Starting phenix.real_space_refine on Thu Jul 25 12:02:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3b_18120/07_2024/8q3b_18120_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3b_18120/07_2024/8q3b_18120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3b_18120/07_2024/8q3b_18120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3b_18120/07_2024/8q3b_18120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3b_18120/07_2024/8q3b_18120_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q3b_18120/07_2024/8q3b_18120_neut.cif" } resolution = 2.69 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 168 5.16 5 C 18712 2.51 5 N 5061 2.21 5 O 5441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 149": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A GLU 1179": "OE1" <-> "OE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 582": "OE1" <-> "OE2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "C GLU 275": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29389 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 11278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11278 Classifications: {'peptide': 1423} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 64, 'TRANS': 1356} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 8553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8553 Classifications: {'peptide': 1104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 48, 'TRANS': 1055} Chain breaks: 8 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 112 Chain: "C" Number of atoms: 2910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2910 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 338} Chain: "D" Number of atoms: 2649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2649 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1665 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 816 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "J" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 635 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "A" 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} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 59 98.567 107.446 63.513 1.00 75.51 S ATOM 471 SG CYS A 62 95.864 109.360 63.460 1.00 63.12 S ATOM 531 SG CYS A 69 95.367 106.005 64.392 1.00 77.85 S ATOM 775 SG CYS A 99 88.068 84.420 23.073 1.00 97.40 S ATOM 797 SG CYS A 102 87.840 87.955 21.646 1.00100.53 S ATOM 1041 SG CYS A 134 85.201 85.475 20.720 1.00114.41 S ATOM 1066 SG CYS A 137 88.791 84.972 19.449 1.00118.07 S ATOM 19350 SG CYS B1180 86.860 113.911 51.944 1.00 58.66 S ATOM 19375 SG CYS B1183 87.097 110.361 50.468 1.00 62.25 S ATOM 19491 SG CYS B1198 90.225 112.240 51.433 1.00 65.03 S ATOM 19513 SG CYS B1201 88.115 113.408 48.449 1.00 73.50 S ATOM 27962 SG CYS I 4 76.123 30.063 35.044 1.00135.73 S ATOM 27982 SG CYS I 7 78.904 31.541 37.253 1.00138.47 S ATOM 28116 SG CYS I 24 76.358 33.883 35.685 1.00135.67 S ATOM 28128 SG CYS I 26 78.968 32.225 33.581 1.00130.43 S ATOM 28498 SG CYS I 73 48.303 21.944 79.935 1.00 96.76 S ATOM 28519 SG CYS I 76 50.616 20.067 82.304 1.00120.92 S ATOM 28676 SG CYS I 96 51.681 23.337 80.876 1.00 95.15 S ATOM 28693 SG CYS I 98 51.465 20.334 78.535 1.00105.92 S ATOM 28798 SG CYS J 7 68.777 77.095 122.097 1.00 63.37 S ATOM 28822 SG CYS J 10 66.813 79.362 124.475 1.00 74.64 S ATOM 29245 SG CYS J 65 65.063 76.665 122.376 1.00 55.15 S ATOM 29251 SG CYS J 66 67.234 75.826 125.431 1.00 53.89 S Time building chain proxies: 15.85, per 1000 atoms: 0.54 Number of scatterers: 29389 At special positions: 0 Unit cell: (133.308, 167.256, 156.492, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 168 16.00 Mg 1 11.99 O 5441 8.00 N 5061 7.00 C 18712 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 - 3.50 Amino acid : False - 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: 10.84 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 69 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 59 " pdb="ZN ZN A1501 " - pdb=" NE2 HIS A 72 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 62 " pdb=" ZN A1502 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 137 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 99 " pdb="ZN ZN A1502 " - pdb=" SG CYS A 134 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1201 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1180 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1183 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1198 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 26 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 24 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 4 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 96 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 73 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 76 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 98 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 66 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 65 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " Number of angles added : 33 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 45 sheets defined 43.0% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 17 through 25 Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 87 through 96 Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.594A pdb=" N TYR A 112 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 166 through 176 removed outlier: 3.518A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'A' and resid 188 through 195 removed outlier: 3.762A pdb=" N HIS A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 225 through 240 removed outlier: 3.590A pdb=" N VAL A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 273 removed outlier: 3.536A pdb=" N ASP A 273 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 342 through 348 Processing helix chain 'A' and resid 358 through 369 Proline residue: A 364 - end of helix Processing helix chain 'A' and resid 450 through 455 removed outlier: 4.175A pdb=" N TYR A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 480 Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.562A pdb=" N PHE A 487 " --> pdb=" O ARG A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 523 through 531 removed outlier: 3.916A pdb=" N PHE A 531 " --> pdb=" O ALA A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 578 through 582 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 615 through 625 Processing helix chain 'A' and resid 625 through 647 removed outlier: 3.760A pdb=" N ASN A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 657 Processing helix chain 'A' and resid 659 through 687 Processing helix chain 'A' and resid 696 through 709 Processing helix chain 'A' and resid 712 through 714 No H-bonds generated for 'chain 'A' and resid 712 through 714' Processing helix chain 'A' and resid 715 through 723 removed outlier: 4.065A pdb=" N ILE A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 Processing helix chain 'A' and resid 741 through 749 Processing helix chain 'A' and resid 781 through 785 Processing helix chain 'A' and resid 797 through 834 Processing helix chain 'A' and resid 854 through 858 removed outlier: 3.529A pdb=" N ASP A 858 " --> pdb=" O TYR A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 891 through 918 removed outlier: 4.236A pdb=" N GLU A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 945 Processing helix chain 'A' and resid 953 through 971 Processing helix chain 'A' and resid 972 through 975 Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.590A pdb=" N GLU A 981 " --> pdb=" O ASN A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1006 removed outlier: 4.506A pdb=" N LEU A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1040 through 1051 Processing helix chain 'A' and resid 1052 through 1062 Processing helix chain 'A' and resid 1074 through 1083 Processing helix chain 'A' and resid 1102 through 1105 removed outlier: 4.076A pdb=" N THR A1105 " --> pdb=" O GLU A1102 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1102 through 1105' Processing helix chain 'A' and resid 1106 through 1118 Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1151 through 1162 Processing helix chain 'A' and resid 1181 through 1189 Processing helix chain 'A' and resid 1191 through 1203 Processing helix chain 'A' and resid 1230 through 1233 Processing helix chain 'A' and resid 1242 through 1256 Processing helix chain 'A' and resid 1299 through 1306 Processing helix chain 'A' and resid 1310 through 1314 removed outlier: 3.909A pdb=" N THR A1313 " --> pdb=" O ASP A1310 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A1314 " --> pdb=" O PRO A1311 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1310 through 1314' Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1327 through 1344 Processing helix chain 'A' and resid 1349 through 1361 removed outlier: 3.854A pdb=" N LEU A1353 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1378 Processing helix chain 'A' and resid 1381 through 1389 Processing helix chain 'A' and resid 1390 through 1402 Processing helix chain 'A' and resid 1410 through 1416 Processing helix chain 'A' and resid 1422 through 1426 Processing helix chain 'A' and resid 1432 through 1440 removed outlier: 3.548A pdb=" N GLU A1438 " --> pdb=" O LYS A1434 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 Processing helix chain 'B' and resid 22 through 38 removed outlier: 3.913A pdb=" N SER B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 53 Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 175 through 183 Processing helix chain 'B' and resid 272 through 280 removed outlier: 3.608A pdb=" N GLY B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 293 removed outlier: 3.602A pdb=" N VAL B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 315 Processing helix chain 'B' and resid 320 through 325 removed outlier: 4.452A pdb=" N HIS B 325 " --> pdb=" O GLN B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 342 removed outlier: 3.645A pdb=" N LYS B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 420 through 450 removed outlier: 3.963A pdb=" N SER B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) Proline residue: B 440 - end of helix Processing helix chain 'B' and resid 476 through 488 Processing helix chain 'B' and resid 514 through 522 Processing helix chain 'B' and resid 526 through 532 removed outlier: 3.873A pdb=" N THR B 530 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 532 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 542 Processing helix chain 'B' and resid 582 through 593 removed outlier: 3.575A pdb=" N LEU B 586 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 611 Processing helix chain 'B' and resid 627 through 642 Processing helix chain 'B' and resid 679 through 697 Processing helix chain 'B' and resid 700 through 705 Processing helix chain 'B' and resid 715 through 724 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 754 through 761 Processing helix chain 'B' and resid 774 through 779 Processing helix chain 'B' and resid 780 through 786 removed outlier: 4.061A pdb=" N SER B 786 " --> pdb=" O ALA B 782 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 792 Processing helix chain 'B' and resid 793 through 800 removed outlier: 4.084A pdb=" N GLU B 800 " --> pdb=" O ARG B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 869 through 874 Processing helix chain 'B' and resid 1011 through 1015 Processing helix chain 'B' and resid 1031 through 1037 removed outlier: 4.709A pdb=" N SER B1035 " --> pdb=" O HIS B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1055 removed outlier: 4.259A pdb=" N MET B1042 " --> pdb=" O THR B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1078 Processing helix chain 'B' and resid 1114 through 1119 Processing helix chain 'B' and resid 1148 through 1159 Processing helix chain 'B' and resid 1160 through 1169 Processing helix chain 'B' and resid 1213 through 1226 Processing helix chain 'C' and resid 19 through 31 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.602A pdb=" N PHE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 230 through 259 Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.599A pdb=" N GLY C 291 " --> pdb=" O THR C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 359 removed outlier: 3.536A pdb=" N ALA C 359 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 118 through 124 removed outlier: 3.504A pdb=" N ALA D 124 " --> pdb=" O GLN D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 195 removed outlier: 3.790A pdb=" N LEU D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 184 " --> pdb=" O LYS D 180 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 208 removed outlier: 3.711A pdb=" N ILE D 200 " --> pdb=" O ASP D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 288 through 314 Processing helix chain 'D' and resid 316 through 334 removed outlier: 4.880A pdb=" N ASN D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ILE D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 17 removed outlier: 4.377A pdb=" N TYR E 11 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLU E 12 " --> pdb=" O THR E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 39 Processing helix chain 'E' and resid 67 through 81 removed outlier: 3.711A pdb=" N MET E 71 " --> pdb=" O HIS E 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU E 81 " --> pdb=" O ASN E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 98 removed outlier: 3.624A pdb=" N LEU E 97 " --> pdb=" O ASP E 93 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 93 through 98' Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.505A pdb=" N LEU E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.614A pdb=" N CYS E 127 " --> pdb=" O HIS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 157 through 161 Processing helix chain 'E' and resid 168 through 175 Processing helix chain 'F' and resid 44 through 49 removed outlier: 3.924A pdb=" N GLY F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.532A pdb=" N ARG F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 90 Processing helix chain 'F' and resid 101 through 112 Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'I' and resid 33 through 37 Processing helix chain 'I' and resid 49 through 60 removed outlier: 3.958A pdb=" N TYR I 53 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE I 55 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N PHE I 56 " --> pdb=" O LYS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 63 No H-bonds generated for 'chain 'I' and resid 61 through 63' Processing helix chain 'J' and resid 14 through 33 removed outlier: 4.361A pdb=" N ALA J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR J 26 " --> pdb=" O ASP J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 51 through 59 Processing helix chain 'J' and resid 63 through 73 removed outlier: 3.508A pdb=" N THR J 73 " --> pdb=" O HIS J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5 removed outlier: 6.315A pdb=" N GLY A 4 " --> pdb=" O MET B1209 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASP B1211 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1404 through 1406 removed outlier: 6.646A pdb=" N VAL B1233 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL A 11 " --> pdb=" O THR B1231 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR B1231 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 13 " --> pdb=" O ASN B1229 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN B1229 " --> pdb=" O PHE A 13 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 83 removed outlier: 10.246A pdb=" N MET A 78 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 10.756A pdb=" N GLN A 202 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 10.212A pdb=" N ALA A 80 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA A 200 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 146 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 7.682A pdb=" N PHE A 444 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR A 326 " --> pdb=" O PHE A 444 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N MET A 446 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N CYS A 328 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 349 through 353 removed outlier: 3.924A pdb=" N ARG A 378 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 408 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N CYS A 376 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 514 through 515 Processing sheet with id=AA9, first strand: chain 'A' and resid 521 through 522 Processing sheet with id=AB1, first strand: chain 'A' and resid 567 through 569 removed outlier: 6.560A pdb=" N GLN A 592 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 753 through 754 Processing sheet with id=AB3, first strand: chain 'A' and resid 837 through 838 removed outlier: 6.531A pdb=" N VAL A 844 " --> pdb=" O VAL A 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 866 through 869 Processing sheet with id=AB5, first strand: chain 'A' and resid 1268 through 1278 removed outlier: 3.760A pdb=" N ILE A1290 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A1275 " --> pdb=" O ASP A1288 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP A1288 " --> pdb=" O ARG A1275 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARG A1277 " --> pdb=" O ARG A1286 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ARG A1286 " --> pdb=" O ARG A1277 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N MET A1094 " --> pdb=" O THR A1295 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB7, first strand: chain 'A' and resid 1207 through 1210 removed outlier: 6.229A pdb=" N ILE A1223 " --> pdb=" O ILE A1176 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A1176 " --> pdb=" O ILE A1223 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE A1225 " --> pdb=" O TRP A1174 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A1174 " --> pdb=" O ILE A1225 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU A1227 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS A1175 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A1131 " --> pdb=" O CYS A1175 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ARG A1177 " --> pdb=" O TRP A1129 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N TRP A1129 " --> pdb=" O ARG A1177 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLU A1179 " --> pdb=" O LEU A1127 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1428 through 1431 removed outlier: 6.764A pdb=" N ILE F 132 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL F 125 " --> pdb=" O GLN F 130 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN F 130 " --> pdb=" O VAL F 125 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR F 56 " --> pdb=" O LYS F 131 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL F 133 " --> pdb=" O THR F 56 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL F 58 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE F 135 " --> pdb=" O VAL F 58 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N PHE B1239 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE F 59 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.546A pdb=" N HIS B 139 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 137 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 93 through 96 removed outlier: 4.521A pdb=" N SER B 158 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU B 130 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 156 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 8.638A pdb=" N ALA B 132 " --> pdb=" O PRO B 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 193 through 195 Processing sheet with id=AC3, first strand: chain 'B' and resid 416 through 419 removed outlier: 6.728A pdb=" N LEU B 204 " --> pdb=" O ASN B 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 213 through 217 removed outlier: 3.616A pdb=" N ILE B 228 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 576 through 578 removed outlier: 4.203A pdb=" N ARG B 668 " --> pdb=" O CYS B 578 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AC7, first strand: chain 'B' and resid 597 through 598 removed outlier: 5.406A pdb=" N TRP B 621 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE B 617 " --> pdb=" O TRP B 621 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 623 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 823 through 826 removed outlier: 3.930A pdb=" N MET B 982 " --> pdb=" O GLU B 885 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ARG B 983 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 834 through 835 Processing sheet with id=AD1, first strand: chain 'B' and resid 1085 through 1086 removed outlier: 6.106A pdb=" N VAL B 865 " --> pdb=" O ALA B1006 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B1008 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N LEU B1026 " --> pdb=" O ASN B 848 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B 850 " --> pdb=" O LEU B1026 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL B1028 " --> pdb=" O ILE B 850 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA B 852 " --> pdb=" O VAL B1028 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE B1102 " --> pdb=" O TYR B 853 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 932 through 935 removed outlier: 3.733A pdb=" N ILE B 934 " --> pdb=" O VAL B 955 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1017 through 1018 Processing sheet with id=AD4, first strand: chain 'B' and resid 1188 through 1190 Processing sheet with id=AD5, first strand: chain 'C' and resid 5 through 12 removed outlier: 5.253A pdb=" N PHE C 5 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LYS C 48 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN C 7 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL C 39 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA C 225 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N HIS C 216 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N HIS C 186 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARG C 218 " --> pdb=" O PHE C 184 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE C 184 " --> pdb=" O ARG C 218 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLY C 220 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 68 through 73 removed outlier: 5.178A pdb=" N ILE C 159 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N SER C 115 " --> pdb=" O ILE C 159 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU C 161 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU C 113 " --> pdb=" O GLU C 161 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 110 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AD8, first strand: chain 'C' and resid 267 through 271 Processing sheet with id=AD9, first strand: chain 'D' and resid 2 through 13 removed outlier: 12.184A pdb=" N TYR D 69 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N ARG D 54 " --> pdb=" O TYR D 69 " (cutoff:3.500A) removed outlier: 11.822A pdb=" N HIS D 71 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N ILE D 52 " --> pdb=" O HIS D 71 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ARG D 73 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N GLY D 50 " --> pdb=" O ARG D 73 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N SER D 75 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE D 48 " --> pdb=" O SER D 75 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL D 77 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE D 44 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 2 through 13 Processing sheet with id=AE2, first strand: chain 'D' and resid 86 through 87 removed outlier: 6.019A pdb=" N THR D 111 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY D 152 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N VAL D 113 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE D 154 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N VAL D 110 " --> pdb=" O SER D 104 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 164 through 166 Processing sheet with id=AE4, first strand: chain 'D' and resid 217 through 219 Processing sheet with id=AE5, first strand: chain 'D' and resid 237 through 238 Processing sheet with id=AE6, first strand: chain 'E' and resid 20 through 21 removed outlier: 6.680A pdb=" N ILE E 52 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE E 89 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N SER E 54 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE E 91 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE E 56 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL E 117 " --> pdb=" O GLU E 86 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 138 through 142 removed outlier: 3.819A pdb=" N LYS E 138 " --> pdb=" O GLU E 185 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N PHE E 181 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N MET E 162 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR E 201 " --> pdb=" O MET E 162 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE E 164 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 12 through 13 removed outlier: 5.318A pdb=" N CYS I 24 " --> pdb=" O GLU I 28 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLU I 28 " --> pdb=" O CYS I 24 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 68 through 69 1320 hydrogen bonds defined for protein. 3639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.58 Time building geometry restraints manager: 11.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9672 1.35 - 1.47: 6880 1.47 - 1.60: 13134 1.60 - 1.73: 1 1.73 - 1.86: 273 Bond restraints: 29960 Sorted by residual: bond pdb=" N PRO E 131 " pdb=" CD PRO E 131 " ideal model delta sigma weight residual 1.473 1.636 -0.163 1.40e-02 5.10e+03 1.36e+02 bond pdb=" N ILE E 130 " pdb=" CA ILE E 130 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.51e+00 bond pdb=" N GLU B1222 " pdb=" CA GLU B1222 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.95e+00 bond pdb=" N MET B1223 " pdb=" CA MET B1223 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.89e+00 bond pdb=" N ASN B 328 " pdb=" CA ASN B 328 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.24e-02 6.50e+03 5.86e+00 ... (remaining 29955 not shown) Histogram of bond angle deviations from ideal: 97.58 - 104.90: 523 104.90 - 112.23: 15116 112.23 - 119.55: 10041 119.55 - 126.87: 14568 126.87 - 134.20: 330 Bond angle restraints: 40578 Sorted by residual: angle pdb=" CB MET B 51 " pdb=" CG MET B 51 " pdb=" SD MET B 51 " ideal model delta sigma weight residual 112.70 125.43 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" CG MET B 51 " pdb=" SD MET B 51 " pdb=" CE MET B 51 " ideal model delta sigma weight residual 100.90 107.90 -7.00 2.20e+00 2.07e-01 1.01e+01 angle pdb=" N TYR B 42 " pdb=" CA TYR B 42 " pdb=" CB TYR B 42 " ideal model delta sigma weight residual 114.17 110.63 3.54 1.14e+00 7.69e-01 9.66e+00 angle pdb=" CA MET B 969 " pdb=" CB MET B 969 " pdb=" CG MET B 969 " ideal model delta sigma weight residual 114.10 120.27 -6.17 2.00e+00 2.50e-01 9.51e+00 angle pdb=" CB MET D 328 " pdb=" CG MET D 328 " pdb=" SD MET D 328 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.42e+00 ... (remaining 40573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 16144 17.90 - 35.80: 1554 35.80 - 53.70: 389 53.70 - 71.60: 136 71.60 - 89.50: 20 Dihedral angle restraints: 18243 sinusoidal: 7366 harmonic: 10877 Sorted by residual: dihedral pdb=" CA HIS E 193 " pdb=" C HIS E 193 " pdb=" N ALA E 194 " pdb=" CA ALA E 194 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASN A 977 " pdb=" C ASN A 977 " pdb=" N ASN A 978 " pdb=" CA ASN A 978 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLN A 68 " pdb=" C GLN A 68 " pdb=" N CYS A 69 " pdb=" CA CYS A 69 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 18240 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 3322 0.037 - 0.074: 836 0.074 - 0.110: 314 0.110 - 0.147: 154 0.147 - 0.184: 5 Chirality restraints: 4631 Sorted by residual: chirality pdb=" CA HIS A 72 " pdb=" N HIS A 72 " pdb=" C HIS A 72 " pdb=" CB HIS A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.44e-01 chirality pdb=" CA ILE A 593 " pdb=" N ILE A 593 " pdb=" C ILE A 593 " pdb=" CB ILE A 593 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA PRO B 794 " pdb=" N PRO B 794 " pdb=" C PRO B 794 " pdb=" CB PRO B 794 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.26e-01 ... (remaining 4628 not shown) Planarity restraints: 5226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 793 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 794 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 794 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 794 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 72 " 0.023 2.00e-02 2.50e+03 2.16e-02 7.01e+00 pdb=" CG HIS A 72 " -0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS A 72 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS A 72 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 72 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 72 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 50 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.14e+00 pdb=" C LEU B 50 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU B 50 " -0.015 2.00e-02 2.50e+03 pdb=" N MET B 51 " -0.013 2.00e-02 2.50e+03 ... (remaining 5223 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 11 2.12 - 2.81: 8506 2.81 - 3.51: 40978 3.51 - 4.20: 69342 4.20 - 4.90: 127491 Nonbonded interactions: 246328 Sorted by model distance: nonbonded pdb=" OD2 ASP A 457 " pdb=" OD2 ASP A 459 " model vdw 1.424 3.040 nonbonded pdb=" O THR J 68 " pdb=" OG1 THR J 72 " model vdw 1.981 2.440 nonbonded pdb=" OG1 THR A1135 " pdb=" OD1 ASN A1173 " model vdw 1.995 2.440 nonbonded pdb=" OD1 ASP A 457 " pdb="MG MG A1503 " model vdw 2.032 2.170 nonbonded pdb=" OE2 GLU A1123 " pdb=" OH TYR I 44 " model vdw 2.035 2.440 ... (remaining 246323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 1.120 Check model and map are aligned: 0.230 Set scattering table: 0.260 Process input model: 81.080 Find NCS groups from input model: 0.270 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: 0.000 Load rotamer database and sin/cos tables:12.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.163 29960 Z= 0.198 Angle : 0.557 12.726 40578 Z= 0.291 Chirality : 0.043 0.184 4631 Planarity : 0.004 0.086 5226 Dihedral : 15.889 89.500 11209 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.52 % Allowed : 19.32 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.94 (0.14), residues: 3688 helix: 1.48 (0.14), residues: 1378 sheet: -0.24 (0.22), residues: 564 loop : 0.38 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 466 HIS 0.020 0.001 HIS A 72 PHE 0.029 0.001 PHE A 810 TYR 0.016 0.001 TYR D 303 ARG 0.021 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 392 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 ASN cc_start: 0.8839 (t0) cc_final: 0.8621 (t0) REVERT: B 62 MET cc_start: 0.7818 (tpp) cc_final: 0.7063 (ptt) REVERT: B 544 ARG cc_start: 0.7469 (mtt-85) cc_final: 0.6931 (mmt180) REVERT: C 274 GLU cc_start: 0.6984 (tm-30) cc_final: 0.6654 (tm-30) REVERT: D 183 ASN cc_start: 0.9038 (t0) cc_final: 0.8819 (t0) REVERT: D 333 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6778 (tmm160) REVERT: I 19 ASN cc_start: 0.8837 (m-40) cc_final: 0.7876 (p0) REVERT: I 31 GLN cc_start: 0.8965 (mm110) cc_final: 0.8733 (tp40) outliers start: 17 outliers final: 5 residues processed: 402 average time/residue: 1.3774 time to fit residues: 650.4901 Evaluate side-chains 376 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 370 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain E residue 125 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 311 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 95 optimal weight: 0.3980 chunk 188 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 chunk 289 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 175 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 356 HIS A1078 GLN A1205 ASN A1375 ASN B 101 HIS B 108 ASN B 207 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN D 272 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29960 Z= 0.265 Angle : 0.531 7.864 40578 Z= 0.277 Chirality : 0.044 0.236 4631 Planarity : 0.004 0.048 5226 Dihedral : 5.305 157.702 4048 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.13 % Allowed : 18.24 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.11 (0.14), residues: 3688 helix: 1.70 (0.14), residues: 1402 sheet: -0.15 (0.22), residues: 571 loop : 0.37 (0.16), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 257 HIS 0.007 0.001 HIS D 323 PHE 0.020 0.001 PHE A 918 TYR 0.016 0.001 TYR B 273 ARG 0.011 0.001 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 389 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 GLU cc_start: 0.7694 (tp30) cc_final: 0.7224 (tp30) REVERT: A 455 ASN cc_start: 0.8909 (t0) cc_final: 0.8666 (t0) REVERT: A 535 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: A 1118 GLU cc_start: 0.8339 (tt0) cc_final: 0.8091 (tt0) REVERT: A 1244 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: B 62 MET cc_start: 0.7771 (tpp) cc_final: 0.7133 (ptt) REVERT: B 251 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.6971 (mmt) REVERT: B 334 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8111 (mm-40) REVERT: B 633 GLN cc_start: 0.8192 (tt0) cc_final: 0.7918 (tt0) REVERT: B 637 MET cc_start: 0.8160 (mmm) cc_final: 0.7780 (mmp) REVERT: D 85 ASP cc_start: 0.8084 (m-30) cc_final: 0.7719 (m-30) REVERT: F 47 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7823 (mm-30) REVERT: F 140 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: I 19 ASN cc_start: 0.8894 (m-40) cc_final: 0.7975 (p0) REVERT: J 52 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8319 (tttp) outliers start: 69 outliers final: 22 residues processed: 423 average time/residue: 1.3409 time to fit residues: 671.2042 Evaluate side-chains 382 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 355 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1244 GLU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 52 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 186 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 278 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 335 optimal weight: 4.9990 chunk 362 optimal weight: 0.7980 chunk 298 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 114 optimal weight: 0.4980 chunk 269 optimal weight: 2.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 349 GLN A 356 HIS A 358 ASN A 721 ASN A1256 ASN B 64 ASN B 207 ASN D 53 GLN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29960 Z= 0.258 Angle : 0.508 8.458 40578 Z= 0.264 Chirality : 0.044 0.175 4631 Planarity : 0.004 0.040 5226 Dihedral : 4.543 78.461 4037 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.47 % Allowed : 18.89 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 1.08 (0.14), residues: 3688 helix: 1.77 (0.14), residues: 1395 sheet: -0.12 (0.22), residues: 563 loop : 0.25 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 257 HIS 0.007 0.001 HIS A 56 PHE 0.020 0.001 PHE A 918 TYR 0.017 0.001 TYR D 303 ARG 0.007 0.000 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 377 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9159 (mmmt) cc_final: 0.8951 (tptp) REVERT: A 123 GLU cc_start: 0.7790 (tp30) cc_final: 0.7292 (tp30) REVERT: A 301 ARG cc_start: 0.7989 (tpt90) cc_final: 0.7427 (tpt170) REVERT: A 500 VAL cc_start: 0.8896 (p) cc_final: 0.8692 (m) REVERT: A 535 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8373 (mp10) REVERT: A 765 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8034 (mp10) REVERT: A 1118 GLU cc_start: 0.8238 (tt0) cc_final: 0.8037 (tm-30) REVERT: A 1421 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8095 (ttm-80) REVERT: B 62 MET cc_start: 0.7748 (tpp) cc_final: 0.7110 (ptt) REVERT: B 251 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7035 (mmt) REVERT: B 281 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8251 (mmm) REVERT: B 334 GLN cc_start: 0.8416 (mm-40) cc_final: 0.7982 (mm-40) REVERT: B 630 GLU cc_start: 0.8074 (mp0) cc_final: 0.7773 (mp0) REVERT: B 633 GLN cc_start: 0.8208 (tt0) cc_final: 0.7916 (tt0) REVERT: B 637 MET cc_start: 0.8252 (mmm) cc_final: 0.7862 (mmp) REVERT: B 970 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7024 (ttm170) REVERT: B 1162 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8631 (mt0) REVERT: D 85 ASP cc_start: 0.8118 (m-30) cc_final: 0.7719 (m-30) REVERT: D 322 ARG cc_start: 0.8733 (mmm-85) cc_final: 0.8339 (mtp85) REVERT: F 140 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: I 19 ASN cc_start: 0.8933 (m-40) cc_final: 0.8068 (p0) REVERT: J 52 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8304 (tttp) REVERT: J 77 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8115 (mtp180) outliers start: 80 outliers final: 30 residues processed: 425 average time/residue: 1.3807 time to fit residues: 689.9970 Evaluate side-chains 397 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 358 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1094 MET Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 970 ARG Chi-restraints excluded: chain B residue 1162 GLN Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 331 optimal weight: 2.9990 chunk 252 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 356 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 319 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 ASN A1375 ASN B 484 GLN D 53 GLN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN J 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 29960 Z= 0.370 Angle : 0.552 8.733 40578 Z= 0.286 Chirality : 0.046 0.211 4631 Planarity : 0.004 0.041 5226 Dihedral : 4.705 77.982 4037 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.87 % Allowed : 18.95 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.85 (0.14), residues: 3688 helix: 1.59 (0.14), residues: 1408 sheet: -0.15 (0.23), residues: 517 loop : 0.04 (0.15), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 257 HIS 0.007 0.001 HIS A 56 PHE 0.021 0.002 PHE A 918 TYR 0.028 0.002 TYR B 192 ARG 0.007 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 366 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8852 (tptt) REVERT: A 254 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8066 (tm) REVERT: A 535 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: A 765 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: A 1118 GLU cc_start: 0.8294 (tt0) cc_final: 0.8076 (tm-30) REVERT: A 1421 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8108 (ttm-80) REVERT: B 62 MET cc_start: 0.7735 (tpp) cc_final: 0.7146 (ptt) REVERT: B 200 TRP cc_start: 0.8802 (m100) cc_final: 0.8598 (m100) REVERT: B 251 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.7060 (mmt) REVERT: B 281 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8359 (mmm) REVERT: B 334 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8124 (mm-40) REVERT: B 633 GLN cc_start: 0.8306 (tt0) cc_final: 0.8005 (tt0) REVERT: B 637 MET cc_start: 0.8315 (mmm) cc_final: 0.7933 (mmp) REVERT: D 85 ASP cc_start: 0.8125 (m-30) cc_final: 0.7712 (m-30) REVERT: F 140 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8480 (mt-10) REVERT: I 1 MET cc_start: 0.7841 (mmm) cc_final: 0.7591 (mmm) REVERT: I 19 ASN cc_start: 0.8974 (m-40) cc_final: 0.8070 (p0) REVERT: J 27 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: J 32 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8550 (tppt) REVERT: J 52 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8293 (tttp) REVERT: J 77 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8139 (mtp180) outliers start: 93 outliers final: 43 residues processed: 424 average time/residue: 1.3637 time to fit residues: 681.3843 Evaluate side-chains 405 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 352 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 297 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 265 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 304 optimal weight: 40.0000 chunk 246 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 320 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1205 ASN A1256 ASN B 364 GLN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 66 ASN J 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 29960 Z= 0.333 Angle : 0.537 9.236 40578 Z= 0.277 Chirality : 0.045 0.250 4631 Planarity : 0.004 0.042 5226 Dihedral : 4.695 78.167 4037 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.62 % Allowed : 19.66 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.79 (0.14), residues: 3688 helix: 1.57 (0.14), residues: 1406 sheet: -0.18 (0.23), residues: 522 loop : -0.01 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 320 HIS 0.006 0.001 HIS A 356 PHE 0.022 0.001 PHE A 918 TYR 0.018 0.001 TYR D 303 ARG 0.007 0.000 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 357 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9136 (mmmt) cc_final: 0.8918 (tptp) REVERT: A 212 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8156 (pt) REVERT: A 254 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8082 (tm) REVERT: A 535 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8380 (mp10) REVERT: A 710 LYS cc_start: 0.8944 (mtpm) cc_final: 0.8574 (mttm) REVERT: A 1118 GLU cc_start: 0.8237 (tt0) cc_final: 0.8020 (tm-30) REVERT: A 1421 ARG cc_start: 0.8518 (ttm-80) cc_final: 0.8134 (ttm-80) REVERT: B 62 MET cc_start: 0.7781 (tpp) cc_final: 0.7167 (ptt) REVERT: B 281 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8352 (mmm) REVERT: B 334 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8117 (mm-40) REVERT: B 633 GLN cc_start: 0.8317 (tt0) cc_final: 0.7985 (tt0) REVERT: B 637 MET cc_start: 0.8286 (mmm) cc_final: 0.7902 (mmp) REVERT: B 970 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7084 (ttm170) REVERT: D 85 ASP cc_start: 0.8112 (m-30) cc_final: 0.7688 (m-30) REVERT: J 27 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7403 (mp0) REVERT: J 32 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (tppt) REVERT: J 52 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8277 (tttp) REVERT: J 77 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8128 (mtp180) outliers start: 85 outliers final: 44 residues processed: 414 average time/residue: 1.4236 time to fit residues: 694.9109 Evaluate side-chains 406 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 353 time to evaluate : 3.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 45 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 970 ARG Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 52 LYS Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 120 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 357 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 chunk 187 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS A1181 ASN A1205 ASN A1375 ASN B 364 GLN C 315 HIS ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN J 48 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29960 Z= 0.229 Angle : 0.511 10.180 40578 Z= 0.263 Chirality : 0.043 0.227 4631 Planarity : 0.004 0.044 5226 Dihedral : 4.587 79.905 4037 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.41 % Allowed : 20.34 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.87 (0.14), residues: 3688 helix: 1.65 (0.14), residues: 1411 sheet: -0.08 (0.23), residues: 516 loop : -0.01 (0.15), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 257 HIS 0.006 0.001 HIS A 356 PHE 0.022 0.001 PHE A 918 TYR 0.014 0.001 TYR D 303 ARG 0.009 0.000 ARG C 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 371 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9124 (mmmt) cc_final: 0.8841 (tptt) REVERT: A 212 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8192 (pt) REVERT: A 254 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8104 (tm) REVERT: A 301 ARG cc_start: 0.7937 (tpt90) cc_final: 0.6926 (tpt90) REVERT: A 707 ASN cc_start: 0.8453 (t0) cc_final: 0.8204 (t0) REVERT: A 710 LYS cc_start: 0.8956 (mtpm) cc_final: 0.8590 (mttm) REVERT: A 765 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: A 1140 LYS cc_start: 0.7679 (tptp) cc_final: 0.7429 (tptp) REVERT: A 1421 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8086 (ttm-80) REVERT: B 62 MET cc_start: 0.7732 (tpp) cc_final: 0.7156 (ptt) REVERT: B 281 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8362 (mmm) REVERT: B 328 ASN cc_start: 0.8276 (t0) cc_final: 0.7981 (t0) REVERT: B 633 GLN cc_start: 0.8269 (tt0) cc_final: 0.7921 (tt0) REVERT: B 637 MET cc_start: 0.8241 (mmm) cc_final: 0.7867 (mmp) REVERT: B 671 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8680 (ptt180) REVERT: B 970 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7176 (ttm170) REVERT: D 85 ASP cc_start: 0.8096 (m-30) cc_final: 0.7671 (m-30) REVERT: F 140 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: J 27 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: J 32 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8516 (tppt) REVERT: J 77 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8138 (mtp180) outliers start: 78 outliers final: 37 residues processed: 424 average time/residue: 1.4145 time to fit residues: 707.2364 Evaluate side-chains 401 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 354 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 551 ASP Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 1093 GLU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 970 ARG Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 344 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 300 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 355 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN I 35 GLN J 48 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 29960 Z= 0.405 Angle : 0.567 10.255 40578 Z= 0.292 Chirality : 0.046 0.222 4631 Planarity : 0.004 0.041 5226 Dihedral : 4.724 76.356 4037 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.75 % Allowed : 20.40 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.71 (0.14), residues: 3688 helix: 1.52 (0.14), residues: 1409 sheet: -0.17 (0.23), residues: 497 loop : -0.11 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 257 HIS 0.006 0.001 HIS A 356 PHE 0.022 0.002 PHE A 918 TYR 0.015 0.002 TYR A 990 ARG 0.014 0.001 ARG B 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 349 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8901 (tptp) REVERT: A 254 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8135 (tm) REVERT: A 535 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8404 (mp10) REVERT: A 707 ASN cc_start: 0.8506 (t0) cc_final: 0.8241 (t0) REVERT: A 710 LYS cc_start: 0.8976 (mtpm) cc_final: 0.8586 (mttm) REVERT: A 765 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8242 (mp10) REVERT: A 1140 LYS cc_start: 0.7790 (tptp) cc_final: 0.7579 (tptp) REVERT: A 1421 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8157 (ttm-80) REVERT: B 62 MET cc_start: 0.7747 (tpp) cc_final: 0.7136 (ptt) REVERT: B 281 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8423 (mmm) REVERT: B 328 ASN cc_start: 0.8417 (t0) cc_final: 0.8113 (t0) REVERT: B 598 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: B 633 GLN cc_start: 0.8353 (tt0) cc_final: 0.7998 (tt0) REVERT: B 637 MET cc_start: 0.8260 (mmm) cc_final: 0.7887 (mmp) REVERT: B 970 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7177 (ttm170) REVERT: D 85 ASP cc_start: 0.8105 (m-30) cc_final: 0.7669 (m-30) REVERT: D 238 ASN cc_start: 0.6851 (t0) cc_final: 0.6391 (t0) REVERT: D 322 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8346 (mtp85) REVERT: J 27 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: J 32 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8523 (tppt) REVERT: J 77 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8127 (mtp180) outliers start: 89 outliers final: 43 residues processed: 416 average time/residue: 1.3908 time to fit residues: 688.2602 Evaluate side-chains 404 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 352 time to evaluate : 3.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 754 SER Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 970 ARG Chi-restraints excluded: chain B residue 1005 ILE Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 220 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 212 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 279 optimal weight: 0.2980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1375 ASN B 364 GLN B 525 ASN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 GLN J 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29960 Z= 0.219 Angle : 0.525 11.099 40578 Z= 0.269 Chirality : 0.043 0.241 4631 Planarity : 0.004 0.045 5226 Dihedral : 4.507 78.078 4035 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.94 % Allowed : 21.17 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.84 (0.14), residues: 3688 helix: 1.62 (0.14), residues: 1415 sheet: -0.09 (0.23), residues: 521 loop : -0.03 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 257 HIS 0.006 0.001 HIS D 159 PHE 0.023 0.001 PHE B 265 TYR 0.013 0.001 TYR C 257 ARG 0.009 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 371 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8909 (tptp) REVERT: A 707 ASN cc_start: 0.8498 (t0) cc_final: 0.8239 (t0) REVERT: A 710 LYS cc_start: 0.8952 (mtpm) cc_final: 0.8586 (mttm) REVERT: A 765 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8241 (mp10) REVERT: A 1421 ARG cc_start: 0.8424 (ttm-80) cc_final: 0.8095 (ttm-80) REVERT: B 62 MET cc_start: 0.7742 (tpp) cc_final: 0.7160 (ptt) REVERT: B 281 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8468 (mmm) REVERT: B 328 ASN cc_start: 0.8320 (t0) cc_final: 0.7952 (t0) REVERT: B 598 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: B 633 GLN cc_start: 0.8292 (tt0) cc_final: 0.7892 (tt0) REVERT: B 637 MET cc_start: 0.8225 (mmm) cc_final: 0.7839 (mmp) REVERT: B 671 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8677 (ptt180) REVERT: B 970 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7149 (ttm170) REVERT: D 85 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: D 238 ASN cc_start: 0.6828 (t0) cc_final: 0.6406 (t0) REVERT: D 322 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8319 (mtp85) REVERT: J 27 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: J 32 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8502 (tppt) REVERT: J 77 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8151 (mtp180) outliers start: 63 outliers final: 34 residues processed: 415 average time/residue: 1.3184 time to fit residues: 646.1287 Evaluate side-chains 404 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 361 time to evaluate : 3.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 442 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 830 ILE Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 916 GLU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 970 ARG Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 323 optimal weight: 10.0000 chunk 340 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 331 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 260 optimal weight: 0.0970 chunk 101 optimal weight: 4.9990 chunk 299 optimal weight: 30.0000 chunk 313 optimal weight: 7.9990 chunk 330 optimal weight: 0.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 HIS I 31 GLN J 48 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29960 Z= 0.243 Angle : 0.536 12.110 40578 Z= 0.273 Chirality : 0.044 0.241 4631 Planarity : 0.004 0.046 5226 Dihedral : 4.476 77.688 4035 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.76 % Allowed : 21.79 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.85 (0.14), residues: 3688 helix: 1.63 (0.14), residues: 1419 sheet: -0.05 (0.23), residues: 514 loop : -0.04 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 327 HIS 0.005 0.001 HIS A 356 PHE 0.024 0.001 PHE B 265 TYR 0.024 0.001 TYR A 46 ARG 0.010 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 364 time to evaluate : 3.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8911 (tptp) REVERT: A 254 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8139 (tm) REVERT: A 707 ASN cc_start: 0.8518 (t0) cc_final: 0.8254 (t0) REVERT: A 710 LYS cc_start: 0.8961 (mtpm) cc_final: 0.8594 (mttm) REVERT: A 765 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: A 1140 LYS cc_start: 0.7923 (tptp) cc_final: 0.7710 (tptp) REVERT: A 1421 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8016 (ttm-80) REVERT: B 62 MET cc_start: 0.7762 (tpp) cc_final: 0.7172 (ptt) REVERT: B 281 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8469 (mmm) REVERT: B 289 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: B 328 ASN cc_start: 0.8339 (t0) cc_final: 0.7936 (t0) REVERT: B 363 ARG cc_start: 0.8557 (ttp-110) cc_final: 0.8238 (ttp-110) REVERT: B 598 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8282 (mp10) REVERT: B 633 GLN cc_start: 0.8292 (tt0) cc_final: 0.7885 (tt0) REVERT: B 637 MET cc_start: 0.8221 (mmm) cc_final: 0.7841 (mmp) REVERT: B 671 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8678 (ptt180) REVERT: D 85 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7652 (m-30) REVERT: D 238 ASN cc_start: 0.6842 (t0) cc_final: 0.6419 (t0) REVERT: D 322 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8333 (mtp85) REVERT: F 140 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8452 (mt-10) REVERT: I 19 ASN cc_start: 0.8968 (m-40) cc_final: 0.8309 (p0) REVERT: J 27 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: J 32 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8496 (tppt) REVERT: J 77 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8144 (mtp180) outliers start: 57 outliers final: 39 residues processed: 403 average time/residue: 1.4043 time to fit residues: 665.4377 Evaluate side-chains 411 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 361 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain B residue 1202 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 217 optimal weight: 5.9990 chunk 350 optimal weight: 0.0570 chunk 213 optimal weight: 30.0000 chunk 166 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 chunk 367 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN A1181 ASN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29960 Z= 0.296 Angle : 0.551 12.150 40578 Z= 0.282 Chirality : 0.045 0.241 4631 Planarity : 0.004 0.056 5226 Dihedral : 4.496 76.901 4035 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.67 % Allowed : 22.04 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.80 (0.14), residues: 3688 helix: 1.59 (0.14), residues: 1419 sheet: -0.00 (0.23), residues: 490 loop : -0.10 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 257 HIS 0.006 0.001 HIS A 356 PHE 0.024 0.001 PHE B 265 TYR 0.021 0.001 TYR A 46 ARG 0.011 0.000 ARG C 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7376 Ramachandran restraints generated. 3688 Oldfield, 0 Emsley, 3688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 361 time to evaluate : 3.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8915 (tptp) REVERT: A 707 ASN cc_start: 0.8522 (t0) cc_final: 0.8260 (t0) REVERT: A 710 LYS cc_start: 0.8967 (mtpm) cc_final: 0.8599 (mttm) REVERT: A 765 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: A 1140 LYS cc_start: 0.7922 (tptp) cc_final: 0.7705 (tptp) REVERT: A 1421 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8019 (ttm-80) REVERT: B 62 MET cc_start: 0.7766 (tpp) cc_final: 0.7173 (ptt) REVERT: B 281 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8494 (mmm) REVERT: B 289 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: B 328 ASN cc_start: 0.8361 (t0) cc_final: 0.7958 (t0) REVERT: B 598 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8276 (mp10) REVERT: B 633 GLN cc_start: 0.8309 (tt0) cc_final: 0.7899 (tt0) REVERT: B 637 MET cc_start: 0.8222 (mmm) cc_final: 0.7843 (mmp) REVERT: D 85 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: D 238 ASN cc_start: 0.6863 (t0) cc_final: 0.6434 (t0) REVERT: D 307 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7812 (tpt) REVERT: D 322 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8324 (mtp85) REVERT: F 140 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8457 (mt-10) REVERT: I 19 ASN cc_start: 0.9015 (m-40) cc_final: 0.8342 (p0) REVERT: J 27 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: J 32 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8502 (tppt) REVERT: J 77 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8149 (mtp180) outliers start: 54 outliers final: 41 residues processed: 396 average time/residue: 1.4730 time to fit residues: 692.6488 Evaluate side-chains 405 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 354 time to evaluate : 3.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 722 SER Chi-restraints excluded: chain A residue 765 GLN Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1242 THR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 281 MET Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 671 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1012 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1177 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 260 PHE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 340 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 159 HIS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 231 MET Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 287 CYS Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 307 MET Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 101 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 102 SER Chi-restraints excluded: chain J residue 16 THR Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 LYS Chi-restraints excluded: chain J residue 77 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 232 optimal weight: 0.6980 chunk 311 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 356 HIS A 447 ASN A1078 GLN ** B 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B1162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1229 ASN ** D 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.092542 restraints weight = 41143.487| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.71 r_work: 0.3143 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29960 Z= 0.186 Angle : 0.524 12.132 40578 Z= 0.267 Chirality : 0.043 0.224 4631 Planarity : 0.004 0.047 5226 Dihedral : 4.383 77.928 4035 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.60 % Allowed : 22.01 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % 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: 0.93 (0.14), residues: 3688 helix: 1.70 (0.14), residues: 1416 sheet: 0.03 (0.23), residues: 514 loop : 0.00 (0.15), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 257 HIS 0.005 0.001 HIS A 356 PHE 0.024 0.001 PHE B 265 TYR 0.020 0.001 TYR A 46 ARG 0.011 0.000 ARG C 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11683.01 seconds wall clock time: 205 minutes 20.51 seconds (12320.51 seconds total)