Starting phenix.real_space_refine on Thu Oct 29 00:27:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.map 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 { model { file = "/net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o6c_0633/10_2026/6o6c_0633.map" } 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 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. Time to flip 12 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/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: {'RNAv2': 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: {'rna3p': 24, None: 2} Not linked: pdbres=" DC M 17 " pdbres="TTD M 18 " Not linked: pdbres="TTD M 18 " pdbres=" DT M 19 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: 5.62, per 1000 atoms: 0.19 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 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... Secondary structure from input PDB file: 140 helices and 48 sheets defined 38.6% alpha, 16.8% beta 19 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 40 through 44 removed outlier: 4.004A pdb=" N THR A 44 " --> pdb=" O MET A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 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 203 through 214 Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 280 Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 288 through 305 removed outlier: 4.060A pdb=" N ALA A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.996A pdb=" N LYS A 330 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 414 through 418 removed outlier: 3.706A pdb=" N SER A 418 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.554A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 510 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 579 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 659 Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 736 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 4.201A pdb=" N THR A 831 " --> pdb=" O THR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 922 through 947 removed outlier: 3.514A pdb=" N LEU A 928 " --> pdb=" O LYS A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 Processing helix chain 'A' and resid 982 through 996 Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.612A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1057 removed outlier: 3.603A pdb=" N VAL A1057 " --> pdb=" O PHE A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1074 Processing helix chain 'A' and resid 1075 through 1079 Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1121 through 1125 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1198 through 1205 Processing helix chain 'A' and resid 1208 through 1221 Processing helix chain 'A' and resid 1247 through 1251 Processing helix chain 'A' and resid 1256 through 1269 Processing helix chain 'A' and resid 1312 through 1317 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1358 Processing helix chain 'A' and resid 1364 through 1375 removed outlier: 3.568A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1405 through 1415 removed outlier: 4.069A pdb=" N GLU A1411 " --> pdb=" O GLU A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 Processing helix chain 'A' and resid 1457 through 1461 Processing helix chain 'A' and resid 1462 through 1467 removed outlier: 3.838A pdb=" N ASP A1467 " --> pdb=" O GLU A1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 28 through 42 removed outlier: 3.887A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.988A pdb=" N SER B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 149 through 155 removed outlier: 3.923A pdb=" N ALA B 153 " --> pdb=" O TYR B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'B' and resid 307 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 369 through 390 removed outlier: 4.471A pdb=" N ALA B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 435 Processing helix chain 'B' and resid 437 through 440 Processing helix chain 'B' and resid 441 through 464 removed outlier: 4.210A pdb=" N ALA B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.839A pdb=" N HIS B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 666 Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 752 through 756 Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.794A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 930 through 934 removed outlier: 3.594A pdb=" N LYS B 934 " --> pdb=" O TYR B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 999 Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.586A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1061 Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1209 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 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 76 through 80 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 removed outlier: 3.593A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 269 Processing helix chain 'D' and resid 6 through 26 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 55 through 59 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 89 through 104 removed outlier: 3.778A pdb=" N THR D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 143 through 147 Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 182 through 189 Processing helix chain 'E' and resid 86 through 103 Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 61 through 65 Processing helix chain 'H' and resid 17 through 27 Processing helix chain 'H' and resid 31 through 39 Processing helix chain 'H' and resid 43 through 52 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 56 through 61 Processing helix chain 'I' and resid 5 through 10 Processing helix chain 'I' and resid 39 through 51 removed outlier: 4.733A pdb=" N LEU I 45 " --> pdb=" O THR I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 111 Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 10.433A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.986A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 315 through 316 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 345 Processing sheet with id=AA7, first strand: chain 'B' and resid 1104 through 1106 Processing sheet with id=AA8, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.109A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 512 through 513 Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 589 removed outlier: 6.507A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 662 through 663 removed outlier: 4.159A pdb=" N PHE A 662 " --> pdb=" O CYS B 829 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 662 through 663 removed outlier: 4.159A pdb=" N PHE A 662 " --> pdb=" O CYS B 829 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) 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=AB5, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB6, first strand: chain 'A' and resid 849 through 850 removed outlier: 6.791A pdb=" N THR A 856 " --> pdb=" O ILE A 864 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB8, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB9, first strand: chain 'A' and resid 1141 through 1142 Processing sheet with id=AC1, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 4.722A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N ILE A1148 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU G 47 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N SER A1150 " --> pdb=" O ARG G 45 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG G 45 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE A1152 " --> pdb=" O VAL G 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1441 through 1444 Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.225A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 68 through 73 removed outlier: 5.225A pdb=" N TYR B 88 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TYR B 137 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE B 90 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG B 135 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AC6, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC7, first strand: chain 'B' and resid 404 through 407 removed outlier: 6.203A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC8, 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: 6.559A pdb=" N LEU B 244 " --> pdb=" O PHE B 250 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE B 250 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AD1, first strand: chain 'B' and resid 544 through 545 removed outlier: 7.061A pdb=" N ALA B 704 " --> pdb=" O GLU B 742 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.483A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AD3, 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=AD4, first strand: chain 'B' and resid 804 through 805 Processing sheet with id=AD5, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD6, first strand: chain 'B' and resid 910 through 912 Processing sheet with id=AD7, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD8, first strand: chain 'B' and resid 1111 through 1112 removed outlier: 3.512A pdb=" N GLN B1117 " --> pdb=" O GLN B1112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1158 through 1163 Processing sheet with id=AE1, first strand: chain 'C' and resid 7 through 14 removed outlier: 6.709A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.787A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.656A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 111 through 114 Processing sheet with id=AE5, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AE6, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.522A pdb=" N TRP D 79 " --> pdb=" O ILE D 109 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL D 111 " --> pdb=" O TRP D 79 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLU D 81 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AE8, 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: 6.634A pdb=" N ILE D 178 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing sheet with id=AE9, 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=AF1, first strand: chain 'G' and resid 15 through 19 Processing sheet with id=AF2, first strand: chain 'G' and resid 70 through 71 Processing sheet with id=AF3, first strand: chain 'I' and resid 19 through 23 1232 hydrogen bonds defined for protein. 3312 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: 8.32 Time building geometry restraints manager: 3.59 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: 101 1.69 - 1.81: 285 Bond restraints: 30821 Sorted by residual: bond pdb=" C2' TTD M 18 " pdb=" C3R TTD M 18 " ideal model delta sigma weight residual 1.520 1.369 0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N1 TTD M 18 " pdb=" C2 TTD M 18 " ideal model delta sigma weight residual 1.353 1.493 -0.140 2.00e-02 2.50e+03 4.91e+01 bond pdb=" C2T TTD M 18 " pdb=" N1T TTD M 18 " ideal model delta sigma weight residual 1.360 1.482 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" C3R TTD M 18 " pdb=" O3R TTD M 18 " ideal model delta sigma weight residual 1.406 1.517 -0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C2 TTD M 18 " pdb=" N3 TTD M 18 " ideal model delta sigma weight residual 1.396 1.507 -0.111 2.00e-02 2.50e+03 3.08e+01 ... (remaining 30816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 41129 3.54 - 7.09: 563 7.09 - 10.63: 148 10.63 - 14.18: 13 14.18 - 17.72: 2 Bond angle restraints: 41855 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 41850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.42: 18377 35.42 - 70.84: 349 70.84 - 106.25: 35 106.25 - 141.67: 4 141.67 - 177.09: 1 Dihedral angle restraints: 18766 sinusoidal: 8142 harmonic: 10624 Sorted by residual: dihedral pdb=" O5' A K 1 " pdb=" C5' A K 1 " pdb=" C4' A K 1 " pdb=" C3' A K 1 " ideal model delta sinusoidal sigma weight residual 60.00 16.07 43.93 3 6.40e+00 2.44e-02 4.34e+01 dihedral pdb=" O5' A K 7 " pdb=" C5' A K 7 " pdb=" C4' A K 7 " pdb=" C3' A K 7 " ideal model delta sinusoidal sigma weight residual 180.00 141.04 38.96 3 6.40e+00 2.44e-02 3.78e+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 ... (remaining 18763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4540 0.108 - 0.216: 147 0.216 - 0.324: 5 0.324 - 0.432: 1 0.432 - 0.539: 2 Chirality restraints: 4695 Sorted by residual: chirality pdb=" C5 TTD M 18 " pdb=" C4 TTD M 18 " pdb=" C6 TTD M 18 " pdb=" C5T TTD M 18 " both_signs ideal model delta sigma weight residual False -3.16 -2.62 -0.54 2.00e-01 2.50e+01 7.28e+00 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 -2.73 -2.25 -0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" C6 TTD M 18 " pdb=" N1 TTD M 18 " pdb=" C5 TTD M 18 " pdb=" C6T TTD M 18 " both_signs ideal model delta sigma weight residual False 2.39 2.71 -0.33 2.00e-01 2.50e+01 2.69e+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: 27919 3.17 - 4.03: 80164 4.03 - 4.90: 149145 Warning: very small nonbonded interaction distances. Nonbonded interactions: 257252 Sorted by model distance: nonbonded pdb=" NH2 ARG A1345 " pdb=" OD1 ASP A1373 " model vdw 0.570 3.120 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 3.120 nonbonded pdb=" NH1 ARG B 857 " pdb=" CD GLU B 945 " model vdw 1.379 3.350 ... (remaining 257247 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 4.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 35.290 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.013 0.615 30843 Z= 0.693 Angle : 1.271 37.552 41861 Z= 0.825 Chirality : 0.054 0.539 4695 Planarity : 0.015 0.179 5249 Dihedral : 12.961 177.091 11892 Min Nonbonded Distance : 0.570 Molprobity Statistics. All-atom Clashscore : 3.76 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (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 ARG 0.003 0.000 ARG F 25 TYR 0.031 0.004 TYR B1091 PHE 0.019 0.003 PHE A 444 TRP 0.017 0.003 TRP A 233 HIS 0.005 0.001 HIS B 363 Details of bonding type rmsd/Z covalent geometry : bond 0.01118 / 0.65 (30821) covalent geometry : angle 1.24811 / 0.82 (41855) hydrogen bonds : bond 0.18852 / 12.72 ( 1265) hydrogen bonds : angle 8.11128 / 5.75 ( 3402) metal coordination : bond 0.27606 / 16.52 ( 20) metal coordination : angle 20.10856 / 9.23 ( 6) Misc. bond : bond 0.03257 / 1.61 ( 2) *********************** 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 to be fit. rotamer outliers: 3 poor density : 750 time to evaluate : 1.031 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: 0.8166 (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: 0.6261 (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: 0.2187 time to fit residues: 251.1568 Evaluate side-chains 438 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 435 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.0870 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 64 ASN A 118 HIS A1270 ASN B 178 ASN B 278 GLN C 17 ASN D 101 GLN F 83 GLN G 89 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 53 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.158578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.119498 restraints weight = 51527.434| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.33 r_work: 0.3422 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30843 Z= 0.180 Angle : 0.776 17.969 41861 Z= 0.403 Chirality : 0.048 0.269 4695 Planarity : 0.008 0.102 5249 Dihedral : 13.105 174.609 4610 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.77 % Allowed : 5.37 % Favored : 93.85 % Rotamer: Outliers : 1.87 % Allowed : 7.01 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.14), residues: 3628 helix: 0.31 (0.14), residues: 1207 sheet: -1.22 (0.21), residues: 517 loop : -0.75 (0.15), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 485 TYR 0.019 0.002 TYR G 15 PHE 0.026 0.002 PHE A 444 TRP 0.019 0.002 TRP B 308 HIS 0.017 0.002 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (30821) covalent geometry : angle 0.76799 / 0.40 (41855) hydrogen bonds : bond 0.06104 / 4.10 ( 1265) hydrogen bonds : angle 6.01942 / 4.26 ( 3402) metal coordination : bond 0.00965 / 0.66 ( 20) metal coordination : angle 9.50733 / 5.25 ( 6) Misc. bond : bond 0.00107 / 0.05 ( 2) *********************** 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 to be fit. rotamer outliers: 60 poor density : 495 time to evaluate : 1.152 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: 0.8326 (m-80) cc_final: 0.7697 (m-10) REVERT: A 344 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8367 (mtt180) REVERT: A 591 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: A 696 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 698 GLN cc_start: 0.8449 (mt0) cc_final: 0.8168 (mt0) REVERT: A 934 LYS cc_start: 0.8838 (tttt) cc_final: 0.8629 (tptt) REVERT: A 1115 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.7888 (p) REVERT: A 1209 MET cc_start: 0.7425 (ttm) cc_final: 0.7223 (ttt) REVERT: A 1436 ILE cc_start: 0.8477 (mt) cc_final: 0.8228 (mt) REVERT: B 239 GLU cc_start: 0.8232 (tt0) cc_final: 0.8020 (tt0) REVERT: B 277 LYS cc_start: 0.8244 (tptt) cc_final: 0.8043 (tppt) REVERT: B 308 TRP cc_start: 0.8078 (p-90) cc_final: 0.7747 (p-90) REVERT: B 458 LYS cc_start: 0.7600 (tttt) cc_final: 0.7256 (tmmt) REVERT: B 603 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 679 TYR cc_start: 0.7921 (m-80) cc_final: 0.7401 (m-80) REVERT: B 839 MET cc_start: 0.8513 (mtm) cc_final: 0.8261 (mtt) REVERT: B 1072 MET cc_start: 0.8648 (mtp) cc_final: 0.8375 (mtp) REVERT: B 1082 MET cc_start: 0.8866 (tpp) cc_final: 0.8494 (mmm) REVERT: B 1150 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7518 (mmp80) REVERT: C 263 THR cc_start: 0.8515 (m) cc_final: 0.8206 (p) REVERT: D 113 GLN cc_start: 0.8222 (tp40) cc_final: 0.8011 (tp40) REVERT: D 215 MET cc_start: 0.6240 (mmm) cc_final: 0.5926 (ptm) REVERT: F 11 GLN cc_start: 0.8125 (tt0) cc_final: 0.7813 (tt0) REVERT: F 52 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8599 (mm-40) REVERT: G 6 PHE cc_start: 0.8046 (m-80) cc_final: 0.7763 (m-80) REVERT: G 10 CYS cc_start: 0.8818 (m) cc_final: 0.8556 (t) REVERT: G 15 TYR cc_start: 0.7833 (t80) cc_final: 0.7441 (t80) REVERT: G 17 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8282 (tpm170) REVERT: G 28 GLU cc_start: 0.9177 (pp20) cc_final: 0.8726 (pm20) REVERT: G 88 SER cc_start: 0.8716 (OUTLIER) cc_final: 0.8172 (m) REVERT: I 2 ASN cc_start: 0.6665 (t0) cc_final: 0.6329 (t0) REVERT: J 40 LEU cc_start: 0.8310 (mt) cc_final: 0.7683 (mp) outliers start: 60 outliers final: 32 residues processed: 532 average time/residue: 0.2060 time to fit residues: 170.2455 Evaluate side-chains 425 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 389 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 416 ARG Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 837 ILE 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 55 VAL Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 452 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain C residue 29 MET Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain F residue 15 VAL 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 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: [62, 82, 229, 12, 197, 238, 221, 187, 7, 358, 188] chunk 62 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 221 optimal weight: 0.5980 chunk 187 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 188 optimal weight: 0.0370 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 GLN A 390 GLN A 517 ASN A1008 GLN B 494 HIS B 587 HIS B1177 HIS D 153 HIS F 83 GLN G 89 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.156519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.117121 restraints weight = 51349.362| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.45 r_work: 0.3360 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30843 Z= 0.181 Angle : 0.703 19.640 41861 Z= 0.362 Chirality : 0.046 0.288 4695 Planarity : 0.006 0.099 5249 Dihedral : 12.702 174.999 4607 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.87 % Favored : 93.52 % Rotamer: Outliers : 2.34 % Allowed : 8.22 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3628 helix: 0.63 (0.15), residues: 1216 sheet: -1.20 (0.21), residues: 526 loop : -0.61 (0.15), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 45 TYR 0.021 0.002 TYR B 259 PHE 0.021 0.002 PHE A 444 TRP 0.021 0.002 TRP A 185 HIS 0.016 0.002 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (30821) covalent geometry : angle 0.69333 / 0.36 (41855) hydrogen bonds : bond 0.05394 / 3.62 ( 1265) hydrogen bonds : angle 5.59036 / 3.97 ( 3402) metal coordination : bond 0.00474 / 0.35 ( 20) metal coordination : angle 9.68300 / 5.52 ( 6) Misc. bond : bond 0.00182 / 0.10 ( 2) *********************** 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 491 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 416 time to evaluate : 1.132 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: A 37 PHE cc_start: 0.8414 (m-80) cc_final: 0.8012 (m-10) REVERT: A 61 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7066 (mm) REVERT: A 122 MET cc_start: 0.8604 (tpt) cc_final: 0.8339 (tpt) REVERT: A 398 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7341 (mt-10) REVERT: A 591 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.7557 (m-80) REVERT: A 696 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8464 (mt-10) REVERT: A 698 GLN cc_start: 0.8361 (mt0) cc_final: 0.8107 (mt0) REVERT: A 903 ASN cc_start: 0.8055 (m-40) cc_final: 0.7711 (t0) REVERT: A 934 LYS cc_start: 0.8863 (tttt) cc_final: 0.8647 (tptt) REVERT: A 1079 MET cc_start: 0.5464 (mmm) cc_final: 0.4960 (mtt) REVERT: A 1225 PHE cc_start: 0.8674 (t80) cc_final: 0.8341 (t80) REVERT: A 1268 LEU cc_start: 0.8015 (tt) cc_final: 0.7321 (pp) REVERT: B 101 MET cc_start: 0.8021 (mmt) cc_final: 0.7735 (mmm) REVERT: B 239 GLU cc_start: 0.8139 (tt0) cc_final: 0.7853 (tt0) REVERT: B 277 LYS cc_start: 0.8253 (tptt) cc_final: 0.8034 (tppt) REVERT: B 308 TRP cc_start: 0.7910 (p-90) cc_final: 0.7672 (p-90) REVERT: B 458 LYS cc_start: 0.7608 (tttt) cc_final: 0.7226 (tmmt) REVERT: B 773 MET cc_start: 0.7678 (mmp) cc_final: 0.7111 (mtt) REVERT: B 1072 MET cc_start: 0.8697 (mtp) cc_final: 0.8487 (mtt) REVERT: B 1082 MET cc_start: 0.8815 (tpp) cc_final: 0.8449 (mmm) REVERT: B 1150 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7514 (mmp80) REVERT: C 40 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 215 MET cc_start: 0.6512 (mmm) cc_final: 0.6090 (ptm) REVERT: F 11 GLN cc_start: 0.8153 (tt0) cc_final: 0.7837 (tt0) REVERT: F 19 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7528 (mtm180) REVERT: F 52 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8565 (mm-40) REVERT: G 34 TYR cc_start: 0.8555 (t80) cc_final: 0.8243 (t80) REVERT: G 81 ARG cc_start: 0.8416 (mmm-85) cc_final: 0.8142 (mmm-85) REVERT: I 2 ASN cc_start: 0.6785 (t0) cc_final: 0.6347 (t0) REVERT: J 66 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7652 (mp10) outliers start: 75 outliers final: 45 residues processed: 465 average time/residue: 0.1961 time to fit residues: 145.5221 Evaluate side-chains 415 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 368 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 135 PHE 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 416 ARG Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1115 SER 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 A residue 1424 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 893 LEU 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 152 LYS 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 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 17 SER 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: [172, 92, 348, 128, 213, 88, 119, 54, 33, 278, 163] chunk 172 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 348 optimal weight: 0.3980 chunk 128 optimal weight: 1.9990 chunk 213 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 163 optimal weight: 0.0050 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 316 GLN A 854 ASN I 2 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.156574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117495 restraints weight = 51092.804| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.40 r_work: 0.3366 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 30843 Z= 0.150 Angle : 0.671 17.685 41861 Z= 0.342 Chirality : 0.045 0.293 4695 Planarity : 0.005 0.094 5249 Dihedral : 12.591 174.047 4607 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.54 % Favored : 93.96 % Rotamer: Outliers : 1.96 % Allowed : 9.25 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.14), residues: 3628 helix: 0.70 (0.15), residues: 1224 sheet: -1.10 (0.21), residues: 525 loop : -0.57 (0.15), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 63 TYR 0.018 0.001 TYR B 890 PHE 0.018 0.001 PHE I 35 TRP 0.019 0.002 TRP A 430 HIS 0.019 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (30821) covalent geometry : angle 0.66270 / 0.34 (41855) hydrogen bonds : bond 0.04819 / 3.24 ( 1265) hydrogen bonds : angle 5.38390 / 3.84 ( 3402) metal coordination : bond 0.00350 / 0.28 ( 20) metal coordination : angle 8.58340 / 4.91 ( 6) Misc. bond : bond 0.00097 / 0.05 ( 2) *********************** 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 472 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 409 time to evaluate : 1.215 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: 0.8502 (m-80) cc_final: 0.8072 (m-10) REVERT: A 132 LYS cc_start: 0.7856 (mmmm) cc_final: 0.7619 (tptt) REVERT: A 398 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7393 (mt-10) REVERT: A 591 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: A 696 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8467 (mt-10) REVERT: A 698 GLN cc_start: 0.8358 (mt0) cc_final: 0.8115 (mt0) REVERT: A 903 ASN cc_start: 0.8059 (m-40) cc_final: 0.7627 (t0) REVERT: A 934 LYS cc_start: 0.8867 (tttt) cc_final: 0.8596 (tptt) REVERT: A 1079 MET cc_start: 0.5489 (mmm) cc_final: 0.5248 (ttm) REVERT: A 1114 PRO cc_start: 0.8493 (Cg_exo) cc_final: 0.8252 (Cg_endo) REVERT: A 1209 MET cc_start: 0.7746 (ttt) cc_final: 0.7221 (mtm) REVERT: A 1225 PHE cc_start: 0.8719 (t80) cc_final: 0.8383 (t80) REVERT: A 1239 ARG cc_start: 0.8742 (ptm160) cc_final: 0.8226 (ttt180) REVERT: A 1279 ILE cc_start: 0.9022 (mm) cc_final: 0.8819 (mm) REVERT: A 1309 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7067 (p0) REVERT: B 101 MET cc_start: 0.8134 (mmt) cc_final: 0.7805 (mmm) REVERT: B 277 LYS cc_start: 0.8308 (tptt) cc_final: 0.8077 (tppt) REVERT: B 308 TRP cc_start: 0.7891 (p-90) cc_final: 0.7586 (p-90) REVERT: B 458 LYS cc_start: 0.7573 (tttt) cc_final: 0.7138 (tmmt) REVERT: B 473 MET cc_start: 0.4877 (ttp) cc_final: 0.4503 (ptp) REVERT: B 773 MET cc_start: 0.7642 (mmp) cc_final: 0.7177 (mtt) REVERT: B 835 GLN cc_start: 0.8326 (tp-100) cc_final: 0.8062 (tp-100) REVERT: B 1072 MET cc_start: 0.8737 (mtp) cc_final: 0.8457 (mtt) REVERT: B 1082 MET cc_start: 0.8857 (tpp) cc_final: 0.8489 (mmm) REVERT: B 1150 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7483 (mmp80) REVERT: C 1 MET cc_start: 0.2359 (mtt) cc_final: 0.1985 (mtt) REVERT: C 264 GLN cc_start: 0.8368 (tp40) cc_final: 0.7948 (tm-30) REVERT: D 215 MET cc_start: 0.6557 (mmm) cc_final: 0.6264 (ptm) REVERT: E 112 GLU cc_start: 0.7920 (pm20) cc_final: 0.7612 (pm20) REVERT: F 1 MET cc_start: 0.4294 (mtp) cc_final: 0.2366 (ptp) REVERT: F 11 GLN cc_start: 0.8206 (tt0) cc_final: 0.7885 (tt0) REVERT: F 19 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7694 (mtm180) REVERT: F 52 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8563 (mm-40) REVERT: G 6 PHE cc_start: 0.8131 (m-80) cc_final: 0.7839 (m-80) REVERT: G 27 PHE cc_start: 0.8325 (m-10) cc_final: 0.8121 (m-10) REVERT: G 34 TYR cc_start: 0.8730 (t80) cc_final: 0.8419 (t80) REVERT: G 44 TYR cc_start: 0.7379 (t80) cc_final: 0.6868 (t80) REVERT: G 81 ARG cc_start: 0.8413 (mmm-85) cc_final: 0.8147 (mmm-85) REVERT: G 87 GLN cc_start: 0.8089 (tp40) cc_final: 0.7688 (tp40) REVERT: H 16 ASP cc_start: 0.8008 (p0) cc_final: 0.7754 (p0) REVERT: I 2 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6272 (t0) REVERT: J 66 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7669 (mp10) outliers start: 63 outliers final: 43 residues processed: 448 average time/residue: 0.1987 time to fit residues: 140.9395 Evaluate side-chains 420 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 374 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 237 THR 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 416 ARG Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1309 ASP Chi-restraints excluded: chain A residue 1331 SER Chi-restraints excluded: chain A residue 1393 ASN Chi-restraints excluded: chain A residue 1406 VAL Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 839 MET 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 119 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 78 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 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 30 ILE 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: [307, 35, 32, 73, 218, 5, 164, 310, 348, 211, 227] chunk 307 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.0020 chunk 73 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 164 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 348 optimal weight: 0.0040 chunk 211 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 124 GLN A 299 HIS A 445 ASN A 854 ASN B1097 HIS B1177 HIS G 89 GLN I 2 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.155384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115400 restraints weight = 51512.769| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.64 r_work: 0.3323 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30843 Z= 0.136 Angle : 0.634 16.544 41861 Z= 0.323 Chirality : 0.044 0.305 4695 Planarity : 0.005 0.091 5249 Dihedral : 12.478 173.729 4607 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.62 % Favored : 93.85 % Rotamer: Outliers : 1.93 % Allowed : 9.75 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3628 helix: 0.88 (0.15), residues: 1225 sheet: -1.03 (0.21), residues: 529 loop : -0.55 (0.15), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1274 TYR 0.016 0.001 TYR A1349 PHE 0.018 0.001 PHE I 35 TRP 0.011 0.001 TRP A 430 HIS 0.021 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (30821) covalent geometry : angle 0.62664 / 0.32 (41855) hydrogen bonds : bond 0.04516 / 3.03 ( 1265) hydrogen bonds : angle 5.19399 / 3.71 ( 3402) metal coordination : bond 0.00303 / 0.24 ( 20) metal coordination : angle 7.97078 / 4.57 ( 6) Misc. bond : bond 0.00083 / 0.04 ( 2) *********************** 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 458 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 396 time to evaluate : 1.094 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: 0.8585 (m-80) cc_final: 0.8117 (m-10) REVERT: A 122 MET cc_start: 0.8639 (tpt) cc_final: 0.8362 (tpp) REVERT: A 132 LYS cc_start: 0.7938 (mmmm) cc_final: 0.7667 (tptt) REVERT: A 291 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8156 (mm-30) REVERT: A 398 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7554 (mt-10) REVERT: A 404 TYR cc_start: 0.7630 (m-80) cc_final: 0.7308 (m-80) REVERT: A 591 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7666 (m-80) REVERT: A 696 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 698 GLN cc_start: 0.8352 (mt0) cc_final: 0.8101 (mt0) REVERT: A 746 MET cc_start: 0.8925 (mtm) cc_final: 0.8467 (mtm) REVERT: A 790 ASP cc_start: 0.7080 (t0) cc_final: 0.6689 (t0) REVERT: A 903 ASN cc_start: 0.8106 (m-40) cc_final: 0.7662 (t0) REVERT: A 934 LYS cc_start: 0.8904 (tttt) cc_final: 0.8593 (tptt) REVERT: A 1079 MET cc_start: 0.5489 (mmm) cc_final: 0.5269 (ttm) REVERT: A 1209 MET cc_start: 0.7810 (ttt) cc_final: 0.7488 (ttt) REVERT: A 1225 PHE cc_start: 0.8772 (t80) cc_final: 0.8413 (t80) REVERT: A 1239 ARG cc_start: 0.8819 (ptm160) cc_final: 0.8546 (ptm160) REVERT: A 1285 MET cc_start: 0.8156 (pmm) cc_final: 0.7612 (pmm) REVERT: B 101 MET cc_start: 0.8207 (mmt) cc_final: 0.7813 (mmm) REVERT: B 277 LYS cc_start: 0.8351 (tptt) cc_final: 0.8097 (tppt) REVERT: B 308 TRP cc_start: 0.7888 (p-90) cc_final: 0.7583 (p-90) REVERT: B 458 LYS cc_start: 0.7440 (tttt) cc_final: 0.6976 (tmmt) REVERT: B 473 MET cc_start: 0.4936 (ttp) cc_final: 0.4321 (ptp) REVERT: B 486 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6171 (m-80) REVERT: B 773 MET cc_start: 0.7732 (mmp) cc_final: 0.7213 (mtt) REVERT: B 1072 MET cc_start: 0.8778 (mtp) cc_final: 0.8507 (mtt) REVERT: B 1082 MET cc_start: 0.8802 (tpp) cc_final: 0.8441 (mmm) REVERT: C 264 GLN cc_start: 0.8355 (tp40) cc_final: 0.7925 (tm-30) REVERT: D 215 MET cc_start: 0.6565 (mmm) cc_final: 0.6258 (ptm) REVERT: F 1 MET cc_start: 0.4298 (mtp) cc_final: 0.2533 (ptp) REVERT: F 11 GLN cc_start: 0.8262 (tt0) cc_final: 0.7948 (tt0) REVERT: F 19 ARG cc_start: 0.8153 (mtp180) cc_final: 0.7736 (mtm180) REVERT: F 52 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8582 (mm-40) REVERT: G 5 ARG cc_start: 0.7943 (mmp-170) cc_final: 0.7699 (mmm160) REVERT: G 6 PHE cc_start: 0.8081 (m-80) cc_final: 0.7659 (m-80) REVERT: G 34 TYR cc_start: 0.8752 (t80) cc_final: 0.8347 (t80) REVERT: G 44 TYR cc_start: 0.7450 (t80) cc_final: 0.7046 (t80) REVERT: G 81 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7853 (mmm-85) REVERT: G 87 GLN cc_start: 0.8086 (tp40) cc_final: 0.7463 (tp40) REVERT: G 89 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7503 (mp10) REVERT: H 16 ASP cc_start: 0.8104 (p0) cc_final: 0.7879 (p0) REVERT: I 1 MET cc_start: 0.5477 (tpp) cc_final: 0.5178 (tpp) REVERT: J 66 GLN cc_start: 0.8262 (tm-30) cc_final: 0.7451 (mp10) outliers start: 62 outliers final: 42 residues processed: 434 average time/residue: 0.1946 time to fit residues: 133.6312 Evaluate side-chains 418 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 373 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLN Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1331 SER 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 1436 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 543 SER 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 603 LEU Chi-restraints excluded: chain B residue 839 MET 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 119 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 36 GLU Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain F residue 15 VAL 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 84 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain J residue 29 TYR 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: [222, 48, 317, 228, 39, 209, 76, 230, 356, 31, 233] chunk 222 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 317 optimal weight: 0.9980 chunk 228 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 230 optimal weight: 0.5980 chunk 356 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 233 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 517 ASN B 121 ASN B 794 ASN B1097 HIS C 135 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.153900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114273 restraints weight = 51187.537| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.65 r_work: 0.3299 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30843 Z= 0.153 Angle : 0.641 17.528 41861 Z= 0.326 Chirality : 0.045 0.310 4695 Planarity : 0.005 0.092 5249 Dihedral : 12.437 173.997 4607 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.90 % Favored : 93.63 % Rotamer: Outliers : 2.15 % Allowed : 9.93 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3628 helix: 0.82 (0.15), residues: 1234 sheet: -0.90 (0.21), residues: 521 loop : -0.56 (0.15), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 7 TYR 0.017 0.001 TYR B1192 PHE 0.019 0.001 PHE I 35 TRP 0.012 0.001 TRP C 170 HIS 0.010 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (30821) covalent geometry : angle 0.63313 / 0.33 (41855) hydrogen bonds : bond 0.04451 / 2.98 ( 1265) hydrogen bonds : angle 5.11970 / 3.66 ( 3402) metal coordination : bond 0.00371 / 0.28 ( 20) metal coordination : angle 8.34170 / 4.78 ( 6) Misc. bond : bond 0.00086 / 0.04 ( 2) *********************** 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 466 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 397 time to evaluate : 1.197 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: A 37 PHE cc_start: 0.8516 (m-80) cc_final: 0.8109 (m-10) REVERT: A 122 MET cc_start: 0.8686 (tpt) cc_final: 0.8392 (tpp) REVERT: A 132 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7632 (tptt) REVERT: A 404 TYR cc_start: 0.7466 (m-80) cc_final: 0.7175 (m-80) REVERT: A 591 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: A 696 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 698 GLN cc_start: 0.8328 (mt0) cc_final: 0.8072 (mt0) REVERT: A 746 MET cc_start: 0.8941 (mtm) cc_final: 0.8423 (mtm) REVERT: A 790 ASP cc_start: 0.6939 (t0) cc_final: 0.6626 (t0) REVERT: A 806 ARG cc_start: 0.6817 (tmt170) cc_final: 0.6317 (tpt90) REVERT: A 903 ASN cc_start: 0.8122 (m-40) cc_final: 0.7793 (t0) REVERT: A 934 LYS cc_start: 0.8818 (tttt) cc_final: 0.8578 (tptt) REVERT: A 1209 MET cc_start: 0.7586 (ttt) cc_final: 0.7221 (ttt) REVERT: A 1225 PHE cc_start: 0.8822 (t80) cc_final: 0.8493 (t80) REVERT: A 1239 ARG cc_start: 0.8795 (ptm160) cc_final: 0.8516 (ptm160) REVERT: A 1259 MET cc_start: 0.9233 (pmm) cc_final: 0.9032 (pmm) REVERT: A 1268 LEU cc_start: 0.8105 (tt) cc_final: 0.7368 (pp) REVERT: A 1285 MET cc_start: 0.7882 (pmm) cc_final: 0.7384 (pmm) REVERT: B 101 MET cc_start: 0.8108 (mmt) cc_final: 0.7716 (mmm) REVERT: B 277 LYS cc_start: 0.8350 (tptt) cc_final: 0.8113 (tppt) REVERT: B 308 TRP cc_start: 0.7886 (p-90) cc_final: 0.7549 (p-90) REVERT: B 458 LYS cc_start: 0.7222 (tttt) cc_final: 0.6792 (tmmt) REVERT: B 473 MET cc_start: 0.5051 (ttp) cc_final: 0.4584 (ptp) REVERT: B 486 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.5967 (m-80) REVERT: B 773 MET cc_start: 0.7592 (mmp) cc_final: 0.7205 (mtt) REVERT: B 1072 MET cc_start: 0.8684 (mtp) cc_final: 0.8423 (mtt) REVERT: B 1082 MET cc_start: 0.8751 (tpp) cc_final: 0.8427 (mmm) REVERT: C 264 GLN cc_start: 0.8474 (tp40) cc_final: 0.8002 (tm-30) REVERT: D 83 CYS cc_start: 0.8090 (t) cc_final: 0.7622 (t) REVERT: F 1 MET cc_start: 0.3932 (mtp) cc_final: 0.2292 (ptp) REVERT: F 11 GLN cc_start: 0.8218 (tt0) cc_final: 0.7941 (tt0) REVERT: F 19 ARG cc_start: 0.8027 (mtp180) cc_final: 0.7711 (mtm180) REVERT: F 52 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8527 (mm-40) REVERT: G 44 TYR cc_start: 0.7435 (t80) cc_final: 0.6983 (t80) REVERT: G 81 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.7882 (mmm-85) REVERT: G 87 GLN cc_start: 0.7980 (tp40) cc_final: 0.7514 (tp40) REVERT: G 89 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7654 (mp10) REVERT: J 66 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7345 (mp10) outliers start: 69 outliers final: 50 residues processed: 442 average time/residue: 0.1938 time to fit residues: 136.7992 Evaluate side-chains 431 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 379 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 237 THR 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 416 ARG Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1331 SER 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 B residue 55 VAL Chi-restraints excluded: chain B residue 95 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 396 ASP Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 543 SER 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 603 LEU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 976 ILE 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 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 C residue 263 THR Chi-restraints excluded: chain D residue 152 LYS 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 58 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain J residue 29 TYR 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: [2, 48, 333, 241, 255, 235, 33, 131, 238, 356, 205] chunk 2 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 333 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 6.9990 chunk 235 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 356 optimal weight: 0.6980 chunk 205 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.154248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114296 restraints weight = 51325.613| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.57 r_work: 0.3304 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30843 Z= 0.145 Angle : 0.632 16.937 41861 Z= 0.321 Chirality : 0.044 0.314 4695 Planarity : 0.005 0.091 5249 Dihedral : 12.382 173.888 4607 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.68 % Favored : 93.83 % Rotamer: Outliers : 2.06 % Allowed : 10.56 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.14), residues: 3628 helix: 0.85 (0.15), residues: 1241 sheet: -0.90 (0.21), residues: 519 loop : -0.54 (0.15), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 7 TYR 0.016 0.001 TYR A1349 PHE 0.019 0.001 PHE I 35 TRP 0.020 0.001 TRP A1228 HIS 0.011 0.001 HIS A 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (30821) covalent geometry : angle 0.62451 / 0.32 (41855) hydrogen bonds : bond 0.04306 / 2.88 ( 1265) hydrogen bonds : angle 5.04380 / 3.60 ( 3402) metal coordination : bond 0.00343 / 0.26 ( 20) metal coordination : angle 8.06528 / 4.63 ( 6) Misc. bond : bond 0.00077 / 0.04 ( 2) *********************** 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 458 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 392 time to evaluate : 0.982 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: A 37 PHE cc_start: 0.8543 (m-80) cc_final: 0.8129 (m-10) REVERT: A 122 MET cc_start: 0.8699 (tpt) cc_final: 0.8405 (tpp) REVERT: A 132 LYS cc_start: 0.7891 (mmmm) cc_final: 0.7636 (tptt) REVERT: A 404 TYR cc_start: 0.7493 (m-80) cc_final: 0.7205 (m-80) REVERT: A 591 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7540 (m-80) REVERT: A 696 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 698 GLN cc_start: 0.8373 (mt0) cc_final: 0.8122 (mt0) REVERT: A 806 ARG cc_start: 0.6733 (tmt170) cc_final: 0.6258 (tpt90) REVERT: A 895 LYS cc_start: 0.8336 (mtmm) cc_final: 0.8044 (mtmm) REVERT: A 903 ASN cc_start: 0.8144 (m-40) cc_final: 0.7783 (t0) REVERT: A 934 LYS cc_start: 0.8818 (tttt) cc_final: 0.8579 (tptt) REVERT: A 1225 PHE cc_start: 0.8838 (t80) cc_final: 0.8535 (t80) REVERT: A 1239 ARG cc_start: 0.8755 (ptm160) cc_final: 0.8244 (ttt180) REVERT: A 1268 LEU cc_start: 0.8081 (tt) cc_final: 0.7346 (pp) REVERT: A 1285 MET cc_start: 0.7670 (pmm) cc_final: 0.7156 (pmm) REVERT: B 101 MET cc_start: 0.8154 (mmt) cc_final: 0.7754 (mmm) REVERT: B 277 LYS cc_start: 0.8300 (tptt) cc_final: 0.8068 (tppt) REVERT: B 308 TRP cc_start: 0.7874 (p-90) cc_final: 0.7600 (p-90) REVERT: B 458 LYS cc_start: 0.7180 (tttt) cc_final: 0.6767 (tmmt) REVERT: B 473 MET cc_start: 0.5007 (ttp) cc_final: 0.4556 (ptp) REVERT: B 486 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6007 (m-80) REVERT: B 773 MET cc_start: 0.7533 (mmp) cc_final: 0.7224 (mtt) REVERT: B 1082 MET cc_start: 0.8770 (tpp) cc_final: 0.8451 (mmm) REVERT: C 264 GLN cc_start: 0.8451 (tp40) cc_final: 0.7999 (tm-30) REVERT: D 58 MET cc_start: 0.8162 (mmm) cc_final: 0.7726 (tmm) REVERT: D 83 CYS cc_start: 0.8037 (t) cc_final: 0.7635 (t) REVERT: F 1 MET cc_start: 0.3943 (mtp) cc_final: 0.2312 (ptp) REVERT: F 11 GLN cc_start: 0.8254 (tt0) cc_final: 0.7974 (tt0) REVERT: F 19 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7660 (mtm180) REVERT: F 52 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8523 (mm-40) REVERT: G 8 ARG cc_start: 0.9079 (mmt180) cc_final: 0.8680 (mmt180) REVERT: G 34 TYR cc_start: 0.8757 (t80) cc_final: 0.8077 (t80) REVERT: G 81 ARG cc_start: 0.8519 (mmm-85) cc_final: 0.7792 (mmm-85) REVERT: G 87 GLN cc_start: 0.7969 (tp40) cc_final: 0.7536 (tp40) REVERT: G 89 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7739 (mp10) REVERT: J 66 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7360 (mp10) REVERT: J 70 ARG cc_start: 0.7757 (tpp80) cc_final: 0.7374 (mmm-85) outliers start: 66 outliers final: 49 residues processed: 434 average time/residue: 0.1974 time to fit residues: 136.3204 Evaluate side-chains 428 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 377 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 295 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1331 SER 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 1424 VAL 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 218 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 GLU 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 543 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 976 ILE 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 119 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 152 LYS 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 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 64 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: [278, 264, 214, 103, 114, 295, 233, 151, 339, 87, 332] chunk 278 optimal weight: 1.9990 chunk 264 optimal weight: 0.8980 chunk 214 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 295 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 chunk 151 optimal weight: 10.0000 chunk 339 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN A1130 GLN B 587 HIS B1193 GLN D 146 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.153251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.113462 restraints weight = 51363.495| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.58 r_work: 0.3271 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30843 Z= 0.182 Angle : 0.662 19.594 41861 Z= 0.335 Chirality : 0.045 0.312 4695 Planarity : 0.005 0.094 5249 Dihedral : 12.376 174.377 4607 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.79 % Favored : 93.72 % Rotamer: Outliers : 2.06 % Allowed : 10.78 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3628 helix: 0.85 (0.15), residues: 1238 sheet: -0.86 (0.21), residues: 515 loop : -0.57 (0.15), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 7 TYR 0.023 0.002 TYR G 44 PHE 0.021 0.002 PHE I 35 TRP 0.019 0.002 TRP A1228 HIS 0.009 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (30821) covalent geometry : angle 0.65301 / 0.33 (41855) hydrogen bonds : bond 0.04434 / 2.97 ( 1265) hydrogen bonds : angle 5.07694 / 3.63 ( 3402) metal coordination : bond 0.00494 / 0.36 ( 20) metal coordination : angle 9.27671 / 5.33 ( 6) Misc. bond : bond 0.00098 / 0.05 ( 2) *********************** 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 464 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 398 time to evaluate : 1.133 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: A 37 PHE cc_start: 0.8555 (m-80) cc_final: 0.8172 (m-10) REVERT: A 122 MET cc_start: 0.8701 (tpt) cc_final: 0.8388 (tpp) REVERT: A 132 LYS cc_start: 0.7954 (mmmm) cc_final: 0.7684 (tptt) REVERT: A 287 HIS cc_start: 0.7946 (p-80) cc_final: 0.7365 (m-70) REVERT: A 404 TYR cc_start: 0.7487 (m-80) cc_final: 0.7203 (m-80) REVERT: A 591 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7577 (m-80) REVERT: A 696 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8299 (mt-10) REVERT: A 698 GLN cc_start: 0.8389 (mt0) cc_final: 0.8148 (mt0) REVERT: A 790 ASP cc_start: 0.6947 (t0) cc_final: 0.6666 (t0) REVERT: A 903 ASN cc_start: 0.8139 (m-40) cc_final: 0.7784 (t0) REVERT: A 934 LYS cc_start: 0.8821 (tttt) cc_final: 0.8597 (tptt) REVERT: A 1225 PHE cc_start: 0.8839 (t80) cc_final: 0.8620 (t80) REVERT: A 1239 ARG cc_start: 0.8720 (ptm160) cc_final: 0.8214 (ttt180) REVERT: A 1285 MET cc_start: 0.7649 (pmm) cc_final: 0.7138 (pmm) REVERT: B 101 MET cc_start: 0.8150 (mmt) cc_final: 0.7699 (mmm) REVERT: B 277 LYS cc_start: 0.8272 (tptt) cc_final: 0.7983 (tppt) REVERT: B 458 LYS cc_start: 0.7321 (tttt) cc_final: 0.6912 (tmmt) REVERT: B 473 MET cc_start: 0.5044 (ttp) cc_final: 0.4642 (ptp) REVERT: B 486 TYR cc_start: 0.7404 (OUTLIER) cc_final: 0.5969 (m-80) REVERT: B 701 ILE cc_start: 0.7845 (mm) cc_final: 0.7388 (pt) REVERT: B 773 MET cc_start: 0.7572 (mmp) cc_final: 0.7279 (mtt) REVERT: B 1082 MET cc_start: 0.8774 (tpp) cc_final: 0.8472 (mmm) REVERT: C 264 GLN cc_start: 0.8474 (tp40) cc_final: 0.8020 (tm-30) REVERT: D 1 MET cc_start: 0.6105 (mpp) cc_final: 0.5450 (mpp) REVERT: D 58 MET cc_start: 0.8204 (mmm) cc_final: 0.7725 (tmm) REVERT: D 83 CYS cc_start: 0.8125 (t) cc_final: 0.7704 (t) REVERT: F 1 MET cc_start: 0.4413 (mtp) cc_final: 0.2784 (ptp) REVERT: F 11 GLN cc_start: 0.8275 (tt0) cc_final: 0.7995 (tt0) REVERT: F 19 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7440 (mtm180) REVERT: F 52 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8558 (mm-40) REVERT: G 81 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.7685 (mmm-85) REVERT: G 87 GLN cc_start: 0.8034 (tp40) cc_final: 0.7544 (tp40) REVERT: G 89 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7767 (mp10) REVERT: J 70 ARG cc_start: 0.7787 (tpp80) cc_final: 0.7399 (mmm-85) outliers start: 66 outliers final: 56 residues processed: 439 average time/residue: 0.1991 time to fit residues: 138.2532 Evaluate side-chains 436 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 378 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 416 ARG Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 932 GLU Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1197 LEU Chi-restraints excluded: chain A residue 1331 SER 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 1424 VAL Chi-restraints excluded: chain A residue 1430 LEU 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 140 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 239 GLU 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 543 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 976 ILE 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 C residue 29 MET Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 152 LYS Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 54 SER 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 84 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain J residue 29 TYR 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: [120, 262, 121, 210, 195, 37, 130, 105, 118, 217, 83] chunk 120 optimal weight: 10.0000 chunk 262 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 210 optimal weight: 0.9990 chunk 195 optimal weight: 0.5980 chunk 37 optimal weight: 0.1980 chunk 130 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 chunk 118 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.154586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114950 restraints weight = 51146.751| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.60 r_work: 0.3303 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30843 Z= 0.137 Angle : 0.633 16.950 41861 Z= 0.321 Chirality : 0.044 0.318 4695 Planarity : 0.004 0.090 5249 Dihedral : 12.315 173.714 4607 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.87 % Favored : 93.66 % Rotamer: Outliers : 1.68 % Allowed : 11.62 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3628 helix: 0.96 (0.15), residues: 1234 sheet: -0.81 (0.22), residues: 498 loop : -0.56 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1422 TYR 0.018 0.001 TYR A1349 PHE 0.021 0.001 PHE G 6 TRP 0.036 0.001 TRP A1228 HIS 0.009 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (30821) covalent geometry : angle 0.62535 / 0.32 (41855) hydrogen bonds : bond 0.04169 / 2.78 ( 1265) hydrogen bonds : angle 5.01164 / 3.59 ( 3402) metal coordination : bond 0.00333 / 0.25 ( 20) metal coordination : angle 8.14677 / 4.68 ( 6) Misc. bond : bond 0.00075 / 0.04 ( 2) *********************** 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 447 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 393 time to evaluate : 1.160 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: A 37 PHE cc_start: 0.8528 (m-80) cc_final: 0.8170 (m-10) REVERT: A 122 MET cc_start: 0.8688 (tpt) cc_final: 0.8370 (tpp) REVERT: A 132 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7677 (tptt) REVERT: A 287 HIS cc_start: 0.7915 (p-80) cc_final: 0.7459 (m-70) REVERT: A 404 TYR cc_start: 0.7488 (m-80) cc_final: 0.7211 (m-80) REVERT: A 591 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: A 696 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 698 GLN cc_start: 0.8389 (mt0) cc_final: 0.8136 (mt0) REVERT: A 790 ASP cc_start: 0.6921 (t0) cc_final: 0.6481 (t0) REVERT: A 806 ARG cc_start: 0.6787 (tmt170) cc_final: 0.6351 (tpt90) REVERT: A 895 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7919 (mtmm) REVERT: A 903 ASN cc_start: 0.8142 (m-40) cc_final: 0.7813 (t0) REVERT: A 934 LYS cc_start: 0.8768 (tttt) cc_final: 0.8564 (tptt) REVERT: A 1239 ARG cc_start: 0.8704 (ptm160) cc_final: 0.8260 (ttt180) REVERT: A 1285 MET cc_start: 0.7508 (pmm) cc_final: 0.7089 (pmm) REVERT: A 1422 ARG cc_start: 0.8341 (ptt-90) cc_final: 0.8083 (ptt-90) REVERT: B 101 MET cc_start: 0.8078 (mmt) cc_final: 0.7683 (mmm) REVERT: B 277 LYS cc_start: 0.8239 (tptt) cc_final: 0.7952 (tppt) REVERT: B 458 LYS cc_start: 0.7211 (tttt) cc_final: 0.6803 (tmmt) REVERT: B 473 MET cc_start: 0.5030 (ttp) cc_final: 0.4647 (ptp) REVERT: B 486 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.5890 (m-80) REVERT: B 1082 MET cc_start: 0.8755 (tpp) cc_final: 0.8443 (mmm) REVERT: C 264 GLN cc_start: 0.8463 (tp40) cc_final: 0.8031 (tm-30) REVERT: D 1 MET cc_start: 0.6259 (mpp) cc_final: 0.5593 (mpp) REVERT: D 58 MET cc_start: 0.8225 (mmm) cc_final: 0.7718 (tmm) REVERT: D 83 CYS cc_start: 0.8092 (t) cc_final: 0.7688 (t) REVERT: D 114 ASN cc_start: 0.8784 (t0) cc_final: 0.8454 (m-40) REVERT: F 1 MET cc_start: 0.4431 (OUTLIER) cc_final: 0.2939 (ptp) REVERT: F 11 GLN cc_start: 0.8247 (tt0) cc_final: 0.7968 (tt0) REVERT: F 19 ARG cc_start: 0.7913 (mtp180) cc_final: 0.7386 (mtm180) REVERT: F 52 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8528 (mm-40) REVERT: G 5 ARG cc_start: 0.7562 (mmp80) cc_final: 0.7214 (mmp80) REVERT: G 34 TYR cc_start: 0.8624 (t80) cc_final: 0.8382 (t80) REVERT: G 81 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.7691 (mmm-85) REVERT: G 87 GLN cc_start: 0.7990 (tp40) cc_final: 0.7337 (tp40) REVERT: H 29 GLU cc_start: 0.7462 (pm20) cc_final: 0.7227 (tm-30) REVERT: J 66 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7438 (mp10) REVERT: J 68 GLU cc_start: 0.8122 (tp30) cc_final: 0.7921 (tp30) outliers start: 54 outliers final: 43 residues processed: 428 average time/residue: 0.1946 time to fit residues: 133.2303 Evaluate side-chains 425 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 379 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 416 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1331 SER 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 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 140 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 486 TYR Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 976 ILE 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 263 THR Chi-restraints excluded: chain D residue 152 LYS 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 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 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 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: [332, 304, 239, 194, 68, 185, 131, 278, 73, 41, 192] chunk 332 optimal weight: 6.9990 chunk 304 optimal weight: 0.6980 chunk 239 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.154348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.114556 restraints weight = 50807.429| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.61 r_work: 0.3297 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30843 Z= 0.149 Angle : 0.646 18.617 41861 Z= 0.327 Chirality : 0.044 0.317 4695 Planarity : 0.005 0.093 5249 Dihedral : 12.286 173.662 4607 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.79 % Favored : 93.74 % Rotamer: Outliers : 1.59 % Allowed : 11.90 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3628 helix: 0.95 (0.15), residues: 1240 sheet: -0.77 (0.22), residues: 498 loop : -0.60 (0.15), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 52 TYR 0.016 0.001 TYR A1349 PHE 0.023 0.001 PHE G 6 TRP 0.026 0.001 TRP A1228 HIS 0.010 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (30821) covalent geometry : angle 0.63722 / 0.33 (41855) hydrogen bonds : bond 0.04143 / 2.77 ( 1265) hydrogen bonds : angle 5.00728 / 3.59 ( 3402) metal coordination : bond 0.00409 / 0.31 ( 20) metal coordination : angle 9.12510 / 5.24 ( 6) Misc. bond : bond 0.00082 / 0.04 ( 2) ********************** 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 431 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 380 time to evaluate : 0.909 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8579 (m-80) cc_final: 0.8216 (m-10) REVERT: A 122 MET cc_start: 0.8699 (tpt) cc_final: 0.8363 (tpp) REVERT: A 132 LYS cc_start: 0.7944 (mmmm) cc_final: 0.7662 (tptt) REVERT: A 404 TYR cc_start: 0.7435 (m-80) cc_final: 0.7161 (m-80) REVERT: A 591 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: A 696 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 698 GLN cc_start: 0.8406 (mt0) cc_final: 0.8157 (mt0) REVERT: A 790 ASP cc_start: 0.6977 (t0) cc_final: 0.6508 (t0) REVERT: A 806 ARG cc_start: 0.6799 (tmt170) cc_final: 0.6367 (tpt90) REVERT: A 895 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7903 (mtmm) REVERT: A 903 ASN cc_start: 0.8179 (m-40) cc_final: 0.7825 (t0) REVERT: A 934 LYS cc_start: 0.8815 (tttt) cc_final: 0.8573 (tptt) REVERT: A 1239 ARG cc_start: 0.8601 (ptm160) cc_final: 0.8290 (ttt180) REVERT: A 1285 MET cc_start: 0.7511 (pmm) cc_final: 0.7090 (pmm) REVERT: A 1422 ARG cc_start: 0.8378 (ptt-90) cc_final: 0.8107 (ptt-90) REVERT: B 101 MET cc_start: 0.8113 (mmt) cc_final: 0.7701 (mmm) REVERT: B 277 LYS cc_start: 0.8239 (tptt) cc_final: 0.7955 (tppt) REVERT: B 458 LYS cc_start: 0.7199 (tttt) cc_final: 0.6782 (tmmt) REVERT: B 473 MET cc_start: 0.5085 (ttp) cc_final: 0.4672 (ptp) REVERT: B 486 TYR cc_start: 0.7285 (OUTLIER) cc_final: 0.5931 (m-80) REVERT: B 701 ILE cc_start: 0.7816 (mm) cc_final: 0.7410 (pt) REVERT: B 1082 MET cc_start: 0.8781 (tpp) cc_final: 0.8464 (mmm) REVERT: C 264 GLN cc_start: 0.8477 (tp40) cc_final: 0.8035 (tm-30) REVERT: D 1 MET cc_start: 0.6335 (mpp) cc_final: 0.5682 (mpp) REVERT: D 58 MET cc_start: 0.8196 (mmm) cc_final: 0.7626 (tmm) REVERT: D 83 CYS cc_start: 0.8133 (t) cc_final: 0.7720 (t) REVERT: D 114 ASN cc_start: 0.8801 (t0) cc_final: 0.8462 (m-40) REVERT: F 1 MET cc_start: 0.4526 (OUTLIER) cc_final: 0.3070 (ptp) REVERT: F 11 GLN cc_start: 0.8284 (tt0) cc_final: 0.7994 (tt0) REVERT: F 19 ARG cc_start: 0.7942 (mtp180) cc_final: 0.7401 (mtm180) REVERT: F 52 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8544 (mm-40) REVERT: G 34 TYR cc_start: 0.8651 (t80) cc_final: 0.8434 (t80) REVERT: G 87 GLN cc_start: 0.7965 (tp40) cc_final: 0.7290 (tp40) REVERT: G 89 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7698 (mp10) REVERT: H 29 GLU cc_start: 0.7412 (pm20) cc_final: 0.7189 (tm-30) REVERT: J 66 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7434 (mp10) outliers start: 51 outliers final: 44 residues processed: 411 average time/residue: 0.1988 time to fit residues: 130.2103 Evaluate side-chains 423 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 376 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 416 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 624 SER Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 1035 TYR Chi-restraints excluded: chain A residue 1331 SER 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 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 140 ILE Chi-restraints excluded: chain B residue 218 SER 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 543 SER Chi-restraints excluded: chain B residue 587 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 839 MET Chi-restraints excluded: chain B residue 976 ILE 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 263 THR Chi-restraints excluded: chain D residue 152 LYS 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 115 TYR Chi-restraints excluded: chain G residue 26 LEU Chi-restraints excluded: chain G residue 43 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 64 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: [12, 327, 197, 63, 152, 180, 290, 24, 116, 176, 9] chunk 12 optimal weight: 3.9990 chunk 327 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 290 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 176 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.152430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.112445 restraints weight = 51237.673| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.62 r_work: 0.3255 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 30843 Z= 0.208 Angle : 0.690 21.962 41861 Z= 0.348 Chirality : 0.046 0.314 4695 Planarity : 0.005 0.093 5249 Dihedral : 12.316 174.473 4607 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.95 % Favored : 93.61 % Rotamer: Outliers : 1.78 % Allowed : 11.71 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3628 helix: 0.93 (0.15), residues: 1223 sheet: -0.75 (0.22), residues: 493 loop : -0.71 (0.15), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 52 TYR 0.018 0.002 TYR B 486 PHE 0.023 0.002 PHE I 35 TRP 0.022 0.002 TRP A1228 HIS 0.010 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (30821) covalent geometry : angle 0.67727 / 0.35 (41855) hydrogen bonds : bond 0.04464 / 3.00 ( 1265) hydrogen bonds : angle 5.09512 / 3.65 ( 3402) metal coordination : bond 0.00569 / 0.43 ( 20) metal coordination : angle 10.82281 / 6.20 ( 6) Misc. bond : bond 0.00107 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8524.02 seconds wall clock time: 146 minutes 16.05 seconds (8776.05 seconds total)