A pdb=" N GLY C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.537A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 3.660A pdb=" N LEU C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 removed outlier: 3.616A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.631A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.517A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 508 Processing helix chain 'C' and resid 519 through 528 removed outlier: 3.668A pdb=" N ARG C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.861A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.899A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN C 613 " --> pdb=" O ILE C 609 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.752A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.530A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 942 through 980 removed outlier: 4.232A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.156A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.706A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 4.023A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.530A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.858A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.726A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.889A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.794A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.537A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.540A pdb=" N TYR D 165 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.726A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 207 removed outlier: 3.799A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (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 263 through 285 removed outlier: 3.543A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.673A pdb=" N VAL D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 377 removed outlier: 3.806A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) 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 415 removed outlier: 3.984A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) 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 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.697A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 Processing helix chain 'D' and resid 614 through 632 removed outlier: 3.525A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.615A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.499A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.615A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 865 through 874 removed outlier: 3.757A pdb=" N GLU D 874 " --> pdb=" O ASP D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.770A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.615A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.699A pdb=" N GLY D1071 " --> pdb=" O THR D1068 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1068 through 1072' Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.839A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.659A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1295 Processing helix chain 'D' and resid 1310 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.619A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.697A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1370 removed outlier: 3.708A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.683A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.930A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.998A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.153A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLY A 151 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.153A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 151 " --> pdb=" O TYR A 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.898A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 13 through 16 removed outlier: 3.524A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 99 through 105 removed outlier: 3.711A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE B 140 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 171 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 108 through 111 removed outlier: 3.843A pdb=" N GLY B 108 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 133 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.814A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.595A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.559A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN C 120 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 118 " --> pdb=" O LEU C 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.635A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.502A pdb=" N GLN C 148 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.680A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 227 through 231 Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.687A pdb=" N MET C 239 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 285 " --> pdb=" O MET C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 255 through 257 removed outlier: 4.351A pdb=" N VAL C 263 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ALA C 257 " --> pdb=" O VAL C 261 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.426A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.375A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 749 through 752 removed outlier: 6.915A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.676A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.145A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 4.322A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.807A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.616A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.622A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 526 through 527 removed outlier: 3.711A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 707 through 708 removed outlier: 3.752A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 848 through 849 removed outlier: 7.235A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU D 857 " --> pdb=" O VAL D 848 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 949 through 951 removed outlier: 4.663A pdb=" N ALA D1018 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 991 through 996 removed outlier: 3.831A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1034 through 1038 removed outlier: 3.746A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1046 through 1048 removed outlier: 3.836A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1188 through 1190 removed outlier: 3.711A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281 removed outlier: 6.844A pdb=" N THR D1301 " --> pdb=" O VAL D1267 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 65 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7678 1.34 - 1.45: 4121 1.45 - 1.57: 14441 1.57 - 1.69: 165 1.69 - 1.81: 182 Bond restraints: 26587 Sorted by residual: bond pdb=" C3' DA F 0 " pdb=" C2' DA F 0 " ideal model delta sigma weight residual 1.516 1.548 -0.032 8.00e-03 1.56e+04 1.58e+01 bond pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " ideal model delta sigma weight residual 1.435 1.481 -0.046 1.30e-02 5.92e+03 1.24e+01 bond pdb=" C3' DC G -7 " pdb=" C2' DC G -7 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.95e+00 bond pdb=" C3' DA F 11 " pdb=" O3' DA F 11 " ideal model delta sigma weight residual 1.435 1.474 -0.039 1.30e-02 5.92e+03 8.80e+00 bond pdb=" C3' DA G 7 " pdb=" C2' DA G 7 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.72e+00 ... (remaining 26582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 35703 2.12 - 4.23: 573 4.23 - 6.35: 36 6.35 - 8.47: 11 8.47 - 10.59: 1 Bond angle restraints: 36324 Sorted by residual: angle pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " pdb=" P DG G -6 " ideal model delta sigma weight residual 119.70 124.86 -5.16 1.20e+00 6.94e-01 1.85e+01 angle pdb=" C3' DA F 11 " pdb=" O3' DA F 11 " pdb=" P DC F 12 " ideal model delta sigma weight residual 119.70 124.72 -5.02 1.20e+00 6.94e-01 1.75e+01 angle pdb=" N3 DT G 11 " pdb=" C4 DT G 11 " pdb=" O4 DT G 11 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT G -2 " pdb=" C4 DT G -2 " pdb=" O4 DT G -2 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT G -11 " pdb=" C4 DT G -11 " pdb=" O4 DT G -11 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 36319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 15633 35.19 - 70.39: 449 70.39 - 105.58: 29 105.58 - 140.78: 1 140.78 - 175.97: 3 Dihedral angle restraints: 16115 sinusoidal: 7139 harmonic: 8976 Sorted by residual: dihedral pdb=" C4' G H -10 " pdb=" C3' G H -10 " pdb=" C2' G H -10 " pdb=" C1' G H -10 " ideal model delta sinusoidal sigma weight residual 36.34 -31.62 67.96 1 3.10e+00 1.04e-01 6.24e+02 dihedral pdb=" O4' G H -10 " pdb=" C4' G H -10 " pdb=" C3' G H -10 " pdb=" C2' G H -10 " ideal model delta sinusoidal sigma weight residual -35.15 20.03 -55.18 1 4.00e+00 6.25e-02 2.57e+02 dihedral pdb=" O4' G H -10 " pdb=" C2' G H -10 " pdb=" C1' G H -10 " pdb=" C3' G H -10 " ideal model delta sinusoidal sigma weight residual 25.59 -33.12 58.71 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 16112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3453 0.057 - 0.114: 602 0.114 - 0.171: 108 0.171 - 0.228: 22 0.228 - 0.285: 21 Chirality restraints: 4206 Sorted by residual: chirality pdb=" P C H -18 " pdb=" OP1 C H -18 " pdb=" OP2 C H -18 " pdb=" O5' C H -18 " both_signs ideal model delta sigma weight residual True 2.17 -2.46 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' G H -10 " pdb=" C3' G H -10 " pdb=" O2' G H -10 " pdb=" C1' G H -10 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" P C H -9 " pdb=" OP1 C H -9 " pdb=" OP2 C H -9 " pdb=" O5' C H -9 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 4203 not shown) Planarity restraints: 4441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 190 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 212 " -0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO B 213 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 213 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 213 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 245 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO D 246 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 246 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 246 " 0.028 5.00e-02 4.00e+02 ... (remaining 4438 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1432 2.73 - 3.27: 22578 3.27 - 3.82: 41563 3.82 - 4.36: 49680 4.36 - 4.90: 85978 Nonbonded interactions: 201231 Sorted by model distance: nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.191 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.226 2.170 nonbonded pdb=" O GLY D 613 " pdb=" OG1 THR D 617 " model vdw 2.298 3.040 nonbonded pdb=" O PHE C 804 " pdb=" OG SER D 638 " model vdw 2.307 3.040 nonbonded pdb=" O SER D1064 " pdb=" OG SER D1064 " model vdw 2.321 3.040 ... (remaining 201226 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 7 through 66 or (resid 67 and (name N or name CA or name C \ or name O or name CB )) or resid 68 through 117 or (resid 118 and (name N or na \ me CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N o \ r name CA or name C or name O or name CB )) or resid 121 through 157 or (resid 1 \ 70 and (name N or name CA or name C or name O or name CB )) or resid 171 through \ 192 or (resid 193 through 194 and (name N or name CA or name C or name O or nam \ e CB )) or resid 195 through 232)) selection = (chain 'B' and (resid 7 through 32 or (resid 33 and (name N or name CA or name C \ or name O or name CB )) or resid 34 through 92 or (resid 93 and (name N or name \ CA or name C or name O or name CB )) or resid 94 through 157 or resid 170 throu \ gh 190 or (resid 191 and (name N or name CA or name C or name O or name CB )) or \ resid 192 through 232)) } 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: 1.040 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 31.130 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 0.467 26594 Z= 0.258 Angle : 0.654 29.860 36330 Z= 0.385 Chirality : 0.049 0.285 4206 Planarity : 0.005 0.057 4441 Dihedral : 15.215 175.971 10339 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -3.59 (0.11), residues: 3105 helix: -2.51 (0.10), residues: 1032 sheet: -1.45 (0.25), residues: 391 loop : -2.57 (0.12), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 218 TYR 0.019 0.001 TYR B 68 PHE 0.010 0.001 PHE C 514 TRP 0.017 0.001 TRP C 807 HIS 0.003 0.000 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.21 (26587) covalent geometry : angle 0.61748 / 0.38 (36324) hydrogen bonds : bond 0.18628 / 12.75 ( 1030) hydrogen bonds : angle 7.03463 / 4.80 ( 2887) metal coordination : bond 0.27846 / 14.24 ( 7) metal coordination : angle 16.88376 / 8.74 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 1.022 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PRO C 847 " (corrupted residue). Skipping it. Corrupt residue: chain: C residue: PRO 847 >>> skipping REVERT: A 205 MET cc_start: 0.8383 (ptp) cc_final: 0.8031 (ptp) REVERT: B 51 MET cc_start: 0.8554 (mmm) cc_final: 0.8228 (mmp) REVERT: B 215 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6552 (tm-30) REVERT: C 419 ILE cc_start: 0.9094 (pt) cc_final: 0.8860 (pt) REVERT: C 1084 ASP cc_start: 0.8523 (m-30) cc_final: 0.8211 (m-30) REVERT: C 1289 GLU cc_start: 0.7969 (tt0) cc_final: 0.7708 (tt0) REVERT: D 155 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7299 (mm-30) REVERT: D 320 ASN cc_start: 0.7338 (m-40) cc_final: 0.7094 (m110) REVERT: D 525 MET cc_start: 0.7971 (ptm) cc_final: 0.7750 (ptm) REVERT: D 556 GLU cc_start: 0.7074 (tt0) cc_final: 0.6446 (pt0) REVERT: D 849 LEU cc_start: 0.8613 (mt) cc_final: 0.8320 (mt) REVERT: E 68 GLU cc_start: 0.7357 (tt0) cc_final: 0.7087 (mp0) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.2220 time to fit residues: 164.8954 Evaluate side-chains 322 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS B 75 GLN B 128 HIS B 132 HIS C 69 GLN C 150 HIS C 273 HIS C 330 HIS C 490 GLN C 582 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 688 GLN C 766 ASN C 952 GLN C1157 GLN C1268 GLN C1313 HIS D 206 ASN D 665 GLN D 667 GLN D 739 GLN D1235 ASN D1279 GLN E 7 GLN E 31 GLN E 72 GLN E 73 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.132293 restraints weight = 31103.821| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.39 r_work: 0.3079 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26594 Z= 0.192 Angle : 0.592 8.311 36330 Z= 0.299 Chirality : 0.046 0.573 4206 Planarity : 0.005 0.049 4441 Dihedral : 14.830 175.870 4394 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.22 % Allowed : 10.77 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.83 (0.13), residues: 3105 helix: -0.02 (0.15), residues: 1051 sheet: -1.03 (0.24), residues: 416 loop : -2.13 (0.13), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 45 TYR 0.018 0.001 TYR C 367 PHE 0.020 0.002 PHE C1025 TRP 0.016 0.001 TRP C 807 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (26587) covalent geometry : angle 0.59031 / 0.30 (36324) hydrogen bonds : bond 0.04258 / 2.92 ( 1030) hydrogen bonds : angle 4.41343 / 3.00 ( 2887) metal coordination : bond 0.02415 / 1.13 ( 7) metal coordination : angle 3.15694 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 331 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8328 (mmtp) cc_final: 0.7752 (mttp) REVERT: A 31 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7789 (mt) REVERT: A 96 ASP cc_start: 0.7477 (t0) cc_final: 0.7277 (t0) REVERT: C 834 GLN cc_start: 0.8495 (mt0) cc_final: 0.8136 (mt0) REVERT: C 1038 GLN cc_start: 0.7347 (tm-30) cc_final: 0.7085 (tm-30) REVERT: D 177 ASP cc_start: 0.6866 (t0) cc_final: 0.6519 (t0) REVERT: D 826 ILE cc_start: 0.6728 (mm) cc_final: 0.6497 (mm) REVERT: E 11 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7525 (tp30) REVERT: E 68 GLU cc_start: 0.7732 (tt0) cc_final: 0.6854 (mp0) REVERT: E 71 GLU cc_start: 0.7632 (tp30) cc_final: 0.7295 (tp30) outliers start: 32 outliers final: 22 residues processed: 353 average time/residue: 0.1952 time to fit residues: 106.5154 Evaluate side-chains 324 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 301 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 271 optimal weight: 0.0010 chunk 63 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 301 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 84 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 275 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 314 optimal weight: 10.0000 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 23 HIS C 120 GLN C 618 GLN C1116 HIS D 206 ASN D 667 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.126567 restraints weight = 31172.231| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.35 r_work: 0.3024 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 26594 Z= 0.177 Angle : 0.559 8.058 36330 Z= 0.284 Chirality : 0.045 0.327 4206 Planarity : 0.004 0.055 4441 Dihedral : 14.884 177.800 4394 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.95 % Allowed : 12.52 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -1.04 (0.14), residues: 3105 helix: 0.94 (0.16), residues: 1060 sheet: -0.66 (0.26), residues: 382 loop : -1.87 (0.13), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 827 TYR 0.014 0.001 TYR A 177 PHE 0.027 0.002 PHE C1025 TRP 0.015 0.001 TRP C 807 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (26587) covalent geometry : angle 0.55713 / 0.28 (36324) hydrogen bonds : bond 0.04598 / 3.14 ( 1030) hydrogen bonds : angle 4.02539 / 2.74 ( 2887) metal coordination : bond 0.00681 / 0.38 ( 7) metal coordination : angle 3.65911 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7818 (t0) cc_final: 0.7572 (t0) REVERT: B 199 ASP cc_start: 0.8347 (m-30) cc_final: 0.7858 (m-30) REVERT: C 36 GLN cc_start: 0.8488 (tt0) cc_final: 0.8008 (tm-30) REVERT: C 88 ARG cc_start: 0.8357 (mtp85) cc_final: 0.7853 (mtp85) REVERT: C 542 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7965 (mtt-85) REVERT: C 611 GLU cc_start: 0.7520 (tt0) cc_final: 0.7299 (tt0) REVERT: C 834 GLN cc_start: 0.8486 (mt0) cc_final: 0.8165 (mt0) REVERT: D 227 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.7081 (t80) REVERT: D 709 ARG cc_start: 0.7681 (ptt180) cc_final: 0.7202 (tpt90) REVERT: D 826 ILE cc_start: 0.6531 (mm) cc_final: 0.6293 (mm) REVERT: D 865 HIS cc_start: 0.7908 (p90) cc_final: 0.7573 (p90) REVERT: D 1243 LEU cc_start: 0.9108 (tp) cc_final: 0.8828 (mp) REVERT: E 11 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7637 (tp30) REVERT: E 35 LYS cc_start: 0.8320 (mttp) cc_final: 0.8088 (mmtp) REVERT: E 68 GLU cc_start: 0.7632 (tt0) cc_final: 0.6739 (mp0) REVERT: E 71 GLU cc_start: 0.7469 (tp30) cc_final: 0.7246 (tp30) outliers start: 51 outliers final: 34 residues processed: 356 average time/residue: 0.1915 time to fit residues: 105.7239 Evaluate side-chains 326 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 106 optimal weight: 0.6980 chunk 313 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 216 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 239 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN E 73 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.126166 restraints weight = 31043.211| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.33 r_work: 0.2997 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26594 Z= 0.151 Angle : 0.522 9.059 36330 Z= 0.265 Chirality : 0.044 0.290 4206 Planarity : 0.004 0.054 4441 Dihedral : 14.825 177.484 4394 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 13.82 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.71 (0.14), residues: 3105 helix: 1.28 (0.16), residues: 1068 sheet: -0.55 (0.26), residues: 382 loop : -1.71 (0.13), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1341 TYR 0.014 0.001 TYR A 177 PHE 0.017 0.001 PHE D 172 TRP 0.008 0.001 TRP C 807 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (26587) covalent geometry : angle 0.52141 / 0.27 (36324) hydrogen bonds : bond 0.04013 / 2.76 ( 1030) hydrogen bonds : angle 3.86488 / 2.63 ( 2887) metal coordination : bond 0.00384 / 0.16 ( 7) metal coordination : angle 2.47966 / 1.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 297 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7810 (t0) cc_final: 0.7579 (t0) REVERT: B 199 ASP cc_start: 0.8347 (m-30) cc_final: 0.7852 (m-30) REVERT: C 36 GLN cc_start: 0.8460 (tt0) cc_final: 0.7985 (tm-30) REVERT: C 88 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7813 (mtp85) REVERT: C 611 GLU cc_start: 0.7578 (tt0) cc_final: 0.7358 (tt0) REVERT: C 1038 GLN cc_start: 0.7454 (tm-30) cc_final: 0.7096 (tm-30) REVERT: D 227 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.7157 (t80) REVERT: D 709 ARG cc_start: 0.7567 (ptt180) cc_final: 0.7228 (tpt90) REVERT: D 712 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: D 826 ILE cc_start: 0.6858 (mm) cc_final: 0.6580 (mm) REVERT: D 865 HIS cc_start: 0.7908 (p90) cc_final: 0.7635 (p90) REVERT: D 1243 LEU cc_start: 0.9103 (tp) cc_final: 0.8815 (mp) REVERT: E 11 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7625 (tp30) REVERT: E 35 LYS cc_start: 0.8312 (mttp) cc_final: 0.8082 (mmtp) REVERT: E 68 GLU cc_start: 0.7558 (tt0) cc_final: 0.6667 (mp0) REVERT: E 71 GLU cc_start: 0.7457 (tp30) cc_final: 0.7236 (tp30) outliers start: 56 outliers final: 37 residues processed: 338 average time/residue: 0.1963 time to fit residues: 102.8267 Evaluate side-chains 325 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 286 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 934 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1058 SER Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1265 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 93 optimal weight: 0.6980 chunk 250 optimal weight: 8.9990 chunk 182 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 193 optimal weight: 0.4980 chunk 229 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.0060 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 712 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.166402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.129347 restraints weight = 30914.578| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.26 r_work: 0.3067 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 26594 Z= 0.100 Angle : 0.479 9.288 36330 Z= 0.242 Chirality : 0.043 0.298 4206 Planarity : 0.003 0.050 4441 Dihedral : 14.753 177.824 4394 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.45 % Allowed : 14.97 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.37 (0.15), residues: 3105 helix: 1.63 (0.17), residues: 1068 sheet: -0.40 (0.26), residues: 382 loop : -1.54 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 371 TYR 0.013 0.001 TYR C 367 PHE 0.015 0.001 PHE D 892 TRP 0.006 0.001 TRP D1193 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (26587) covalent geometry : angle 0.47821 / 0.24 (36324) hydrogen bonds : bond 0.03477 / 2.40 ( 1030) hydrogen bonds : angle 3.70030 / 2.52 ( 2887) metal coordination : bond 0.00240 / 0.10 ( 7) metal coordination : angle 1.96042 / 1.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 303 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7799 (t0) cc_final: 0.7576 (t0) REVERT: C 88 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7840 (mtp85) REVERT: C 611 GLU cc_start: 0.7622 (tt0) cc_final: 0.7364 (tt0) REVERT: C 1038 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7018 (tm-30) REVERT: D 227 PHE cc_start: 0.8788 (OUTLIER) cc_final: 0.7097 (t80) REVERT: D 709 ARG cc_start: 0.7472 (ptt180) cc_final: 0.7014 (tpt90) REVERT: D 712 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: D 826 ILE cc_start: 0.6807 (mm) cc_final: 0.6566 (mm) REVERT: D 865 HIS cc_start: 0.7899 (p90) cc_final: 0.7650 (p90) REVERT: D 1243 LEU cc_start: 0.9103 (tp) cc_final: 0.8818 (mp) REVERT: E 11 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7669 (tp30) REVERT: E 35 LYS cc_start: 0.8330 (mttp) cc_final: 0.8124 (mmtp) REVERT: E 68 GLU cc_start: 0.7585 (tt0) cc_final: 0.6440 (mp0) REVERT: E 71 GLU cc_start: 0.7474 (tp30) cc_final: 0.7248 (tp30) outliers start: 38 outliers final: 29 residues processed: 331 average time/residue: 0.1903 time to fit residues: 97.8457 Evaluate side-chains 316 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1275 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 233 optimal weight: 0.0980 chunk 154 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 275 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 213 optimal weight: 0.0870 chunk 119 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 99 optimal weight: 0.0170 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS D 229 GLN D 712 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.165927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126379 restraints weight = 31086.509| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.41 r_work: 0.3000 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26594 Z= 0.112 Angle : 0.482 9.495 36330 Z= 0.243 Chirality : 0.043 0.301 4206 Planarity : 0.003 0.047 4441 Dihedral : 14.726 178.031 4394 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.25 % Allowed : 14.78 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.20 (0.15), residues: 3105 helix: 1.78 (0.17), residues: 1061 sheet: -0.29 (0.26), residues: 386 loop : -1.45 (0.14), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1341 TYR 0.012 0.001 TYR C 367 PHE 0.015 0.001 PHE C 80 TRP 0.006 0.001 TRP D1193 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (26587) covalent geometry : angle 0.48177 / 0.24 (36324) hydrogen bonds : bond 0.03509 / 2.42 ( 1030) hydrogen bonds : angle 3.63600 / 2.47 ( 2887) metal coordination : bond 0.00273 / 0.12 ( 7) metal coordination : angle 1.90909 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 291 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7900 (t0) cc_final: 0.7648 (t0) REVERT: C 88 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7765 (mtp85) REVERT: C 611 GLU cc_start: 0.7639 (tt0) cc_final: 0.7376 (tt0) REVERT: C 1038 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7035 (tm-30) REVERT: D 227 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.6946 (t80) REVERT: D 698 MET cc_start: 0.8638 (mmm) cc_final: 0.8279 (tpp) REVERT: D 712 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.6825 (pm20) REVERT: D 826 ILE cc_start: 0.6715 (mm) cc_final: 0.6464 (mm) REVERT: D 865 HIS cc_start: 0.7809 (p90) cc_final: 0.7546 (p90) REVERT: D 1243 LEU cc_start: 0.9101 (tp) cc_final: 0.8857 (mp) REVERT: E 11 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7641 (tp30) REVERT: E 35 LYS cc_start: 0.8269 (mttp) cc_final: 0.8066 (mmtp) REVERT: E 68 GLU cc_start: 0.7568 (tt0) cc_final: 0.6389 (mp0) REVERT: E 71 GLU cc_start: 0.7344 (tp30) cc_final: 0.7111 (tp30) outliers start: 59 outliers final: 47 residues processed: 335 average time/residue: 0.1911 time to fit residues: 99.6855 Evaluate side-chains 336 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1058 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1159 ILE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 210 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 150 optimal weight: 4.9990 chunk 288 optimal weight: 0.7980 chunk 113 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 266 optimal weight: 7.9990 chunk 313 optimal weight: 9.9990 chunk 173 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS D 712 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123795 restraints weight = 31120.057| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.46 r_work: 0.2935 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 26594 Z= 0.213 Angle : 0.577 9.668 36330 Z= 0.292 Chirality : 0.046 0.292 4206 Planarity : 0.004 0.058 4441 Dihedral : 14.838 178.634 4394 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.52 % Allowed : 15.20 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.36 (0.15), residues: 3105 helix: 1.55 (0.17), residues: 1060 sheet: -0.35 (0.26), residues: 398 loop : -1.48 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 45 TYR 0.019 0.002 TYR A 177 PHE 0.015 0.002 PHE C 80 TRP 0.009 0.001 TRP D1193 HIS 0.007 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.21 (26587) covalent geometry : angle 0.57567 / 0.29 (36324) hydrogen bonds : bond 0.04589 / 3.13 ( 1030) hydrogen bonds : angle 3.77482 / 2.58 ( 2887) metal coordination : bond 0.00498 / 0.23 ( 7) metal coordination : angle 2.82250 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: B 199 ASP cc_start: 0.8387 (m-30) cc_final: 0.7856 (m-30) REVERT: C 30 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7801 (tt) REVERT: C 88 ARG cc_start: 0.8324 (mtp85) cc_final: 0.7749 (mtp85) REVERT: C 611 GLU cc_start: 0.7732 (tt0) cc_final: 0.7480 (tt0) REVERT: D 227 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.6954 (t80) REVERT: D 267 ASP cc_start: 0.8268 (t70) cc_final: 0.7849 (t0) REVERT: D 504 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: D 709 ARG cc_start: 0.7441 (ptt180) cc_final: 0.6951 (tpt90) REVERT: D 712 GLN cc_start: 0.7311 (OUTLIER) cc_final: 0.7001 (pm20) REVERT: D 826 ILE cc_start: 0.6870 (mm) cc_final: 0.6602 (mm) REVERT: D 865 HIS cc_start: 0.7867 (p90) cc_final: 0.7623 (p90) REVERT: E 11 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7529 (tp30) REVERT: E 35 LYS cc_start: 0.8232 (mttp) cc_final: 0.8028 (mmtp) REVERT: E 68 GLU cc_start: 0.7582 (tt0) cc_final: 0.6330 (mp0) REVERT: E 71 GLU cc_start: 0.7340 (tp30) cc_final: 0.7077 (tp30) outliers start: 66 outliers final: 55 residues processed: 343 average time/residue: 0.1896 time to fit residues: 101.3491 Evaluate side-chains 341 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 282 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 800 LEU Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1058 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1317 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 160 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 196 optimal weight: 0.0670 chunk 260 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 overall best weight: 0.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS C1134 GLN D 712 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.126147 restraints weight = 31234.712| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.48 r_work: 0.2938 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26594 Z= 0.120 Angle : 0.503 9.553 36330 Z= 0.254 Chirality : 0.043 0.311 4206 Planarity : 0.003 0.053 4441 Dihedral : 14.792 178.914 4394 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.29 % Allowed : 15.73 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.14 (0.15), residues: 3105 helix: 1.76 (0.17), residues: 1061 sheet: -0.25 (0.26), residues: 396 loop : -1.37 (0.14), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 371 TYR 0.012 0.001 TYR C 367 PHE 0.018 0.001 PHE C 80 TRP 0.008 0.001 TRP D1020 HIS 0.003 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (26587) covalent geometry : angle 0.50206 / 0.25 (36324) hydrogen bonds : bond 0.03745 / 2.59 ( 1030) hydrogen bonds : angle 3.65503 / 2.49 ( 2887) metal coordination : bond 0.00330 / 0.14 ( 7) metal coordination : angle 1.91025 / 1.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8962 (mt) cc_final: 0.8702 (mp) REVERT: C 88 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7657 (mtp85) REVERT: C 611 GLU cc_start: 0.7658 (tt0) cc_final: 0.7382 (tt0) REVERT: C 1037 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7894 (m) REVERT: D 227 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.6780 (t80) REVERT: D 267 ASP cc_start: 0.8197 (t70) cc_final: 0.7773 (t0) REVERT: D 504 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: D 698 MET cc_start: 0.8629 (mmm) cc_final: 0.8333 (tpp) REVERT: D 712 GLN cc_start: 0.7381 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: D 826 ILE cc_start: 0.6778 (mm) cc_final: 0.6508 (mm) REVERT: D 865 HIS cc_start: 0.7740 (p90) cc_final: 0.7491 (p90) REVERT: E 11 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7527 (tp30) REVERT: E 65 ASP cc_start: 0.7953 (m-30) cc_final: 0.7689 (m-30) REVERT: E 68 GLU cc_start: 0.7510 (tt0) cc_final: 0.6256 (mp0) outliers start: 60 outliers final: 49 residues processed: 331 average time/residue: 0.1685 time to fit residues: 87.4496 Evaluate side-chains 332 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1058 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1317 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 67 optimal weight: 20.0000 chunk 225 optimal weight: 4.9990 chunk 223 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 300 optimal weight: 6.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 66 HIS D 712 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.160642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123429 restraints weight = 31147.073| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.42 r_work: 0.2937 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 26594 Z= 0.204 Angle : 0.569 9.774 36330 Z= 0.287 Chirality : 0.046 0.308 4206 Planarity : 0.004 0.056 4441 Dihedral : 14.849 179.310 4394 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.48 % Allowed : 15.54 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 3105 helix: 1.60 (0.17), residues: 1061 sheet: -0.28 (0.26), residues: 404 loop : -1.39 (0.14), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 45 TYR 0.018 0.001 TYR A 177 PHE 0.021 0.002 PHE C 80 TRP 0.010 0.001 TRP D1193 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.20 (26587) covalent geometry : angle 0.56844 / 0.29 (36324) hydrogen bonds : bond 0.04480 / 3.06 ( 1030) hydrogen bonds : angle 3.74882 / 2.56 ( 2887) metal coordination : bond 0.00517 / 0.24 ( 7) metal coordination : angle 2.67134 / 1.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 284 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: C 30 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7763 (tt) REVERT: C 88 ARG cc_start: 0.8339 (mtp85) cc_final: 0.7749 (mtp85) REVERT: C 611 GLU cc_start: 0.7740 (tt0) cc_final: 0.7495 (tt0) REVERT: C 1037 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8047 (m) REVERT: D 227 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7003 (t80) REVERT: D 267 ASP cc_start: 0.8279 (t70) cc_final: 0.7859 (t0) REVERT: D 504 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: D 709 ARG cc_start: 0.7507 (ptt180) cc_final: 0.6892 (tpt90) REVERT: D 712 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: D 826 ILE cc_start: 0.6996 (mm) cc_final: 0.6729 (mm) REVERT: D 865 HIS cc_start: 0.7812 (p90) cc_final: 0.7577 (p90) REVERT: E 11 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7547 (tp30) REVERT: E 68 GLU cc_start: 0.7562 (tt0) cc_final: 0.6354 (mp0) outliers start: 65 outliers final: 56 residues processed: 334 average time/residue: 0.1821 time to fit residues: 95.0354 Evaluate side-chains 337 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1058 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1317 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 25 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 213 optimal weight: 0.8980 chunk 296 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 250 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 216 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 712 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.162473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.125099 restraints weight = 31011.828| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.40 r_work: 0.2966 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26594 Z= 0.119 Angle : 0.511 9.642 36330 Z= 0.258 Chirality : 0.043 0.324 4206 Planarity : 0.003 0.054 4441 Dihedral : 14.801 179.398 4394 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.18 % Allowed : 15.88 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.05 (0.15), residues: 3105 helix: 1.80 (0.17), residues: 1060 sheet: -0.15 (0.26), residues: 400 loop : -1.29 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1149 TYR 0.013 0.001 TYR A 177 PHE 0.039 0.001 PHE D 172 TRP 0.009 0.001 TRP D1193 HIS 0.004 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (26587) covalent geometry : angle 0.51004 / 0.26 (36324) hydrogen bonds : bond 0.03763 / 2.60 ( 1030) hydrogen bonds : angle 3.65731 / 2.49 ( 2887) metal coordination : bond 0.00341 / 0.15 ( 7) metal coordination : angle 1.94904 / 1.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6210 Ramachandran restraints generated. 3105 Oldfield, 0 Emsley, 3105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 286 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.7885 (ttp-170) REVERT: C 30 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7643 (tt) REVERT: C 88 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7812 (mtp85) REVERT: C 611 GLU cc_start: 0.7700 (tt0) cc_final: 0.7436 (tt0) REVERT: C 1037 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7946 (m) REVERT: C 1340 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6858 (pt0) REVERT: D 227 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.6983 (t80) REVERT: D 267 ASP cc_start: 0.8226 (t70) cc_final: 0.7814 (t0) REVERT: D 504 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7976 (pm20) REVERT: D 709 ARG cc_start: 0.7502 (ptt180) cc_final: 0.6900 (tpt90) REVERT: D 712 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: D 826 ILE cc_start: 0.6942 (mm) cc_final: 0.6671 (mm) REVERT: D 865 HIS cc_start: 0.7812 (p90) cc_final: 0.7587 (p90) REVERT: E 11 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7536 (tp30) REVERT: E 65 ASP cc_start: 0.8114 (m-30) cc_final: 0.7854 (m-30) REVERT: E 68 GLU cc_start: 0.7512 (tt0) cc_final: 0.6308 (mp0) outliers start: 57 outliers final: 50 residues processed: 331 average time/residue: 0.1779 time to fit residues: 92.1712 Evaluate side-chains 337 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1092 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1219 GLU Chi-restraints excluded: chain C residue 1340 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 712 GLN Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1058 SER Chi-restraints excluded: chain D residue 1107 VAL Chi-restraints excluded: chain D residue 1155 ILE Chi-restraints excluded: chain D residue 1176 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1275 LEU Chi-restraints excluded: chain D residue 1317 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 90 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 712 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.164581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127145 restraints weight = 30712.554| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.24 r_work: 0.2965 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26594 Z= 0.146 Angle : 0.527 9.780 36330 Z= 0.266 Chirality : 0.044 0.327 4206 Planarity : 0.004 0.052 4441 Dihedral : 14.797 179.688 4394 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.37 % Allowed : 15.73 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.04 (0.15), residues: 3105 helix: 1.76 (0.17), residues: 1062 sheet: -0.12 (0.26), residues: 419 loop : -1.27 (0.14), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1149 TYR 0.014 0.001 TYR A 177 PHE 0.043 0.001 PHE D 172 TRP 0.010 0.001 TRP D1193 HIS 0.005 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (26587) covalent geometry : angle 0.52625 / 0.27 (36324) hydrogen bonds : bond 0.03944 / 2.72 ( 1030) hydrogen bonds : angle 3.65576 / 2.49 ( 2887) metal coordination : bond 0.00386 / 0.16 ( 7) metal coordination : angle 2.11963 / 1.16 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6255.53 seconds wall clock time: 107 minutes 48.23 seconds (6468.23 seconds total)