Starting phenix.real_space_refine on Sun Jun 22 20:16:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ypa_33997/06_2025/7ypa_33997.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ypa_33997/06_2025/7ypa_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_33997/06_2025/7ypa_33997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ypa_33997/06_2025/7ypa_33997.map" model { file = "/net/cci-nas-00/data/ceres_data/7ypa_33997/06_2025/7ypa_33997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ypa_33997/06_2025/7ypa_33997.cif" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'ARG:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 8, '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: {'TYR:plan': 1, 'GLU:plan': 4, '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: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 13} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "I" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna3p': 9} 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: 14.12, per 1000 atoms: 0.54 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: 5.82 Conformation dependent library (CDL) restraints added in 3.1 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: 9.66 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: 14.80 Time building geometry restraints manager: 7.15 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' DC G -7 " pdb=" O3' DC G -7 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.83e+00 bond pdb=" C ALA D 426 " pdb=" N PRO D 427 " ideal model delta sigma weight residual 1.334 1.377 -0.044 2.34e-02 1.83e+03 3.47e+00 bond pdb=" C GLU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 1.334 1.377 -0.043 2.34e-02 1.83e+03 3.36e+00 bond pdb=" CA LEU D1261 " pdb=" CB LEU D1261 " ideal model delta sigma weight residual 1.526 1.553 -0.026 1.53e-02 4.27e+03 2.99e+00 bond pdb=" C3' DA F 11 " pdb=" O3' DA F 11 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 2.95e+00 ... (remaining 26582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 35813 2.12 - 4.23: 464 4.23 - 6.35: 35 6.35 - 8.47: 11 8.47 - 10.59: 1 Bond angle restraints: 36324 Sorted by residual: angle pdb=" C ASP D 902 " pdb=" N LEU D 903 " pdb=" CA LEU D 903 " ideal model delta sigma weight residual 121.54 129.08 -7.54 1.91e+00 2.74e-01 1.56e+01 angle pdb=" C THR D 703 " pdb=" N GLU D 704 " pdb=" CA GLU D 704 " ideal model delta sigma weight residual 122.08 127.24 -5.16 1.47e+00 4.63e-01 1.23e+01 angle pdb=" C GLY D 73 " pdb=" N LYS D 74 " pdb=" CA LYS D 74 " ideal model delta sigma weight residual 125.02 131.08 -6.06 1.76e+00 3.23e-01 1.19e+01 angle pdb=" C ARG A 191 " pdb=" N VAL A 192 " pdb=" CA VAL A 192 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.64e+00 3.72e-01 1.11e+01 angle pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " pdb=" P DG G -6 " ideal model delta sigma weight residual 120.20 124.86 -4.66 1.50e+00 4.44e-01 9.67e+00 ... (remaining 36319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.19: 15715 35.19 - 70.39: 477 70.39 - 105.58: 39 105.58 - 140.78: 1 140.78 - 175.97: 3 Dihedral angle restraints: 16235 sinusoidal: 7259 harmonic: 8976 Sorted by residual: dihedral pdb=" C4' DC G -7 " pdb=" C3' DC G -7 " pdb=" O3' DC G -7 " pdb=" P DG G -6 " ideal model delta sinusoidal sigma weight residual -140.00 35.97 -175.97 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA F -1 " pdb=" C3' DA F -1 " pdb=" O3' DA F -1 " pdb=" P DA F 0 " ideal model delta sinusoidal sigma weight residual 220.00 76.80 143.20 1 3.50e+01 8.16e-04 1.41e+01 dihedral pdb=" C4' DA F 11 " pdb=" C3' DA F 11 " pdb=" O3' DA F 11 " pdb=" P DC F 12 " ideal model delta sinusoidal sigma weight residual -140.00 3.12 -143.12 1 3.50e+01 8.16e-04 1.41e+01 ... (remaining 16232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3257 0.046 - 0.092: 673 0.092 - 0.138: 244 0.138 - 0.185: 28 0.185 - 0.231: 4 Chirality restraints: 4206 Sorted by residual: chirality pdb=" CB ILE E 13 " pdb=" CA ILE E 13 " pdb=" CG1 ILE E 13 " pdb=" CG2 ILE E 13 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" P DC F 12 " pdb=" OP1 DC F 12 " pdb=" OP2 DC F 12 " pdb=" O5' DC F 12 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE C 232 " pdb=" CA ILE C 232 " pdb=" CG1 ILE C 232 " pdb=" CG2 ILE C 232 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+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: 1.250 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: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 72.500 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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= 0.209 Angle : 0.626 29.860 36330 Z= 0.340 Chirality : 0.044 0.231 4206 Planarity : 0.005 0.057 4441 Dihedral : 15.656 175.971 10459 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.001 TRP C 807 HIS 0.003 0.000 HIS D 777 PHE 0.010 0.001 PHE C 514 TYR 0.019 0.001 TYR B 68 ARG 0.002 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.18628 ( 1030) hydrogen bonds : angle 7.03463 ( 2887) metal coordination : bond 0.27846 ( 7) metal coordination : angle 16.88376 ( 6) covalent geometry : bond 0.00266 (26587) covalent geometry : angle 0.58680 (36324) *********************** 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 : 2.686 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: 0.5148 time to fit residues: 382.9609 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 : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 151 optimal weight: 0.3980 chunk 184 optimal weight: 4.9990 chunk 287 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 75 GLN B 128 HIS B 132 HIS C 69 GLN C 120 GLN C 150 HIS C 273 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 C1268 GLN C1313 HIS D 206 ASN 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.173373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.136071 restraints weight = 31241.382| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.30 r_work: 0.3179 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1509 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= 0.112 Angle : 0.468 6.770 36330 Z= 0.245 Chirality : 0.040 0.187 4206 Planarity : 0.004 0.047 4441 Dihedral : 15.701 175.806 4514 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.15 % Allowed : 9.74 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 3105 helix: -0.04 (0.15), residues: 1060 sheet: -1.01 (0.25), residues: 399 loop : -2.09 (0.13), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 807 HIS 0.004 0.001 HIS C1313 PHE 0.013 0.001 PHE C1025 TYR 0.015 0.001 TYR C 367 ARG 0.005 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 1030) hydrogen bonds : angle 4.26960 ( 2887) metal coordination : bond 0.00982 ( 7) metal coordination : angle 3.37997 ( 6) covalent geometry : bond 0.00247 (26587) covalent geometry : angle 0.46559 (36324) *********************** 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 364 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 334 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8127 (mmtp) cc_final: 0.7646 (mttp) REVERT: A 96 ASP cc_start: 0.7412 (t0) cc_final: 0.7180 (t0) REVERT: A 205 MET cc_start: 0.8838 (ptp) cc_final: 0.8369 (ptp) REVERT: B 51 MET cc_start: 0.8756 (mmm) cc_final: 0.8397 (mmp) REVERT: C 88 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7806 (mtp85) REVERT: C 834 GLN cc_start: 0.8472 (mt0) cc_final: 0.8224 (mt0) REVERT: C 1038 GLN cc_start: 0.7398 (tm-30) cc_final: 0.7183 (tm-30) REVERT: C 1232 MET cc_start: 0.8563 (mmm) cc_final: 0.7798 (mmm) REVERT: C 1241 ASP cc_start: 0.8359 (m-30) cc_final: 0.8101 (m-30) REVERT: C 1289 GLU cc_start: 0.8086 (tt0) cc_final: 0.7875 (tt0) REVERT: D 155 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7766 (tp30) REVERT: D 177 ASP cc_start: 0.6946 (t0) cc_final: 0.6568 (t0) REVERT: D 525 MET cc_start: 0.8369 (ptm) cc_final: 0.8168 (ptm) REVERT: D 826 ILE cc_start: 0.6875 (mm) cc_final: 0.6616 (mm) REVERT: E 11 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7575 (tp30) REVERT: E 68 GLU cc_start: 0.7737 (tt0) cc_final: 0.6881 (mp0) REVERT: E 71 GLU cc_start: 0.7699 (tp30) cc_final: 0.7339 (tp30) outliers start: 30 outliers final: 22 residues processed: 354 average time/residue: 0.4109 time to fit residues: 222.9650 Evaluate side-chains 324 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 302 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 139 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 131 THR Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 569 ILE 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 C residue 1178 LYS Chi-restraints excluded: chain D residue 158 GLN Chi-restraints excluded: chain D residue 232 ASN 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 1159 ILE 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 293 optimal weight: 8.9990 chunk 273 optimal weight: 9.9990 chunk 302 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 8 optimal weight: 0.0170 chunk 226 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 89 optimal weight: 0.0270 chunk 195 optimal weight: 0.9980 chunk 59 optimal weight: 0.0070 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 618 GLN C1157 GLN D 206 ASN D 665 GLN D 739 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.136266 restraints weight = 31118.489| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.20 r_work: 0.3157 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26594 Z= 0.086 Angle : 0.426 7.784 36330 Z= 0.222 Chirality : 0.039 0.164 4206 Planarity : 0.003 0.044 4441 Dihedral : 15.617 179.112 4514 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.03 % Allowed : 11.57 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3105 helix: 1.14 (0.16), residues: 1060 sheet: -0.65 (0.26), residues: 373 loop : -1.79 (0.13), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 807 HIS 0.003 0.000 HIS D 777 PHE 0.013 0.001 PHE C 337 TYR 0.009 0.001 TYR D 144 ARG 0.006 0.000 ARG D1341 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 1030) hydrogen bonds : angle 3.73567 ( 2887) metal coordination : bond 0.00215 ( 7) metal coordination : angle 2.21244 ( 6) covalent geometry : bond 0.00193 (26587) covalent geometry : angle 0.42520 (36324) *********************** 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 335 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 308 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7543 (t0) cc_final: 0.7225 (t0) REVERT: A 205 MET cc_start: 0.8961 (ptp) cc_final: 0.8541 (ptp) REVERT: C 80 PHE cc_start: 0.8783 (m-80) cc_final: 0.8503 (m-80) REVERT: C 368 ARG cc_start: 0.8402 (mtm110) cc_final: 0.8173 (mtm110) REVERT: C 779 ARG cc_start: 0.8633 (ttt90) cc_final: 0.8422 (ttp80) REVERT: C 1038 GLN cc_start: 0.7389 (tm-30) cc_final: 0.7144 (tm-30) REVERT: C 1241 ASP cc_start: 0.8667 (m-30) cc_final: 0.8466 (m-30) REVERT: D 155 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7777 (tp30) REVERT: D 177 ASP cc_start: 0.7063 (t0) cc_final: 0.6812 (t0) REVERT: D 227 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.7047 (t80) REVERT: D 709 ARG cc_start: 0.7777 (ptt180) cc_final: 0.6938 (tpt90) REVERT: D 803 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8168 (p) REVERT: D 826 ILE cc_start: 0.6956 (mm) cc_final: 0.6637 (mm) REVERT: E 11 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7718 (tp30) REVERT: E 68 GLU cc_start: 0.7595 (tt0) cc_final: 0.6673 (mp0) outliers start: 27 outliers final: 19 residues processed: 328 average time/residue: 0.4196 time to fit residues: 213.8249 Evaluate side-chains 308 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 287 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 156 SER 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 131 THR 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 658 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1027 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 133 optimal weight: 5.9990 chunk 146 optimal weight: 0.0050 chunk 285 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 301 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 102 optimal weight: 0.0170 chunk 73 optimal weight: 8.9990 overall best weight: 0.5434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 618 GLN C 834 GLN D 712 GLN D 739 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.171357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134388 restraints weight = 31242.445| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.26 r_work: 0.3138 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2030 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= 0.092 Angle : 0.425 6.802 36330 Z= 0.221 Chirality : 0.039 0.160 4206 Planarity : 0.003 0.036 4441 Dihedral : 15.609 178.200 4514 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.41 % Allowed : 12.33 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3105 helix: 1.62 (0.17), residues: 1062 sheet: -0.36 (0.26), residues: 374 loop : -1.54 (0.13), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 807 HIS 0.003 0.000 HIS D 777 PHE 0.017 0.001 PHE D 172 TYR 0.007 0.001 TYR C1229 ARG 0.004 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 1030) hydrogen bonds : angle 3.54240 ( 2887) metal coordination : bond 0.00189 ( 7) metal coordination : angle 1.92598 ( 6) covalent geometry : bond 0.00209 (26587) covalent geometry : angle 0.42388 (36324) *********************** 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 334 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 297 time to evaluate : 2.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7577 (t0) cc_final: 0.7294 (t0) REVERT: C 79 VAL cc_start: 0.8459 (m) cc_final: 0.8185 (p) REVERT: C 88 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7823 (mtp85) REVERT: C 368 ARG cc_start: 0.8347 (mtm110) cc_final: 0.8106 (mtm110) REVERT: C 1038 GLN cc_start: 0.7298 (tm-30) cc_final: 0.7089 (tm-30) REVERT: D 155 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7894 (tp30) REVERT: D 225 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7093 (mm-30) REVERT: D 227 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7111 (t80) REVERT: D 803 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8237 (p) REVERT: D 826 ILE cc_start: 0.6956 (mm) cc_final: 0.6640 (mm) REVERT: E 11 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7624 (tp30) REVERT: E 68 GLU cc_start: 0.7543 (tt0) cc_final: 0.6683 (mp0) outliers start: 37 outliers final: 27 residues processed: 323 average time/residue: 0.4152 time to fit residues: 208.3646 Evaluate side-chains 320 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 291 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 131 THR 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 635 THR Chi-restraints excluded: chain C residue 658 GLN 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 111 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN 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 803 VAL Chi-restraints excluded: chain D residue 821 MET 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 1261 LEU Chi-restraints excluded: chain D residue 1275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 97 optimal weight: 0.7980 chunk 131 optimal weight: 0.0040 chunk 122 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 157 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 107 optimal weight: 0.0030 chunk 163 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.134317 restraints weight = 31139.278| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.29 r_work: 0.3137 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26594 Z= 0.085 Angle : 0.415 6.942 36330 Z= 0.216 Chirality : 0.039 0.185 4206 Planarity : 0.003 0.038 4441 Dihedral : 15.588 178.338 4514 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.41 % Allowed : 13.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3105 helix: 1.83 (0.17), residues: 1071 sheet: -0.09 (0.26), residues: 381 loop : -1.42 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 807 HIS 0.003 0.000 HIS D 777 PHE 0.018 0.001 PHE D 172 TYR 0.008 0.001 TYR D 140 ARG 0.003 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.02853 ( 1030) hydrogen bonds : angle 3.42644 ( 2887) metal coordination : bond 0.00173 ( 7) metal coordination : angle 1.63533 ( 6) covalent geometry : bond 0.00193 (26587) covalent geometry : angle 0.41435 (36324) *********************** 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 346 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 309 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7595 (t0) cc_final: 0.7294 (t0) REVERT: A 170 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.7937 (ttp-170) REVERT: C 79 VAL cc_start: 0.8394 (m) cc_final: 0.8152 (p) REVERT: C 88 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7826 (mtp85) REVERT: C 185 ASP cc_start: 0.7919 (m-30) cc_final: 0.7694 (m-30) REVERT: C 208 ILE cc_start: 0.8521 (mt) cc_final: 0.8092 (pt) REVERT: C 368 ARG cc_start: 0.8315 (mtm110) cc_final: 0.8059 (mtm110) REVERT: C 611 GLU cc_start: 0.7454 (tt0) cc_final: 0.7212 (tt0) REVERT: C 1038 GLN cc_start: 0.7291 (tm-30) cc_final: 0.7070 (tm-30) REVERT: D 155 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7649 (tp30) REVERT: D 225 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7198 (mm-30) REVERT: D 227 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.6984 (t80) REVERT: D 803 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8200 (p) REVERT: D 826 ILE cc_start: 0.6992 (mm) cc_final: 0.6658 (mm) REVERT: D 1152 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7158 (tt0) REVERT: E 11 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7631 (tp30) REVERT: E 68 GLU cc_start: 0.7533 (tt0) cc_final: 0.6673 (mp0) outliers start: 37 outliers final: 27 residues processed: 336 average time/residue: 0.5496 time to fit residues: 293.4943 Evaluate side-chains 325 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 54 CYS 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 131 THR 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 635 THR Chi-restraints excluded: chain C residue 658 GLN 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 111 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN 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 803 VAL Chi-restraints excluded: chain D residue 821 MET 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 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 219 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 210 optimal weight: 0.0970 chunk 153 optimal weight: 0.7980 chunk 306 optimal weight: 0.0270 chunk 34 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 305 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 618 GLN D 365 GLN D 739 GLN E 73 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.170755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.133199 restraints weight = 31073.775| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.26 r_work: 0.3117 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26594 Z= 0.088 Angle : 0.416 7.476 36330 Z= 0.216 Chirality : 0.039 0.149 4206 Planarity : 0.003 0.038 4441 Dihedral : 15.585 178.516 4514 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.37 % Allowed : 13.67 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.15), residues: 3105 helix: 2.00 (0.17), residues: 1072 sheet: 0.10 (0.27), residues: 381 loop : -1.31 (0.14), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 807 HIS 0.003 0.000 HIS D 777 PHE 0.018 0.001 PHE D 172 TYR 0.007 0.001 TYR A 177 ARG 0.007 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 1030) hydrogen bonds : angle 3.34373 ( 2887) metal coordination : bond 0.00175 ( 7) metal coordination : angle 1.58052 ( 6) covalent geometry : bond 0.00202 (26587) covalent geometry : angle 0.41552 (36324) *********************** 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 346 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 310 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 ARG cc_start: 0.8420 (ttp-170) cc_final: 0.8017 (ttp-170) REVERT: C 79 VAL cc_start: 0.8481 (m) cc_final: 0.8190 (p) REVERT: C 88 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7748 (mtp85) REVERT: C 185 ASP cc_start: 0.8250 (m-30) cc_final: 0.8029 (m-30) REVERT: C 368 ARG cc_start: 0.8248 (mtm110) cc_final: 0.8020 (mtm110) REVERT: C 611 GLU cc_start: 0.7586 (tt0) cc_final: 0.7299 (tt0) REVERT: C 658 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8092 (pt0) REVERT: C 1038 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 1174 GLU cc_start: 0.8062 (tp30) cc_final: 0.7852 (mt-10) REVERT: D 155 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7709 (tp30) REVERT: D 225 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7338 (mm-30) REVERT: D 227 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.6867 (t80) REVERT: D 803 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8219 (p) REVERT: D 826 ILE cc_start: 0.7035 (mm) cc_final: 0.6676 (mm) REVERT: D 1152 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7140 (tt0) REVERT: D 1243 LEU cc_start: 0.9089 (tp) cc_final: 0.8888 (mp) REVERT: E 11 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7753 (tp30) REVERT: E 68 GLU cc_start: 0.7599 (tt0) cc_final: 0.6657 (mp0) outliers start: 36 outliers final: 24 residues processed: 336 average time/residue: 0.4598 time to fit residues: 243.8671 Evaluate side-chains 317 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 290 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain B residue 54 CYS 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 131 THR 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 658 GLN Chi-restraints excluded: chain C residue 1011 LEU 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 111 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET 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 1275 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 264 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 306 optimal weight: 5.9990 chunk 196 optimal weight: 0.6980 chunk 303 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN D 365 GLN D 720 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.168786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129398 restraints weight = 31026.460| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.31 r_work: 0.3071 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26594 Z= 0.103 Angle : 0.433 8.533 36330 Z= 0.225 Chirality : 0.040 0.146 4206 Planarity : 0.003 0.041 4441 Dihedral : 15.629 178.940 4514 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.60 % Allowed : 13.86 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 3105 helix: 2.07 (0.17), residues: 1069 sheet: 0.14 (0.26), residues: 391 loop : -1.24 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 807 HIS 0.003 0.001 HIS D 777 PHE 0.017 0.001 PHE D 172 TYR 0.009 0.001 TYR A 177 ARG 0.005 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.03134 ( 1030) hydrogen bonds : angle 3.34740 ( 2887) metal coordination : bond 0.00237 ( 7) metal coordination : angle 1.86849 ( 6) covalent geometry : bond 0.00241 (26587) covalent geometry : angle 0.43283 (36324) *********************** 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 343 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 301 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7693 (t0) cc_final: 0.7487 (t0) REVERT: A 205 MET cc_start: 0.8763 (ptm) cc_final: 0.8411 (ptm) REVERT: C 79 VAL cc_start: 0.8506 (m) cc_final: 0.8262 (p) REVERT: C 88 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7830 (mtp85) REVERT: C 185 ASP cc_start: 0.7964 (m-30) cc_final: 0.7733 (m-30) REVERT: C 208 ILE cc_start: 0.8565 (mt) cc_final: 0.8182 (pt) REVERT: C 368 ARG cc_start: 0.8282 (mtm110) cc_final: 0.8042 (mtm110) REVERT: C 371 ARG cc_start: 0.7311 (mmt90) cc_final: 0.6848 (mmt90) REVERT: C 611 GLU cc_start: 0.7513 (tt0) cc_final: 0.7279 (tt0) REVERT: C 658 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.8022 (pt0) REVERT: C 1038 GLN cc_start: 0.7339 (tm-30) cc_final: 0.7035 (tm-30) REVERT: D 155 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7575 (tp30) REVERT: D 225 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7249 (mm-30) REVERT: D 227 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7013 (t80) REVERT: D 803 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8275 (p) REVERT: D 826 ILE cc_start: 0.7116 (mm) cc_final: 0.6769 (mm) REVERT: D 1243 LEU cc_start: 0.9021 (tp) cc_final: 0.8806 (mp) REVERT: E 11 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7628 (tp30) REVERT: E 68 GLU cc_start: 0.7520 (tt0) cc_final: 0.6653 (mp0) outliers start: 42 outliers final: 30 residues processed: 329 average time/residue: 0.4147 time to fit residues: 210.7427 Evaluate side-chains 320 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 287 time to evaluate : 2.704 ------------------------------------------------------------------------------- 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 54 CYS 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 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 615 VAL Chi-restraints excluded: chain C residue 658 GLN Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 111 THR 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 666 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET 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 1058 SER 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 83 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 224 optimal weight: 4.9990 chunk 196 optimal weight: 0.0010 chunk 266 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 289 optimal weight: 0.5980 chunk 226 optimal weight: 0.0270 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.168225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.128469 restraints weight = 30975.931| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.30 r_work: 0.3073 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26594 Z= 0.101 Angle : 0.433 9.099 36330 Z= 0.225 Chirality : 0.040 0.146 4206 Planarity : 0.003 0.043 4441 Dihedral : 15.630 179.188 4514 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.57 % Allowed : 14.20 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.15), residues: 3105 helix: 2.11 (0.17), residues: 1071 sheet: 0.23 (0.26), residues: 402 loop : -1.19 (0.14), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.003 0.001 HIS D 777 PHE 0.017 0.001 PHE C 80 TYR 0.010 0.001 TYR A 177 ARG 0.006 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 1030) hydrogen bonds : angle 3.33185 ( 2887) metal coordination : bond 0.00243 ( 7) metal coordination : angle 1.73867 ( 6) covalent geometry : bond 0.00237 (26587) covalent geometry : angle 0.43278 (36324) *********************** 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 333 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 292 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7754 (t0) cc_final: 0.7485 (t0) REVERT: A 170 ARG cc_start: 0.8368 (ttp-170) cc_final: 0.7935 (ttp-170) REVERT: A 205 MET cc_start: 0.8783 (ptm) cc_final: 0.8449 (ptm) REVERT: C 79 VAL cc_start: 0.8482 (m) cc_final: 0.8264 (p) REVERT: C 88 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7818 (mtp85) REVERT: C 185 ASP cc_start: 0.7939 (m-30) cc_final: 0.7707 (m-30) REVERT: C 368 ARG cc_start: 0.8286 (mtm110) cc_final: 0.8046 (mtm110) REVERT: C 371 ARG cc_start: 0.7298 (mmt90) cc_final: 0.6862 (mmt90) REVERT: C 545 PHE cc_start: 0.8398 (m-80) cc_final: 0.8018 (m-80) REVERT: C 611 GLU cc_start: 0.7525 (tt0) cc_final: 0.7299 (tt0) REVERT: C 1038 GLN cc_start: 0.7461 (tm-30) cc_final: 0.7124 (tm-30) REVERT: D 155 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7630 (tp30) REVERT: D 225 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7230 (mm-30) REVERT: D 227 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.6991 (t80) REVERT: D 803 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8239 (p) REVERT: D 826 ILE cc_start: 0.7132 (mm) cc_final: 0.6766 (mm) REVERT: D 1152 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7111 (tt0) REVERT: D 1243 LEU cc_start: 0.9018 (tp) cc_final: 0.8795 (mp) REVERT: E 11 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7526 (tp30) REVERT: E 68 GLU cc_start: 0.7523 (tt0) cc_final: 0.6635 (mp0) outliers start: 41 outliers final: 33 residues processed: 321 average time/residue: 0.4099 time to fit residues: 202.5329 Evaluate side-chains 322 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 287 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU 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 54 CYS 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 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 615 VAL Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain D residue 111 THR 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 666 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 981 GLU 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 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 64 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 219 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 316 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 224 optimal weight: 0.0040 chunk 230 optimal weight: 1.9990 chunk 229 optimal weight: 0.7980 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.126231 restraints weight = 30936.847| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.23 r_work: 0.3024 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26594 Z= 0.134 Angle : 0.469 9.811 36330 Z= 0.243 Chirality : 0.041 0.150 4206 Planarity : 0.003 0.046 4441 Dihedral : 15.727 179.567 4514 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.45 % Allowed : 14.32 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3105 helix: 2.05 (0.17), residues: 1063 sheet: 0.18 (0.26), residues: 400 loop : -1.17 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1193 HIS 0.004 0.001 HIS D 777 PHE 0.018 0.001 PHE C 80 TYR 0.013 0.001 TYR A 177 ARG 0.005 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 1030) hydrogen bonds : angle 3.42330 ( 2887) metal coordination : bond 0.00384 ( 7) metal coordination : angle 2.35296 ( 6) covalent geometry : bond 0.00324 (26587) covalent geometry : angle 0.46799 (36324) *********************** 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 327 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 289 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 ASP cc_start: 0.7559 (t0) cc_final: 0.7323 (t0) REVERT: C 88 ARG cc_start: 0.8297 (mtp85) cc_final: 0.7865 (mtp85) REVERT: C 185 ASP cc_start: 0.7992 (m-30) cc_final: 0.7768 (m-30) REVERT: C 371 ARG cc_start: 0.7283 (mmt90) cc_final: 0.6829 (mmt90) REVERT: C 618 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: C 1038 GLN cc_start: 0.7507 (tm-30) cc_final: 0.7006 (tm-30) REVERT: D 66 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8404 (mtpp) REVERT: D 155 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7619 (tp30) REVERT: D 225 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7268 (mm-30) REVERT: D 227 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.7000 (t80) REVERT: D 485 MET cc_start: 0.8888 (tpt) cc_final: 0.8385 (tpt) REVERT: D 803 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8362 (p) REVERT: D 826 ILE cc_start: 0.7247 (mm) cc_final: 0.6916 (mm) REVERT: D 1243 LEU cc_start: 0.9034 (tp) cc_final: 0.8807 (mp) REVERT: E 11 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7553 (tp30) REVERT: E 68 GLU cc_start: 0.7478 (tt0) cc_final: 0.6587 (mp0) outliers start: 38 outliers final: 33 residues processed: 316 average time/residue: 0.4252 time to fit residues: 208.1445 Evaluate side-chains 313 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 2.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU 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 90 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 153 VAL 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 615 VAL Chi-restraints excluded: chain C residue 618 GLN 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 1094 VAL Chi-restraints excluded: chain C residue 1163 THR 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 666 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 981 GLU 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 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 87 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN C1116 HIS 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 = 0.160560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.122501 restraints weight = 30983.304| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.29 r_work: 0.3023 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 26594 Z= 0.225 Angle : 0.582 11.015 36330 Z= 0.302 Chirality : 0.045 0.154 4206 Planarity : 0.005 0.062 4441 Dihedral : 15.984 179.312 4514 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.37 % Allowed : 14.62 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.15), residues: 3105 helix: 1.61 (0.16), residues: 1068 sheet: -0.01 (0.26), residues: 419 loop : -1.27 (0.14), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D1193 HIS 0.008 0.001 HIS D 419 PHE 0.029 0.002 PHE C 80 TYR 0.022 0.002 TYR A 177 ARG 0.008 0.001 ARG C1246 Details of bonding type rmsd hydrogen bonds : bond 0.04752 ( 1030) hydrogen bonds : angle 3.73055 ( 2887) metal coordination : bond 0.00585 ( 7) metal coordination : angle 3.43418 ( 6) covalent geometry : bond 0.00553 (26587) covalent geometry : angle 0.58009 (36324) ********************** 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 329 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 293 time to evaluate : 2.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8410 (mmtp) cc_final: 0.8048 (mttp) REVERT: A 96 ASP cc_start: 0.7876 (t0) cc_final: 0.7675 (t0) REVERT: A 205 MET cc_start: 0.9037 (ptm) cc_final: 0.8396 (ptp) REVERT: C 88 ARG cc_start: 0.8480 (mtp85) cc_final: 0.7981 (mtp85) REVERT: C 185 ASP cc_start: 0.8262 (m-30) cc_final: 0.8057 (m-30) REVERT: C 371 ARG cc_start: 0.7300 (mmt90) cc_final: 0.6831 (mmt90) REVERT: C 862 LEU cc_start: 0.8249 (mp) cc_final: 0.7868 (mt) REVERT: D 155 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7712 (tp30) REVERT: D 227 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7072 (t80) REVERT: D 267 ASP cc_start: 0.8471 (t70) cc_final: 0.8075 (t0) REVERT: D 485 MET cc_start: 0.9125 (tpt) cc_final: 0.8811 (tpt) REVERT: D 826 ILE cc_start: 0.7411 (mm) cc_final: 0.7124 (mm) REVERT: E 68 GLU cc_start: 0.7711 (tt0) cc_final: 0.6473 (mp0) REVERT: E 71 GLU cc_start: 0.7341 (tp30) cc_final: 0.7062 (tp30) REVERT: E 75 GLN cc_start: 0.6548 (tm-30) cc_final: 0.6009 (tp40) outliers start: 36 outliers final: 31 residues processed: 320 average time/residue: 0.4145 time to fit residues: 204.7948 Evaluate side-chains 310 residues out of total 2666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 278 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU 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 90 VAL 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 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 1094 VAL Chi-restraints excluded: chain C residue 1163 THR 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 666 GLU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 821 MET Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 981 GLU 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 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 47 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 85 optimal weight: 0.1980 chunk 191 optimal weight: 0.8980 chunk 267 optimal weight: 9.9990 chunk 179 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 618 GLN C1134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125929 restraints weight = 31021.063| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.28 r_work: 0.3005 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26594 Z= 0.106 Angle : 0.464 10.770 36330 Z= 0.242 Chirality : 0.040 0.150 4206 Planarity : 0.003 0.051 4441 Dihedral : 15.828 178.573 4514 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.26 % Allowed : 15.01 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3105 helix: 1.97 (0.17), residues: 1062 sheet: 0.12 (0.26), residues: 408 loop : -1.14 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D1193 HIS 0.003 0.001 HIS D 777 PHE 0.030 0.001 PHE C 80 TYR 0.011 0.001 TYR C 47 ARG 0.005 0.000 ARG C 371 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 1030) hydrogen bonds : angle 3.50212 ( 2887) metal coordination : bond 0.00259 ( 7) metal coordination : angle 1.92927 ( 6) covalent geometry : bond 0.00247 (26587) covalent geometry : angle 0.46360 (36324) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14991.22 seconds wall clock time: 260 minutes 9.69 seconds (15609.69 seconds total)