Starting phenix.real_space_refine on Thu Mar 21 13:21:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/03_2024/6o6c_0633_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 53 5.49 5 Mg 1 5.21 5 S 175 5.16 5 C 18833 2.51 5 N 5256 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 846": "OE1" <-> "OE2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B GLU 875": "OE1" <-> "OE2" Residue "B GLU 1041": "OE1" <-> "OE2" Residue "B GLU 1120": "OE1" <-> "OE2" Residue "B GLU 1134": "OE1" <-> "OE2" Residue "B GLU 1149": "OE1" <-> "OE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30166 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 11351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1446, 11351 Classifications: {'peptide': 1446} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1379} Chain breaks: 5 Chain: "B" Number of atoms: 9284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1165, 9284 Classifications: {'peptide': 1165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 1115} Chain breaks: 3 Chain: "C" Number of atoms: 2125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2125 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "D" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1760 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "E" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "F" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1161 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "G" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 935 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "H" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "I" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 895 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 364 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "K" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna3p': 8} Chain: "L" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 340 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "M" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Unusual residues: {'TTD': 1} Classifications: {'DNA': 26, 'undetermined': 1} Link IDs: {'p': 1, 'rna3p': 24, None: 1} Not linked: pdbres=" DC M 17 " pdbres="TTD M 18 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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 1240 SG CYS A 167 87.971 72.182 121.396 1.00 99.25 S ATOM 468 SG CYS A 67 43.826 77.457 102.799 1.00 63.76 S ATOM 490 SG CYS A 70 41.686 80.963 104.524 1.00 56.91 S ATOM 20141 SG CYS B1163 53.709 89.367 110.873 1.00 79.55 S ATOM 20284 SG CYS B1182 52.991 86.230 111.318 1.00 47.63 S ATOM 20303 SG CYS B1185 56.094 86.852 113.537 1.00 60.87 S ATOM 21305 SG CYS C 86 13.014 86.577 42.888 1.00 73.52 S ATOM 21355 SG CYS C 92 11.157 83.522 41.382 1.00 74.47 S ATOM 21378 SG CYS C 95 14.664 84.145 41.547 1.00 53.50 S ATOM 26614 SG CYS G 32 123.548 41.303 75.543 1.00 0.00 S ATOM 26963 SG CYS G 78 115.785 58.709 29.522 1.00102.80 S ATOM 27327 SG CYS H 7 43.650 79.903 30.168 1.00 30.04 S ATOM 27350 SG CYS H 10 43.095 83.465 28.238 1.00 36.49 S ATOM 27630 SG CYS H 45 46.258 82.950 27.716 1.00 61.73 S ATOM 27636 SG CYS H 46 43.608 80.379 26.422 1.00 47.29 S ATOM 28755 SG CYS J 31 32.093 43.965 53.492 1.00 60.51 S ATOM 28775 SG CYS J 34 30.655 42.558 49.157 1.00 64.64 S ATOM 28902 SG CYS J 51 33.105 40.926 52.084 1.00 53.00 S Time building chain proxies: 15.41, per 1000 atoms: 0.51 Number of scatterers: 30166 At special positions: 0 Unit cell: (151.96, 163.56, 136.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 175 16.00 P 53 15.00 Mg 1 11.99 O 5840 8.00 N 5256 7.00 C 18833 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.49 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 32 " pdb=" ZN G 202 " pdb="ZN ZN G 202 " - pdb=" ND1 HIS G 108 " pdb="ZN ZN G 202 " - pdb=" SG CYS G 78 " pdb=" ZN H 101 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 7 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 10 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 46 " pdb="ZN ZN H 101 " - pdb=" SG CYS H 45 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 51 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 31 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 34 " Number of angles added : 6 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 138 helices and 35 sheets defined 32.8% alpha, 13.1% beta 19 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 14.98 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 41 through 43 No H-bonds generated for 'chain 'A' and resid 41 through 43' Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 143 removed outlier: 3.969A pdb=" N ALA A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 261 through 279 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.502A pdb=" N SER A 294 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 300 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR A 302 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.816A pdb=" N SER A 476 " --> pdb=" O SER A 473 " (cutoff:3.500A) Proline residue: A 477 - end of helix Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 574 through 580 removed outlier: 3.736A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 622 No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 658 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 735 Processing helix chain 'A' and resid 742 through 749 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 810 through 844 removed outlier: 4.201A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 923 through 946 removed outlier: 3.514A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 Processing helix chain 'A' and resid 983 through 995 Processing helix chain 'A' and resid 1005 through 1014 Processing helix chain 'A' and resid 1016 through 1025 Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'A' and resid 1039 through 1056 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix removed outlier: 4.610A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1122 through 1124 No H-bonds generated for 'chain 'A' and resid 1122 through 1124' Processing helix chain 'A' and resid 1128 through 1138 Processing helix chain 'A' and resid 1143 through 1146 Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1220 Processing helix chain 'A' and resid 1248 through 1250 No H-bonds generated for 'chain 'A' and resid 1248 through 1250' Processing helix chain 'A' and resid 1257 through 1268 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 5.213A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1339 Processing helix chain 'A' and resid 1341 through 1359 removed outlier: 4.239A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1396 through 1401 removed outlier: 4.445A pdb=" N SER A1401 " --> pdb=" O LEU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1406 through 1414 removed outlier: 4.069A pdb=" N GLU A1411 " --> pdb=" O GLU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1428 No H-bonds generated for 'chain 'A' and resid 1425 through 1428' Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'A' and resid 1458 through 1460 No H-bonds generated for 'chain 'A' and resid 1458 through 1460' Processing helix chain 'A' and resid 1463 through 1467 removed outlier: 3.838A pdb=" N ASP A1467 " --> pdb=" O GLU A1463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1463 through 1467' Processing helix chain 'B' and resid 19 through 22 No H-bonds generated for 'chain 'B' and resid 19 through 22' Processing helix chain 'B' and resid 29 through 41 removed outlier: 3.575A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.988A pdb=" N SER B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 64 Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 145 through 148 Processing helix chain 'B' and resid 150 through 156 removed outlier: 4.204A pdb=" N SER B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 191 Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 308 through 322 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 368 through 389 removed outlier: 5.521A pdb=" N LYS B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 434 Processing helix chain 'B' and resid 438 through 440 No H-bonds generated for 'chain 'B' and resid 438 through 440' Processing helix chain 'B' and resid 442 through 463 removed outlier: 4.210A pdb=" N ALA B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 495 removed outlier: 3.839A pdb=" N HIS B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 552 through 560 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 666 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 700 Processing helix chain 'B' and resid 745 through 748 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 759 through 761 No H-bonds generated for 'chain 'B' and resid 759 through 761' Processing helix chain 'B' and resid 764 through 776 removed outlier: 3.935A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 removed outlier: 3.650A pdb=" N LEU B 812 " --> pdb=" O MET B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 931 through 933 No H-bonds generated for 'chain 'B' and resid 931 through 933' Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1014 through 1016 No H-bonds generated for 'chain 'B' and resid 1014 through 1016' Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1062 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1122 through 1124 No H-bonds generated for 'chain 'B' and resid 1122 through 1124' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1151 Processing helix chain 'B' and resid 1198 through 1210 removed outlier: 3.703A pdb=" N MET B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.580A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 3.593A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 268 Processing helix chain 'D' and resid 6 through 26 removed outlier: 3.557A pdb=" N VAL D 23 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 35 No H-bonds generated for 'chain 'D' and resid 32 through 35' Processing helix chain 'D' and resid 39 through 46 Processing helix chain 'D' and resid 55 through 58 Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 90 through 103 removed outlier: 3.778A pdb=" N THR D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 No H-bonds generated for 'chain 'D' and resid 118 through 121' Processing helix chain 'D' and resid 144 through 146 No H-bonds generated for 'chain 'D' and resid 144 through 146' Processing helix chain 'D' and resid 158 through 167 Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'E' and resid 87 through 102 Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'H' and resid 18 through 26 Processing helix chain 'H' and resid 32 through 38 Processing helix chain 'H' and resid 44 through 51 removed outlier: 4.929A pdb=" N MET H 49 " --> pdb=" O CYS H 45 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE H 50 " --> pdb=" O CYS H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 62 removed outlier: 3.877A pdb=" N ARG H 62 " --> pdb=" O GLU H 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 9 Processing helix chain 'I' and resid 40 through 52 removed outlier: 4.733A pdb=" N LEU I 45 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN I 52 " --> pdb=" O ALA I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 110 Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= C, first strand: chain 'A' and resid 173 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 5.970A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 375 through 379 Processing sheet with id= G, first strand: chain 'A' and resid 878 through 882 Processing sheet with id= H, first strand: chain 'A' and resid 1116 through 1119 Processing sheet with id= I, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.722A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 606 through 608 removed outlier: 6.215A pdb=" N ILE A 608 " --> pdb=" O ILE A 612 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE A 612 " --> pdb=" O ILE A 608 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 68 through 73 Processing sheet with id= L, first strand: chain 'B' and resid 95 through 97 removed outlier: 6.083A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= N, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= O, first strand: chain 'B' and resid 404 through 407 Processing sheet with id= P, first strand: chain 'B' and resid 222 through 227 removed outlier: 3.581A pdb=" N ARG B 241 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ARG B 241 " --> pdb=" O SER B 252 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER B 252 " --> pdb=" O ARG B 241 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= R, first strand: chain 'B' and resid 614 through 618 removed outlier: 6.229A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 637 through 639 Processing sheet with id= T, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.016A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1086 through 1089 removed outlier: 4.481A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 872 through 874 Processing sheet with id= W, first strand: chain 'B' and resid 979 through 981 removed outlier: 7.465A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id= Y, first strand: chain 'C' and resid 176 through 180 removed outlier: 3.657A pdb=" N GLU C 12 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE C 21 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE C 10 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER C 23 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL C 8 " --> pdb=" O SER C 23 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 43 through 46 Processing sheet with id= AA, first strand: chain 'C' and resid 49 through 54 removed outlier: 6.405A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AC, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.976A pdb=" N THR D 107 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N GLU D 81 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE D 109 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR D 131 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N PHE D 110 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU D 133 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N TYR D 112 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE D 135 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'D' and resid 152 through 155 removed outlier: 3.831A pdb=" N LYS D 152 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N MET D 215 " --> pdb=" O PRO D 176 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE D 178 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 133 through 137 Processing sheet with id= AF, first strand: chain 'F' and resid 95 through 98 removed outlier: 6.668A pdb=" N GLU F 27 " --> pdb=" O SER F 13 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL F 15 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG F 25 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 14 through 19 Processing sheet with id= AH, first strand: chain 'G' and resid 84 through 87 Processing sheet with id= AI, first strand: chain 'I' and resid 19 through 23 931 hydrogen bonds defined for protein. 2523 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 13.34 Time building geometry restraints manager: 12.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5032 1.30 - 1.43: 7725 1.43 - 1.56: 17678 1.56 - 1.69: 102 1.69 - 1.81: 285 Bond restraints: 30822 Sorted by residual: bond pdb=" CA THR F 68 " pdb=" C THR F 68 " ideal model delta sigma weight residual 1.524 1.565 -0.041 1.26e-02 6.30e+03 1.05e+01 bond pdb=" CA MET A1063 " pdb=" C MET A1063 " ideal model delta sigma weight residual 1.530 1.494 0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" CA PRO A 244 " pdb=" C PRO A 244 " ideal model delta sigma weight residual 1.517 1.544 -0.027 9.30e-03 1.16e+04 8.54e+00 bond pdb=" C5R TTD M 18 " pdb=" O5R TTD M 18 " ideal model delta sigma weight residual 1.437 1.493 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" O3R TTD M 18 " pdb=" PB TTD M 18 " ideal model delta sigma weight residual 1.647 1.702 -0.055 2.00e-02 2.50e+03 7.69e+00 ... (remaining 30817 not shown) Histogram of bond angle deviations from ideal: 88.80 - 97.83: 5 97.83 - 106.86: 1209 106.86 - 115.89: 19573 115.89 - 124.92: 20504 124.92 - 133.95: 568 Bond angle restraints: 41859 Sorted by residual: angle pdb=" C GLY A 638 " pdb=" N PRO A 639 " pdb=" CA PRO A 639 " ideal model delta sigma weight residual 119.32 129.54 -10.22 1.14e+00 7.69e-01 8.04e+01 angle pdb=" C SER A 599 " pdb=" N PRO A 600 " pdb=" CA PRO A 600 " ideal model delta sigma weight residual 119.56 128.49 -8.93 1.01e+00 9.80e-01 7.82e+01 angle pdb=" C VAL A 491 " pdb=" N PRO A 492 " pdb=" CA PRO A 492 " ideal model delta sigma weight residual 119.78 128.84 -9.06 1.03e+00 9.43e-01 7.74e+01 angle pdb=" C ALA I 3 " pdb=" N PRO I 4 " pdb=" CA PRO I 4 " ideal model delta sigma weight residual 120.03 128.39 -8.36 9.90e-01 1.02e+00 7.13e+01 angle pdb=" C PHE F 47 " pdb=" N PRO F 48 " pdb=" CA PRO F 48 " ideal model delta sigma weight residual 119.76 128.33 -8.57 1.03e+00 9.43e-01 6.92e+01 ... (remaining 41854 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 18360 35.42 - 70.84: 350 70.84 - 106.25: 28 106.25 - 141.67: 0 141.67 - 177.09: 2 Dihedral angle restraints: 18740 sinusoidal: 8116 harmonic: 10624 Sorted by residual: dihedral pdb=" C4' TTD M 18 " pdb=" C5R TTD M 18 " pdb=" O5R TTD M 18 " pdb=" PB TTD M 18 " ideal model delta sinusoidal sigma weight residual 241.46 91.57 149.89 1 3.00e+01 1.11e-03 1.99e+01 dihedral pdb=" CA PHE C 20 " pdb=" C PHE C 20 " pdb=" N ILE C 21 " pdb=" CA ILE C 21 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C4' DT M 9 " pdb=" C3' DT M 9 " pdb=" O3' DT M 9 " pdb=" P DC M 10 " ideal model delta sinusoidal sigma weight residual -140.00 37.09 -177.09 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 18737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 4112 0.082 - 0.164: 576 0.164 - 0.247: 5 0.247 - 0.329: 1 0.329 - 0.411: 1 Chirality restraints: 4695 Sorted by residual: chirality pdb=" C3' DT M 9 " pdb=" C4' DT M 9 " pdb=" O3' DT M 9 " pdb=" C2' DT M 9 " both_signs ideal model delta sigma weight residual False -2.66 -2.25 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" C1R TTD M 18 " pdb=" C2R TTD M 18 " pdb=" N1T TTD M 18 " pdb=" O4R TTD M 18 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CA VAL A 999 " pdb=" N VAL A 999 " pdb=" C VAL A 999 " pdb=" CB VAL A 999 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4692 not shown) Planarity restraints: 5249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 68 " 0.118 5.00e-02 4.00e+02 1.79e-01 5.14e+01 pdb=" N PRO F 69 " -0.310 5.00e-02 4.00e+02 pdb=" CA PRO F 69 " 0.097 5.00e-02 4.00e+02 pdb=" CD PRO F 69 " 0.094 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 567 " -0.105 5.00e-02 4.00e+02 1.56e-01 3.90e+01 pdb=" N PRO A 568 " 0.270 5.00e-02 4.00e+02 pdb=" CA PRO A 568 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO A 568 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1213 " -0.103 5.00e-02 4.00e+02 1.55e-01 3.85e+01 pdb=" N PRO B1214 " 0.268 5.00e-02 4.00e+02 pdb=" CA PRO B1214 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO B1214 " -0.076 5.00e-02 4.00e+02 ... (remaining 5246 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.44: 5 1.44 - 2.30: 19 2.30 - 3.17: 28190 3.17 - 4.03: 80771 4.03 - 4.90: 149423 Warning: very small nonbonded interaction distances. Nonbonded interactions: 258408 Sorted by model distance: nonbonded pdb=" NH2 ARG A1345 " pdb=" OD1 ASP A1373 " model vdw 0.570 2.520 nonbonded pdb=" CZ ARG A1345 " pdb=" OD1 ASP A1373 " model vdw 0.998 3.270 nonbonded pdb=" NH2 ARG A1345 " pdb=" CG ASP A1373 " model vdw 1.046 3.350 nonbonded pdb=" NH1 ARG B 857 " pdb=" OE2 GLU B 945 " model vdw 1.361 2.520 nonbonded pdb=" NH1 ARG B 857 " pdb=" CD GLU B 945 " model vdw 1.379 3.350 ... (remaining 258403 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: 2.590 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: 12.740 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 92.940 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.011 0.056 30822 Z= 0.715 Angle : 1.232 13.918 41859 Z= 0.816 Chirality : 0.052 0.411 4695 Planarity : 0.015 0.179 5249 Dihedral : 12.671 177.091 11866 Min Nonbonded Distance : 0.570 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 2.54 % Allowed : 6.73 % Favored : 90.74 % Rotamer: Outliers : 0.09 % Allowed : 0.31 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % 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: -1.64 (0.13), residues: 3628 helix: -0.79 (0.13), residues: 1211 sheet: -1.32 (0.22), residues: 492 loop : -1.15 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 233 HIS 0.005 0.001 HIS B 363 PHE 0.019 0.003 PHE A 444 TYR 0.031 0.004 TYR B1091 ARG 0.003 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 750 time to evaluate : 3.232 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8409 (m-80) cc_final: 0.8163 (m-10) REVERT: A 124 GLN cc_start: 0.8867 (mt0) cc_final: 0.8634 (mp10) REVERT: A 260 ASP cc_start: 0.7161 (t70) cc_final: 0.6718 (t0) REVERT: A 696 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7987 (mt-10) REVERT: A 903 ASN cc_start: 0.7763 (m-40) cc_final: 0.7406 (t0) REVERT: A 934 LYS cc_start: 0.9040 (tttt) cc_final: 0.8759 (tptt) REVERT: A 1192 LEU cc_start: 0.6210 (mp) cc_final: 0.5938 (tt) REVERT: A 1206 ASP cc_start: 0.8642 (t0) cc_final: 0.8425 (t70) REVERT: A 1276 VAL cc_start: 0.8813 (t) cc_final: 0.8585 (m) REVERT: A 1422 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7942 (ptt-90) REVERT: B 62 ILE cc_start: 0.8610 (mt) cc_final: 0.8326 (mm) REVERT: B 336 ARG cc_start: 0.9210 (ptt90) cc_final: 0.8805 (ptt90) REVERT: B 458 LYS cc_start: 0.7426 (tttt) cc_final: 0.7167 (tmmt) REVERT: B 835 GLN cc_start: 0.7202 (tp-100) cc_final: 0.5977 (tp-100) REVERT: B 839 MET cc_start: 0.8238 (mtm) cc_final: 0.7833 (mtt) REVERT: B 885 MET cc_start: 0.4617 (ttp) cc_final: 0.3567 (ttp) REVERT: B 1072 MET cc_start: 0.8550 (mtp) cc_final: 0.8239 (mtp) REVERT: B 1082 MET cc_start: 0.9064 (tpp) cc_final: 0.8662 (mmm) REVERT: B 1150 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7546 (mmp80) REVERT: C 263 THR cc_start: 0.8350 (m) cc_final: 0.8121 (p) REVERT: D 50 MET cc_start: 0.9465 (mmm) cc_final: 0.8786 (tpp) REVERT: D 112 TYR cc_start: 0.6466 (m-10) cc_final: 0.6260 (m-10) REVERT: E 110 ASP cc_start: 0.8540 (m-30) cc_final: 0.8252 (m-30) REVERT: E 123 LYS cc_start: 0.8493 (tttp) cc_final: 0.8246 (tttm) REVERT: F 110 ASP cc_start: 0.7895 (m-30) cc_final: 0.7632 (m-30) REVERT: G 6 PHE cc_start: 0.7776 (m-80) cc_final: 0.7486 (m-80) REVERT: G 90 GLN cc_start: 0.6396 (tt0) cc_final: 0.6143 (tp40) outliers start: 3 outliers final: 3 residues processed: 752 average time/residue: 0.4918 time to fit residues: 554.6110 Evaluate side-chains 438 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 435 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain B residue 783 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 0.0870 chunk 276 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 186 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 chunk 331 optimal weight: 9.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 390 GLN A1270 ASN B 178 ASN B 278 GLN B 484 ASN B 587 HIS B 986 GLN D 101 GLN F 83 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30822 Z= 0.242 Angle : 0.678 16.389 41859 Z= 0.357 Chirality : 0.044 0.382 4695 Planarity : 0.007 0.104 5249 Dihedral : 12.946 179.092 4584 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.72 % Allowed : 5.37 % Favored : 93.91 % Rotamer: Outliers : 2.18 % Allowed : 6.85 % Favored : 90.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % 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: 3628 helix: 0.21 (0.14), residues: 1230 sheet: -1.18 (0.21), residues: 519 loop : -0.74 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 308 HIS 0.016 0.001 HIS B 572 PHE 0.027 0.002 PHE B 781 TYR 0.020 0.002 TYR A1349 ARG 0.009 0.001 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 485 time to evaluate : 3.432 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8572 (m-80) cc_final: 0.7789 (m-10) REVERT: A 61 ILE cc_start: 0.6411 (OUTLIER) cc_final: 0.6015 (mt) REVERT: A 124 GLN cc_start: 0.8863 (mt0) cc_final: 0.8645 (mp10) REVERT: A 260 ASP cc_start: 0.7264 (t70) cc_final: 0.6787 (t0) REVERT: A 280 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8654 (mm-30) REVERT: A 341 MET cc_start: 0.8209 (mmm) cc_final: 0.7942 (mmt) REVERT: A 696 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8154 (mt-10) REVERT: A 698 GLN cc_start: 0.8500 (mt0) cc_final: 0.8195 (mt0) REVERT: A 1115 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7936 (p) REVERT: B 101 MET cc_start: 0.8276 (mmt) cc_final: 0.8004 (mmm) REVERT: B 308 TRP cc_start: 0.7796 (p-90) cc_final: 0.6737 (p-90) REVERT: B 311 LEU cc_start: 0.8675 (mt) cc_final: 0.8112 (pp) REVERT: B 336 ARG cc_start: 0.9243 (ptt90) cc_final: 0.8908 (ptt90) REVERT: B 458 LYS cc_start: 0.7334 (tttt) cc_final: 0.7012 (tmmt) REVERT: B 839 MET cc_start: 0.8526 (mtm) cc_final: 0.8279 (mtt) REVERT: B 1072 MET cc_start: 0.8624 (mtp) cc_final: 0.8337 (mtp) REVERT: B 1082 MET cc_start: 0.9103 (tpp) cc_final: 0.8755 (mmm) REVERT: B 1150 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7503 (mmp80) REVERT: C 263 THR cc_start: 0.8437 (m) cc_final: 0.8215 (p) REVERT: D 50 MET cc_start: 0.9179 (mmm) cc_final: 0.8875 (ppp) REVERT: D 57 MET cc_start: 0.8581 (tpp) cc_final: 0.8153 (tpt) REVERT: E 153 VAL cc_start: 0.8748 (t) cc_final: 0.8516 (p) REVERT: F 1 MET cc_start: 0.3026 (OUTLIER) cc_final: 0.1656 (ptp) REVERT: G 88 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8075 (m) REVERT: I 2 ASN cc_start: 0.6635 (t0) cc_final: 0.6370 (t0) REVERT: J 40 LEU cc_start: 0.8215 (mt) cc_final: 0.7243 (mt) REVERT: J 66 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7400 (mp10) outliers start: 70 outliers final: 38 residues processed: 528 average time/residue: 0.4486 time to fit residues: 366.7601 Evaluate side-chains 440 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 397 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain E residue 112 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 332 optimal weight: 4.9990 chunk 358 optimal weight: 0.6980 chunk 295 optimal weight: 9.9990 chunk 329 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS A 316 GLN A 445 ASN A 854 ASN A1130 GLN B 224 GLN B 794 ASN B 986 GLN ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN D 153 HIS F 131 ASN G 12 ASN G 89 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 30822 Z= 0.456 Angle : 0.749 11.102 41859 Z= 0.388 Chirality : 0.048 0.416 4695 Planarity : 0.007 0.104 5249 Dihedral : 13.010 178.591 4581 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.17 % Favored : 93.19 % Rotamer: Outliers : 2.90 % Allowed : 8.07 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % 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: 3628 helix: 0.18 (0.14), residues: 1227 sheet: -1.11 (0.21), residues: 510 loop : -0.83 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 185 HIS 0.016 0.002 HIS A 109 PHE 0.034 0.003 PHE B 781 TYR 0.022 0.002 TYR B 486 ARG 0.010 0.001 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 414 time to evaluate : 3.384 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8679 (m-80) cc_final: 0.8091 (m-10) REVERT: A 91 PHE cc_start: 0.8259 (m-10) cc_final: 0.8012 (m-10) REVERT: A 122 MET cc_start: 0.8453 (tpt) cc_final: 0.8191 (tpt) REVERT: A 124 GLN cc_start: 0.8908 (mt0) cc_final: 0.8646 (mp10) REVERT: A 277 GLU cc_start: 0.8435 (tt0) cc_final: 0.8183 (pt0) REVERT: A 280 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8698 (mm-30) REVERT: A 404 TYR cc_start: 0.7733 (m-80) cc_final: 0.7323 (m-80) REVERT: A 412 ARG cc_start: 0.5805 (mtp85) cc_final: 0.5420 (mtt-85) REVERT: A 696 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8268 (mt-10) REVERT: A 698 GLN cc_start: 0.8601 (mt0) cc_final: 0.8297 (mt0) REVERT: A 903 ASN cc_start: 0.7524 (m-40) cc_final: 0.7072 (t0) REVERT: A 1079 MET cc_start: 0.5617 (mmm) cc_final: 0.5139 (mtt) REVERT: A 1114 PRO cc_start: 0.8517 (Cg_exo) cc_final: 0.8266 (Cg_endo) REVERT: A 1209 MET cc_start: 0.9086 (ttt) cc_final: 0.8684 (mtm) REVERT: A 1309 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7098 (p0) REVERT: B 101 MET cc_start: 0.8563 (mmt) cc_final: 0.8199 (mmm) REVERT: B 259 TYR cc_start: 0.7094 (m-80) cc_final: 0.6512 (m-80) REVERT: B 458 LYS cc_start: 0.7403 (tttt) cc_final: 0.7068 (tmmt) REVERT: B 473 MET cc_start: 0.5437 (ttm) cc_final: 0.4912 (ptm) REVERT: B 486 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.5867 (m-80) REVERT: B 494 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8202 (m-70) REVERT: B 773 MET cc_start: 0.7747 (mmp) cc_final: 0.7516 (mtt) REVERT: B 839 MET cc_start: 0.8812 (mtm) cc_final: 0.8582 (mtt) REVERT: B 986 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8351 (mt0) REVERT: B 1072 MET cc_start: 0.8862 (mtp) cc_final: 0.8599 (mtt) REVERT: C 264 GLN cc_start: 0.8331 (tp40) cc_final: 0.7879 (tm-30) REVERT: D 50 MET cc_start: 0.9176 (mmm) cc_final: 0.8833 (ppp) REVERT: D 54 GLN cc_start: 0.8829 (pt0) cc_final: 0.8558 (pm20) REVERT: D 57 MET cc_start: 0.8690 (tpp) cc_final: 0.8288 (tpt) REVERT: D 199 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8181 (mp) REVERT: E 153 VAL cc_start: 0.9078 (t) cc_final: 0.8792 (p) REVERT: F 1 MET cc_start: 0.3260 (OUTLIER) cc_final: 0.1788 (ptp) REVERT: F 52 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8549 (mm-40) REVERT: G 34 TYR cc_start: 0.8485 (t80) cc_final: 0.8194 (t80) REVERT: G 81 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8031 (mmm-85) REVERT: J 63 ARG cc_start: 0.6587 (mmm160) cc_final: 0.6147 (mmm160) REVERT: J 66 GLN cc_start: 0.8109 (tm-30) cc_final: 0.7613 (mp10) outliers start: 93 outliers final: 65 residues processed: 478 average time/residue: 0.4491 time to fit residues: 335.4219 Evaluate side-chains 444 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 373 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1028 THR Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1278 ASN Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1421 CYS Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 114 ASN Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 158 optimal weight: 0.0980 chunk 222 optimal weight: 0.5980 chunk 333 optimal weight: 0.8980 chunk 352 optimal weight: 0.4980 chunk 174 optimal weight: 0.9990 chunk 315 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN B1177 HIS D 54 GLN I 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30822 Z= 0.184 Angle : 0.600 11.389 41859 Z= 0.307 Chirality : 0.043 0.405 4695 Planarity : 0.005 0.093 5249 Dihedral : 12.846 176.370 4581 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.26 % Favored : 94.24 % Rotamer: Outliers : 1.84 % Allowed : 9.31 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.48 (0.14), residues: 3628 helix: 0.60 (0.15), residues: 1221 sheet: -1.03 (0.21), residues: 506 loop : -0.66 (0.15), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 572 HIS 0.018 0.001 HIS A 109 PHE 0.021 0.001 PHE I 35 TYR 0.018 0.001 TYR A1349 ARG 0.007 0.000 ARG A1135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 411 time to evaluate : 3.268 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8652 (m-80) cc_final: 0.8045 (m-10) REVERT: A 122 MET cc_start: 0.8414 (tpt) cc_final: 0.8150 (tpt) REVERT: A 124 GLN cc_start: 0.8916 (mt0) cc_final: 0.8631 (mp10) REVERT: A 126 LEU cc_start: 0.8754 (mp) cc_final: 0.8496 (mp) REVERT: A 277 GLU cc_start: 0.8419 (tt0) cc_final: 0.8150 (pt0) REVERT: A 280 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8675 (mm-30) REVERT: A 696 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 698 GLN cc_start: 0.8404 (mt0) cc_final: 0.8131 (mt0) REVERT: A 903 ASN cc_start: 0.7591 (m-40) cc_final: 0.7128 (t0) REVERT: B 101 MET cc_start: 0.8409 (mmt) cc_final: 0.8012 (mmm) REVERT: B 259 TYR cc_start: 0.7027 (m-80) cc_final: 0.6580 (m-80) REVERT: B 311 LEU cc_start: 0.8660 (mt) cc_final: 0.8073 (pp) REVERT: B 458 LYS cc_start: 0.7317 (tttt) cc_final: 0.6973 (tmmt) REVERT: B 473 MET cc_start: 0.5257 (ttm) cc_final: 0.4697 (ptm) REVERT: B 486 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: B 494 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.7907 (m-70) REVERT: B 773 MET cc_start: 0.7632 (mmp) cc_final: 0.7298 (mtt) REVERT: B 839 MET cc_start: 0.8767 (mtm) cc_final: 0.8529 (mtt) REVERT: B 1082 MET cc_start: 0.9018 (tpp) cc_final: 0.8697 (mmm) REVERT: C 264 GLN cc_start: 0.8448 (tp40) cc_final: 0.7968 (tm-30) REVERT: D 50 MET cc_start: 0.9398 (mmm) cc_final: 0.8993 (tmm) REVERT: D 54 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: D 57 MET cc_start: 0.8647 (tpp) cc_final: 0.8231 (tpt) REVERT: D 199 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7996 (mp) REVERT: E 153 VAL cc_start: 0.8928 (t) cc_final: 0.8600 (p) REVERT: F 1 MET cc_start: 0.3287 (mtp) cc_final: 0.2138 (ptp) REVERT: F 52 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8532 (mm-40) REVERT: G 44 TYR cc_start: 0.5137 (t80) cc_final: 0.4663 (t80) REVERT: G 45 ARG cc_start: 0.7430 (tpt-90) cc_final: 0.7194 (tpt-90) REVERT: G 81 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: I 2 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6568 (t0) REVERT: I 88 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8335 (mtpt) REVERT: J 63 ARG cc_start: 0.6621 (mmm160) cc_final: 0.6287 (mmm160) REVERT: J 66 GLN cc_start: 0.7907 (tm-30) cc_final: 0.7581 (mp10) outliers start: 59 outliers final: 40 residues processed: 448 average time/residue: 0.4488 time to fit residues: 314.8232 Evaluate side-chains 428 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 382 time to evaluate : 3.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain D residue 54 GLN Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 316 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN B 587 HIS B 986 GLN D 54 GLN I 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 30822 Z= 0.266 Angle : 0.610 11.166 41859 Z= 0.312 Chirality : 0.044 0.420 4695 Planarity : 0.005 0.095 5249 Dihedral : 12.827 176.892 4581 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.84 % Favored : 93.66 % Rotamer: Outliers : 2.58 % Allowed : 9.22 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.41 (0.14), residues: 3628 helix: 0.68 (0.15), residues: 1221 sheet: -1.01 (0.21), residues: 521 loop : -0.61 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 170 HIS 0.008 0.001 HIS A 281 PHE 0.023 0.002 PHE A1225 TYR 0.022 0.001 TYR B1198 ARG 0.007 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 391 time to evaluate : 3.577 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8663 (m-80) cc_final: 0.8135 (m-10) REVERT: A 122 MET cc_start: 0.8460 (tpt) cc_final: 0.8140 (tpt) REVERT: A 124 GLN cc_start: 0.8936 (mt0) cc_final: 0.8638 (mp10) REVERT: A 126 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8490 (mp) REVERT: A 277 GLU cc_start: 0.8462 (tt0) cc_final: 0.8177 (pt0) REVERT: A 280 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8660 (mm-30) REVERT: A 696 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 698 GLN cc_start: 0.8410 (mt0) cc_final: 0.8164 (mt0) REVERT: A 790 ASP cc_start: 0.6876 (t0) cc_final: 0.6369 (t0) REVERT: A 903 ASN cc_start: 0.7610 (m-40) cc_final: 0.7137 (t0) REVERT: A 1209 MET cc_start: 0.9009 (ttt) cc_final: 0.8682 (mtm) REVERT: B 101 MET cc_start: 0.8481 (mmt) cc_final: 0.8073 (mmm) REVERT: B 259 TYR cc_start: 0.7012 (m-80) cc_final: 0.6560 (m-80) REVERT: B 296 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: B 458 LYS cc_start: 0.7283 (tttt) cc_final: 0.6926 (tmmt) REVERT: B 473 MET cc_start: 0.5149 (ttm) cc_final: 0.4664 (ptm) REVERT: B 486 TYR cc_start: 0.6854 (OUTLIER) cc_final: 0.5916 (m-80) REVERT: B 494 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.7943 (m-70) REVERT: B 679 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.6988 (m-80) REVERT: B 773 MET cc_start: 0.7599 (mmp) cc_final: 0.7286 (mtt) REVERT: B 839 MET cc_start: 0.8829 (mtm) cc_final: 0.8599 (mtt) REVERT: B 1098 MET cc_start: 0.8857 (mtm) cc_final: 0.8654 (mtm) REVERT: C 264 GLN cc_start: 0.8468 (tp40) cc_final: 0.7983 (tm-30) REVERT: D 50 MET cc_start: 0.9410 (mmm) cc_final: 0.9023 (tmm) REVERT: D 54 GLN cc_start: 0.8880 (pt0) cc_final: 0.8677 (pm20) REVERT: D 57 MET cc_start: 0.8664 (tpp) cc_final: 0.8293 (tpt) REVERT: D 83 CYS cc_start: 0.8251 (t) cc_final: 0.7800 (t) REVERT: D 199 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (mp) REVERT: E 153 VAL cc_start: 0.9007 (t) cc_final: 0.8587 (p) REVERT: F 1 MET cc_start: 0.3723 (OUTLIER) cc_final: 0.2665 (ptp) REVERT: F 52 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8521 (mm-40) REVERT: G 34 TYR cc_start: 0.8502 (t80) cc_final: 0.8087 (t80) REVERT: G 45 ARG cc_start: 0.7526 (tpt-90) cc_final: 0.7253 (tpt-90) REVERT: G 72 ASP cc_start: 0.8546 (p0) cc_final: 0.7951 (m-30) REVERT: G 81 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7780 (mmm-85) REVERT: G 87 GLN cc_start: 0.7921 (tp40) cc_final: 0.7233 (tp40) REVERT: I 2 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.6051 (t0) REVERT: I 40 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7918 (p-80) REVERT: I 88 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8301 (mtpt) REVERT: J 63 ARG cc_start: 0.6715 (mmm160) cc_final: 0.6246 (mmm160) REVERT: J 66 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7583 (mp10) outliers start: 83 outliers final: 57 residues processed: 442 average time/residue: 0.4331 time to fit residues: 302.3550 Evaluate side-chains 453 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 386 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 8.9990 chunk 317 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 353 optimal weight: 1.9990 chunk 293 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 185 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 986 GLN B1025 HIS I 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 30822 Z= 0.401 Angle : 0.671 11.371 41859 Z= 0.345 Chirality : 0.046 0.418 4695 Planarity : 0.005 0.099 5249 Dihedral : 12.922 178.453 4581 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.15 % Favored : 93.27 % Rotamer: Outliers : 3.21 % Allowed : 9.47 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.62 (0.14), residues: 3628 helix: 0.49 (0.15), residues: 1220 sheet: -0.97 (0.22), residues: 502 loop : -0.79 (0.15), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 170 HIS 0.008 0.002 HIS A 281 PHE 0.022 0.002 PHE I 105 TYR 0.020 0.002 TYR B 486 ARG 0.007 0.001 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 392 time to evaluate : 3.363 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8687 (m-80) cc_final: 0.8144 (m-10) REVERT: A 122 MET cc_start: 0.8471 (tpt) cc_final: 0.8139 (tpt) REVERT: A 124 GLN cc_start: 0.8980 (mt0) cc_final: 0.8752 (mp10) REVERT: A 126 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 146 MET cc_start: 0.7810 (pmm) cc_final: 0.7402 (pmm) REVERT: A 277 GLU cc_start: 0.8449 (tt0) cc_final: 0.8198 (pt0) REVERT: A 696 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8219 (mt-10) REVERT: A 698 GLN cc_start: 0.8467 (mt0) cc_final: 0.8158 (mt0) REVERT: A 790 ASP cc_start: 0.6981 (t0) cc_final: 0.6612 (t0) REVERT: A 903 ASN cc_start: 0.7648 (m-40) cc_final: 0.7144 (t0) REVERT: B 101 MET cc_start: 0.8601 (mmt) cc_final: 0.8152 (mmm) REVERT: B 296 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: B 458 LYS cc_start: 0.7426 (tttt) cc_final: 0.7071 (tmmt) REVERT: B 473 MET cc_start: 0.5386 (ttm) cc_final: 0.4947 (ptm) REVERT: B 486 TYR cc_start: 0.7270 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: B 494 HIS cc_start: 0.8897 (OUTLIER) cc_final: 0.8094 (m-70) REVERT: B 679 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7213 (m-80) REVERT: B 835 GLN cc_start: 0.8334 (tp-100) cc_final: 0.7975 (tp-100) REVERT: C 84 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7407 (mtm110) REVERT: C 264 GLN cc_start: 0.8504 (tp40) cc_final: 0.7986 (tm-30) REVERT: D 50 MET cc_start: 0.9394 (mmm) cc_final: 0.9078 (tmm) REVERT: D 57 MET cc_start: 0.8761 (tpp) cc_final: 0.8315 (tpt) REVERT: D 199 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8071 (mp) REVERT: F 1 MET cc_start: 0.4422 (OUTLIER) cc_final: 0.3028 (ptp) REVERT: F 52 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8504 (mm-40) REVERT: G 34 TYR cc_start: 0.8535 (t80) cc_final: 0.8084 (t80) REVERT: G 72 ASP cc_start: 0.8535 (p0) cc_final: 0.7947 (m-30) REVERT: G 81 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7800 (mmm-85) REVERT: G 87 GLN cc_start: 0.7936 (tp40) cc_final: 0.7443 (tp40) REVERT: G 89 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7087 (mp10) REVERT: I 2 ASN cc_start: 0.6475 (t0) cc_final: 0.6275 (t0) REVERT: I 38 GLU cc_start: 0.7983 (tp30) cc_final: 0.7620 (mm-30) REVERT: I 40 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8042 (p-80) REVERT: J 66 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7465 (mp10) REVERT: J 70 ARG cc_start: 0.7704 (tpp80) cc_final: 0.7498 (mmm-85) outliers start: 103 outliers final: 71 residues processed: 458 average time/residue: 0.4438 time to fit residues: 320.8234 Evaluate side-chains 456 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 377 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1162 ILE Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain I residue 25 THR Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 197 optimal weight: 0.4980 chunk 351 optimal weight: 0.5980 chunk 220 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 162 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 986 GLN C 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30822 Z= 0.215 Angle : 0.587 11.322 41859 Z= 0.301 Chirality : 0.043 0.422 4695 Planarity : 0.005 0.094 5249 Dihedral : 12.796 176.919 4581 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.71 % Favored : 93.74 % Rotamer: Outliers : 2.62 % Allowed : 10.65 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.42 (0.14), residues: 3628 helix: 0.65 (0.15), residues: 1227 sheet: -0.86 (0.21), residues: 522 loop : -0.67 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 170 HIS 0.009 0.001 HIS A 281 PHE 0.019 0.001 PHE I 35 TYR 0.018 0.001 TYR A1349 ARG 0.007 0.000 ARG G 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 398 time to evaluate : 3.472 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8678 (m-80) cc_final: 0.8159 (m-10) REVERT: A 122 MET cc_start: 0.8526 (tpt) cc_final: 0.8184 (tpt) REVERT: A 124 GLN cc_start: 0.8961 (mt0) cc_final: 0.8733 (mp10) REVERT: A 126 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8654 (mp) REVERT: A 146 MET cc_start: 0.7910 (pmm) cc_final: 0.7136 (mmt) REVERT: A 399 HIS cc_start: 0.4656 (OUTLIER) cc_final: 0.4188 (p-80) REVERT: A 696 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 698 GLN cc_start: 0.8437 (mt0) cc_final: 0.8126 (mt0) REVERT: A 790 ASP cc_start: 0.6763 (t0) cc_final: 0.6332 (t0) REVERT: A 903 ASN cc_start: 0.7713 (m-40) cc_final: 0.7233 (t0) REVERT: B 101 MET cc_start: 0.8527 (mmt) cc_final: 0.8106 (mmm) REVERT: B 259 TYR cc_start: 0.7204 (m-80) cc_final: 0.6420 (m-80) REVERT: B 458 LYS cc_start: 0.7334 (tttt) cc_final: 0.7003 (tmmt) REVERT: B 473 MET cc_start: 0.5356 (ttm) cc_final: 0.4926 (ptm) REVERT: B 486 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: B 494 HIS cc_start: 0.8721 (OUTLIER) cc_final: 0.7908 (m-70) REVERT: B 679 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: C 84 ARG cc_start: 0.7694 (mtm110) cc_final: 0.7355 (mtm110) REVERT: C 264 GLN cc_start: 0.8495 (tp40) cc_final: 0.7970 (pt0) REVERT: D 50 MET cc_start: 0.9357 (mmm) cc_final: 0.9049 (tmm) REVERT: D 57 MET cc_start: 0.8619 (tpp) cc_final: 0.8312 (tpt) REVERT: D 199 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7895 (mp) REVERT: F 1 MET cc_start: 0.4309 (OUTLIER) cc_final: 0.3012 (ptp) REVERT: F 52 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8526 (mm-40) REVERT: G 34 TYR cc_start: 0.8471 (t80) cc_final: 0.8000 (t80) REVERT: G 72 ASP cc_start: 0.8572 (p0) cc_final: 0.7979 (m-30) REVERT: G 73 ARG cc_start: 0.7561 (mmm-85) cc_final: 0.6876 (mmm-85) REVERT: G 81 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.7814 (mmm-85) REVERT: G 87 GLN cc_start: 0.7798 (tp40) cc_final: 0.7258 (tp40) REVERT: I 2 ASN cc_start: 0.6357 (t0) cc_final: 0.5968 (t0) REVERT: I 40 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7666 (p-80) REVERT: J 66 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7466 (mp10) REVERT: J 70 ARG cc_start: 0.7630 (tpp80) cc_final: 0.7351 (mmm-85) outliers start: 84 outliers final: 57 residues processed: 447 average time/residue: 0.4459 time to fit residues: 313.4096 Evaluate side-chains 444 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 379 time to evaluate : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 976 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 0.0050 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 223 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 276 optimal weight: 0.5980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1078 GLN B 986 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30822 Z= 0.211 Angle : 0.585 11.152 41859 Z= 0.299 Chirality : 0.043 0.430 4695 Planarity : 0.004 0.094 5249 Dihedral : 12.753 176.561 4581 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.82 % Favored : 93.66 % Rotamer: Outliers : 2.34 % Allowed : 11.06 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.33 (0.14), residues: 3628 helix: 0.73 (0.15), residues: 1232 sheet: -0.74 (0.21), residues: 520 loop : -0.64 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 170 HIS 0.008 0.001 HIS A 399 PHE 0.018 0.001 PHE I 35 TYR 0.025 0.001 TYR B1198 ARG 0.006 0.000 ARG G 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 388 time to evaluate : 3.629 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8678 (m-80) cc_final: 0.8174 (m-10) REVERT: A 122 MET cc_start: 0.8492 (tpt) cc_final: 0.8121 (tpt) REVERT: A 124 GLN cc_start: 0.9006 (mt0) cc_final: 0.8752 (mp10) REVERT: A 126 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8657 (mp) REVERT: A 146 MET cc_start: 0.7908 (pmm) cc_final: 0.7337 (pmm) REVERT: A 399 HIS cc_start: 0.4601 (OUTLIER) cc_final: 0.4117 (p-80) REVERT: A 696 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8108 (mt-10) REVERT: A 698 GLN cc_start: 0.8433 (mt0) cc_final: 0.8139 (mt0) REVERT: A 790 ASP cc_start: 0.6772 (t0) cc_final: 0.6348 (t0) REVERT: A 903 ASN cc_start: 0.7749 (m-40) cc_final: 0.7255 (t0) REVERT: B 101 MET cc_start: 0.8533 (mmt) cc_final: 0.8126 (mmm) REVERT: B 259 TYR cc_start: 0.7215 (m-80) cc_final: 0.6433 (m-80) REVERT: B 458 LYS cc_start: 0.7292 (tttt) cc_final: 0.6943 (tmmt) REVERT: B 473 MET cc_start: 0.5529 (ttm) cc_final: 0.5061 (ptm) REVERT: B 486 TYR cc_start: 0.6840 (OUTLIER) cc_final: 0.5751 (m-80) REVERT: B 494 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7845 (m-70) REVERT: B 679 TYR cc_start: 0.8285 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: C 84 ARG cc_start: 0.7664 (mtm110) cc_final: 0.7331 (mtm110) REVERT: C 264 GLN cc_start: 0.8446 (tp40) cc_final: 0.7980 (pt0) REVERT: D 50 MET cc_start: 0.9344 (mmm) cc_final: 0.9009 (tmm) REVERT: D 57 MET cc_start: 0.8603 (tpp) cc_final: 0.8388 (tpt) REVERT: D 199 ILE cc_start: 0.8146 (OUTLIER) cc_final: 0.7817 (mp) REVERT: F 1 MET cc_start: 0.4784 (OUTLIER) cc_final: 0.3602 (ptp) REVERT: F 52 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8522 (mm-40) REVERT: G 34 TYR cc_start: 0.8479 (t80) cc_final: 0.7947 (t80) REVERT: G 72 ASP cc_start: 0.8587 (p0) cc_final: 0.7993 (m-30) REVERT: G 73 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.6906 (mmm-85) REVERT: G 81 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7801 (mmm-85) REVERT: G 87 GLN cc_start: 0.7828 (tp40) cc_final: 0.7224 (tp40) REVERT: G 89 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7177 (mp10) REVERT: I 40 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7552 (p-80) REVERT: J 66 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7459 (mp10) REVERT: J 70 ARG cc_start: 0.7617 (tpp80) cc_final: 0.7285 (mmm-85) outliers start: 75 outliers final: 55 residues processed: 433 average time/residue: 0.4442 time to fit residues: 304.9750 Evaluate side-chains 443 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 380 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 34 ASP Chi-restraints excluded: chain F residue 108 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 2.9990 chunk 337 optimal weight: 0.2980 chunk 307 optimal weight: 0.8980 chunk 327 optimal weight: 0.5980 chunk 336 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 142 optimal weight: 0.4980 chunk 257 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 chunk 310 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN F 71 ASN I 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30822 Z= 0.198 Angle : 0.578 11.735 41859 Z= 0.294 Chirality : 0.043 0.431 4695 Planarity : 0.004 0.093 5249 Dihedral : 12.701 176.329 4581 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.84 % Favored : 93.63 % Rotamer: Outliers : 2.30 % Allowed : 11.24 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.28 (0.14), residues: 3628 helix: 0.77 (0.15), residues: 1237 sheet: -0.67 (0.22), residues: 515 loop : -0.63 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 170 HIS 0.009 0.001 HIS A 399 PHE 0.018 0.001 PHE I 35 TYR 0.025 0.001 TYR B1198 ARG 0.006 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 386 time to evaluate : 3.401 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8695 (m-80) cc_final: 0.8202 (m-10) REVERT: A 122 MET cc_start: 0.8496 (tpt) cc_final: 0.8265 (tpt) REVERT: A 124 GLN cc_start: 0.9007 (mt0) cc_final: 0.8735 (mp10) REVERT: A 146 MET cc_start: 0.7665 (pmm) cc_final: 0.7158 (pmm) REVERT: A 399 HIS cc_start: 0.4599 (OUTLIER) cc_final: 0.4150 (p-80) REVERT: A 696 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 698 GLN cc_start: 0.8566 (mt0) cc_final: 0.8275 (mt0) REVERT: A 790 ASP cc_start: 0.6732 (t0) cc_final: 0.6325 (t0) REVERT: A 903 ASN cc_start: 0.7774 (m-40) cc_final: 0.7266 (t0) REVERT: B 101 MET cc_start: 0.8515 (mmt) cc_final: 0.8115 (mmm) REVERT: B 259 TYR cc_start: 0.7140 (m-80) cc_final: 0.6566 (m-80) REVERT: B 312 GLU cc_start: 0.9328 (tt0) cc_final: 0.9097 (mt-10) REVERT: B 458 LYS cc_start: 0.7301 (tttt) cc_final: 0.6961 (tmmt) REVERT: B 473 MET cc_start: 0.5553 (ttm) cc_final: 0.5066 (ptm) REVERT: B 486 TYR cc_start: 0.6871 (OUTLIER) cc_final: 0.5824 (m-80) REVERT: B 494 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7937 (m-70) REVERT: B 679 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: C 84 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7357 (mtm110) REVERT: C 264 GLN cc_start: 0.8415 (tp40) cc_final: 0.7970 (pt0) REVERT: D 50 MET cc_start: 0.9307 (mmm) cc_final: 0.8946 (tmm) REVERT: D 199 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7788 (mp) REVERT: F 1 MET cc_start: 0.4579 (OUTLIER) cc_final: 0.3478 (ptp) REVERT: F 52 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8528 (mm-40) REVERT: G 34 TYR cc_start: 0.8456 (t80) cc_final: 0.7911 (t80) REVERT: G 72 ASP cc_start: 0.8595 (p0) cc_final: 0.8009 (m-30) REVERT: G 81 ARG cc_start: 0.8255 (mmm-85) cc_final: 0.7782 (mmm-85) REVERT: G 87 GLN cc_start: 0.7898 (tp40) cc_final: 0.7266 (tp40) REVERT: G 89 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7212 (mp10) REVERT: I 2 ASN cc_start: 0.6732 (OUTLIER) cc_final: 0.6310 (t0) REVERT: I 40 HIS cc_start: 0.7882 (OUTLIER) cc_final: 0.7384 (p-80) REVERT: J 66 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7450 (mp10) outliers start: 74 outliers final: 56 residues processed: 432 average time/residue: 0.4484 time to fit residues: 305.2869 Evaluate side-chains 436 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 372 time to evaluate : 4.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain I residue 2 ASN Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 346 optimal weight: 0.0970 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 240 optimal weight: 0.6980 chunk 363 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 289 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 223 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 986 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30822 Z= 0.202 Angle : 0.583 11.072 41859 Z= 0.296 Chirality : 0.043 0.433 4695 Planarity : 0.004 0.094 5249 Dihedral : 12.669 176.202 4581 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.68 % Favored : 93.83 % Rotamer: Outliers : 2.02 % Allowed : 11.55 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.14), residues: 3628 helix: 0.81 (0.15), residues: 1240 sheet: -0.59 (0.22), residues: 512 loop : -0.61 (0.15), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 170 HIS 0.009 0.001 HIS A 281 PHE 0.018 0.001 PHE I 35 TYR 0.025 0.001 TYR B1198 ARG 0.006 0.000 ARG B 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7256 Ramachandran restraints generated. 3628 Oldfield, 0 Emsley, 3628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 382 time to evaluate : 3.381 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8691 (m-80) cc_final: 0.8202 (m-10) REVERT: A 122 MET cc_start: 0.8432 (tpt) cc_final: 0.8205 (tpp) REVERT: A 124 GLN cc_start: 0.8999 (mt0) cc_final: 0.8724 (mp10) REVERT: A 146 MET cc_start: 0.7676 (pmm) cc_final: 0.6921 (mmm) REVERT: A 399 HIS cc_start: 0.4539 (OUTLIER) cc_final: 0.4109 (p-80) REVERT: A 696 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8113 (mt-10) REVERT: A 698 GLN cc_start: 0.8571 (mt0) cc_final: 0.8284 (mt0) REVERT: A 790 ASP cc_start: 0.6712 (t0) cc_final: 0.6320 (t0) REVERT: A 903 ASN cc_start: 0.7785 (m-40) cc_final: 0.7268 (t0) REVERT: A 1285 MET cc_start: 0.7778 (ptt) cc_final: 0.7529 (ptt) REVERT: B 259 TYR cc_start: 0.7135 (m-80) cc_final: 0.6557 (m-80) REVERT: B 312 GLU cc_start: 0.9299 (tt0) cc_final: 0.9086 (mt-10) REVERT: B 458 LYS cc_start: 0.7246 (tttt) cc_final: 0.6910 (tmmt) REVERT: B 473 MET cc_start: 0.5413 (ttm) cc_final: 0.5053 (ptm) REVERT: B 486 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: B 494 HIS cc_start: 0.8507 (OUTLIER) cc_final: 0.7978 (m-70) REVERT: B 679 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7049 (m-80) REVERT: C 84 ARG cc_start: 0.7677 (mtm110) cc_final: 0.7173 (mtm110) REVERT: C 264 GLN cc_start: 0.8417 (tp40) cc_final: 0.7973 (pt0) REVERT: D 50 MET cc_start: 0.9300 (mmm) cc_final: 0.8894 (tmm) REVERT: D 58 MET cc_start: 0.8402 (ttp) cc_final: 0.8137 (tmm) REVERT: D 170 LEU cc_start: 0.8892 (mt) cc_final: 0.8644 (mt) REVERT: D 199 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7788 (mp) REVERT: F 1 MET cc_start: 0.4510 (OUTLIER) cc_final: 0.3516 (ptp) REVERT: G 34 TYR cc_start: 0.8433 (t80) cc_final: 0.7878 (t80) REVERT: G 81 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7869 (mmm-85) REVERT: G 87 GLN cc_start: 0.7907 (tp40) cc_final: 0.7312 (tp40) REVERT: G 89 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7206 (mp10) REVERT: I 40 HIS cc_start: 0.7867 (OUTLIER) cc_final: 0.7395 (p-80) REVERT: J 66 GLN cc_start: 0.7759 (tm-30) cc_final: 0.7392 (mp10) outliers start: 65 outliers final: 56 residues processed: 423 average time/residue: 0.4362 time to fit residues: 291.4871 Evaluate side-chains 440 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 377 time to evaluate : 3.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 HIS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 399 HIS Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 974 ASP Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER Chi-restraints excluded: chain A residue 1267 MET Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1355 VAL Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 494 HIS Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 679 TYR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 899 ILE Chi-restraints excluded: chain B residue 986 GLN Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1152 MET Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 54 SER Chi-restraints excluded: chain F residue 114 VAL Chi-restraints excluded: chain F residue 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain I residue 40 HIS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 308 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 266 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 290 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 297 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN B 986 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.153164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113760 restraints weight = 51006.830| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.44 r_work: 0.3308 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30822 Z= 0.208 Angle : 0.580 11.017 41859 Z= 0.296 Chirality : 0.043 0.436 4695 Planarity : 0.004 0.094 5249 Dihedral : 12.639 176.126 4581 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.87 % Favored : 93.66 % Rotamer: Outliers : 2.18 % Allowed : 11.43 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % 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: -0.19 (0.14), residues: 3628 helix: 0.83 (0.15), residues: 1238 sheet: -0.55 (0.22), residues: 516 loop : -0.60 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 170 HIS 0.010 0.001 HIS A 281 PHE 0.018 0.001 PHE I 35 TYR 0.024 0.001 TYR B1198 ARG 0.014 0.000 ARG B 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7805.31 seconds wall clock time: 141 minutes 5.23 seconds (8465.23 seconds total)