Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 14:35:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_0633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_0633.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_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_0633/04_2023/6o6c_0633_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_0633_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_0633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_0633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_0633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o6c_0633/04_2023/6o6c_0633_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 15.64, per 1000 atoms: 0.52 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: 12.66 Conformation dependent library (CDL) restraints added in 4.5 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: 11.91 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: 13.73 Time building geometry restraints manager: 13.30 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: 18315 35.42 - 70.84: 320 70.84 - 106.25: 27 106.25 - 141.67: 0 141.67 - 177.09: 2 Dihedral angle restraints: 18664 sinusoidal: 8040 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 18661 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: 3.360 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.090 Check model and map are aligned: 0.530 Set scattering table: 0.260 Process input model: 88.780 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.840 ------------------------------------------------------------------------------- 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 : 12.337 177.091 11790 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 % 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 *********************** 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 : 3.651 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 outliers start: 3 outliers final: 3 residues processed: 752 average time/residue: 0.5024 time to fit residues: 566.8455 Evaluate side-chains 427 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 424 time to evaluate : 3.513 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3083 time to fit residues: 6.7874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 110 optimal weight: 0.9990 chunk 173 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 331 optimal weight: 5.9990 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 124 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2579 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= 0.245 Angle : 0.683 16.842 41859 Z= 0.358 Chirality : 0.045 0.386 4695 Planarity : 0.007 0.101 5249 Dihedral : 12.083 179.417 4503 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.74 % Allowed : 5.26 % Favored : 93.99 % Rotamer Outliers : 2.12 % 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: -0.78 (0.14), residues: 3628 helix: 0.19 (0.14), residues: 1234 sheet: -1.17 (0.21), residues: 519 loop : -0.73 (0.15), residues: 1875 *********************** 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 547 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 479 time to evaluate : 3.328 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: symmetry clash outliers start: 68 outliers final: 37 residues processed: 522 average time/residue: 0.4634 time to fit residues: 377.7255 Evaluate side-chains 429 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 392 time to evaluate : 3.516 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2945 time to fit residues: 24.8344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 225 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 332 optimal weight: 4.9990 chunk 358 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 chunk 329 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 266 optimal weight: 0.3980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 HIS A 299 HIS A 316 GLN A 854 ASN A1130 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN B 986 GLN B1025 HIS ** B1177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN ** D 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.077 30822 Z= 0.552 Angle : 0.817 15.672 41859 Z= 0.422 Chirality : 0.052 0.543 4695 Planarity : 0.007 0.105 5249 Dihedral : 12.285 179.307 4503 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.39 % Favored : 92.94 % Rotamer Outliers : 2.09 % 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: -1.00 (0.14), residues: 3628 helix: 0.04 (0.14), residues: 1214 sheet: -1.23 (0.21), residues: 507 loop : -0.91 (0.14), residues: 1907 *********************** 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 475 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 408 time to evaluate : 3.850 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 outliers start: 67 outliers final: 43 residues processed: 449 average time/residue: 0.4994 time to fit residues: 351.1056 Evaluate side-chains 410 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 367 time to evaluate : 3.588 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2869 time to fit residues: 27.9907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 0.7980 chunk 249 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 158 optimal weight: 0.0000 chunk 222 optimal weight: 0.6980 chunk 333 optimal weight: 5.9990 chunk 352 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 315 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS B 224 GLN B 494 HIS B1177 HIS D 153 HIS ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 30822 Z= 0.208 Angle : 0.617 11.402 41859 Z= 0.318 Chirality : 0.044 0.449 4695 Planarity : 0.005 0.093 5249 Dihedral : 12.111 176.847 4503 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.49 % Favored : 93.99 % Rotamer Outliers : 0.84 % 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: -0.64 (0.14), residues: 3628 helix: 0.45 (0.15), residues: 1219 sheet: -1.06 (0.21), residues: 513 loop : -0.76 (0.15), residues: 1896 *********************** 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 440 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 413 time to evaluate : 3.379 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 outliers start: 27 outliers final: 16 residues processed: 425 average time/residue: 0.4759 time to fit residues: 313.3038 Evaluate side-chains 393 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 377 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2932 time to fit residues: 13.4382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 0.0020 chunk 200 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 301 optimal weight: 0.0870 chunk 243 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 316 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 0.6768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 ASN ** F 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 30822 Z= 0.215 Angle : 0.602 11.169 41859 Z= 0.309 Chirality : 0.044 0.432 4695 Planarity : 0.005 0.094 5249 Dihedral : 12.021 176.498 4503 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.93 % Favored : 93.55 % Rotamer Outliers : 1.31 % 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: 0.61 (0.15), residues: 1230 sheet: -0.96 (0.22), residues: 497 loop : -0.69 (0.15), residues: 1901 *********************** 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 438 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 396 time to evaluate : 3.914 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 outliers start: 42 outliers final: 19 residues processed: 420 average time/residue: 0.4759 time to fit residues: 312.3979 Evaluate side-chains 392 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 373 time to evaluate : 3.563 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3106 time to fit residues: 16.0050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 207 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 353 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 185 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1078 GLN ** A1432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 135 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.091 30822 Z= 0.555 Angle : 0.777 13.082 41859 Z= 0.400 Chirality : 0.050 0.402 4695 Planarity : 0.006 0.102 5249 Dihedral : 12.301 179.984 4503 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.81 % Favored : 92.56 % Rotamer Outliers : 1.90 % 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: -0.95 (0.14), residues: 3628 helix: 0.14 (0.15), residues: 1229 sheet: -0.95 (0.21), residues: 511 loop : -1.01 (0.14), residues: 1888 *********************** 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 437 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 376 time to evaluate : 3.279 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 outliers start: 61 outliers final: 36 residues processed: 408 average time/residue: 0.4848 time to fit residues: 311.5432 Evaluate side-chains 391 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 355 time to evaluate : 3.495 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3096 time to fit residues: 25.3440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 201 optimal weight: 2.9990 chunk 257 optimal weight: 0.4980 chunk 199 optimal weight: 0.5980 chunk 297 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 351 optimal weight: 0.6980 chunk 220 optimal weight: 0.7980 chunk 214 optimal weight: 0.5980 chunk 162 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 484 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 30822 Z= 0.213 Angle : 0.607 11.380 41859 Z= 0.312 Chirality : 0.043 0.410 4695 Planarity : 0.005 0.094 5249 Dihedral : 12.116 177.194 4503 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.87 % Favored : 93.61 % Rotamer Outliers : 0.81 % 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: 1228 sheet: -0.98 (0.21), residues: 518 loop : -0.80 (0.15), residues: 1882 *********************** 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 406 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 380 time to evaluate : 3.526 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 outliers start: 26 outliers final: 13 residues processed: 394 average time/residue: 0.4911 time to fit residues: 304.7029 Evaluate side-chains 378 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 365 time to evaluate : 3.625 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3125 time to fit residues: 12.4331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 210 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 223 optimal weight: 0.5980 chunk 239 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 276 optimal weight: 0.7980 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 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 927 GLN F 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.4479 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= 0.218 Angle : 0.608 14.130 41859 Z= 0.310 Chirality : 0.043 0.418 4695 Planarity : 0.005 0.093 5249 Dihedral : 12.058 176.656 4503 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.98 % Favored : 93.52 % Rotamer Outliers : 0.56 % 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: -0.52 (0.14), residues: 3628 helix: 0.60 (0.15), residues: 1231 sheet: -0.90 (0.21), residues: 518 loop : -0.76 (0.15), residues: 1879 *********************** 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 393 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 375 time to evaluate : 4.204 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 outliers start: 18 outliers final: 5 residues processed: 382 average time/residue: 0.4908 time to fit residues: 292.8472 Evaluate side-chains 369 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 364 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3024 time to fit residues: 7.7450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 0.5980 chunk 337 optimal weight: 8.9990 chunk 307 optimal weight: 2.9990 chunk 327 optimal weight: 0.5980 chunk 336 optimal weight: 1.9990 chunk 197 optimal weight: 0.0170 chunk 142 optimal weight: 10.0000 chunk 257 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 chunk 296 optimal weight: 3.9990 chunk 310 optimal weight: 2.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 30822 Z= 0.182 Angle : 0.595 12.969 41859 Z= 0.300 Chirality : 0.043 0.417 4695 Planarity : 0.004 0.091 5249 Dihedral : 11.983 175.963 4503 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.76 % Favored : 93.77 % Rotamer Outliers : 0.50 % 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: -0.36 (0.14), residues: 3628 helix: 0.74 (0.15), residues: 1231 sheet: -0.80 (0.22), residues: 501 loop : -0.68 (0.15), residues: 1896 *********************** 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 403 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 387 time to evaluate : 3.564 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 outliers start: 16 outliers final: 10 residues processed: 392 average time/residue: 0.4836 time to fit residues: 297.3753 Evaluate side-chains 377 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 367 time to evaluate : 3.445 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3505 time to fit residues: 10.7665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 211 optimal weight: 0.3980 chunk 164 optimal weight: 5.9990 chunk 240 optimal weight: 0.9980 chunk 363 optimal weight: 10.0000 chunk 334 optimal weight: 1.9990 chunk 289 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 794 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 30822 Z= 0.350 Angle : 0.664 13.365 41859 Z= 0.338 Chirality : 0.045 0.416 4695 Planarity : 0.005 0.096 5249 Dihedral : 12.069 177.322 4503 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.17 % Favored : 93.36 % Rotamer Outliers : 0.37 % 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: -0.52 (0.14), residues: 3628 helix: 0.59 (0.15), residues: 1232 sheet: -0.87 (0.22), residues: 500 loop : -0.77 (0.15), residues: 1896 ********************** 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 382 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 370 time to evaluate : 3.909 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 outliers start: 12 outliers final: 6 residues processed: 374 average time/residue: 0.4812 time to fit residues: 283.2253 Evaluate side-chains 360 residues out of total 3211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 354 time to evaluate : 3.445 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3281 time to fit residues: 8.2829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 308 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 266 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 290 optimal weight: 0.4980 chunk 121 optimal weight: 9.9990 chunk 297 optimal weight: 0.0970 chunk 36 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.152679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.113168 restraints weight = 50750.696| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.49 r_work: 0.3288 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 30822 Z= 0.204 Angle : 0.609 13.171 41859 Z= 0.309 Chirality : 0.043 0.417 4695 Planarity : 0.004 0.092 5249 Dihedral : 11.991 176.209 4503 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.87 % Favored : 93.72 % Rotamer Outliers : 0.40 % 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: -0.39 (0.14), residues: 3628 helix: 0.70 (0.15), residues: 1227 sheet: -0.79 (0.22), residues: 506 loop : -0.69 (0.15), residues: 1895 =============================================================================== Job complete usr+sys time: 7392.44 seconds wall clock time: 134 minutes 39.24 seconds (8079.24 seconds total)