Starting phenix.real_space_refine on Thu Feb 15 11:07:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/02_2024/7dsh_30833_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/02_2024/7dsh_30833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/02_2024/7dsh_30833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/02_2024/7dsh_30833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/02_2024/7dsh_30833_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dsh_30833/02_2024/7dsh_30833_updated.pdb" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 7764 2.51 5 N 2004 2.21 5 O 2242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 544": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A ARG 701": "NH1" <-> "NH2" Residue "A ARG 703": "NH1" <-> "NH2" Residue "A ARG 713": "NH1" <-> "NH2" Residue "A ARG 731": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A ARG 909": "NH1" <-> "NH2" Residue "A ARG 953": "NH1" <-> "NH2" Residue "A ARG 966": "NH1" <-> "NH2" Residue "A TYR 1040": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "A ARG 1104": "NH1" <-> "NH2" Residue "A ARG 1178": "NH1" <-> "NH2" Residue "A ARG 1257": "NH1" <-> "NH2" Residue "A ARG 1268": "NH1" <-> "NH2" Residue "A PHE 1287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A TYR 1314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1371": "NH1" <-> "NH2" Residue "A ARG 1393": "NH1" <-> "NH2" Residue "A ARG 1434": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 73": "NH1" <-> "NH2" Residue "B TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12071 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9066 Classifications: {'peptide': 1138} Link IDs: {'PTRANS': 35, 'TRANS': 1102} Chain breaks: 1 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2934 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.78, per 1000 atoms: 0.56 Number of scatterers: 12071 At special positions: 0 Unit cell: (148.755, 108.665, 130.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 3 15.00 Mg 1 11.99 O 2242 8.00 N 2004 7.00 C 7764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN B 240 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.64 Conformation dependent library (CDL) restraints added in 2.4 seconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 9 sheets defined 29.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 221 through 231 removed outlier: 3.657A pdb=" N GLY A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 removed outlier: 4.255A pdb=" N ILE A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ARG A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'A' and resid 550 through 570 removed outlier: 3.807A pdb=" N VAL A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 600 through 608 removed outlier: 3.579A pdb=" N ALA A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 633 removed outlier: 3.657A pdb=" N THR A 626 " --> pdb=" O GLU A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 697 through 699 No H-bonds generated for 'chain 'A' and resid 697 through 699' Processing helix chain 'A' and resid 709 through 725 removed outlier: 3.614A pdb=" N GLU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP A 724 " --> pdb=" O ALA A 720 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 725 " --> pdb=" O LYS A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 774 Processing helix chain 'A' and resid 799 through 811 removed outlier: 3.807A pdb=" N ALA A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 804 " --> pdb=" O ASP A 800 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL A 805 " --> pdb=" O GLU A 801 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 810 " --> pdb=" O ALA A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 923 through 935 Processing helix chain 'A' and resid 943 through 950 removed outlier: 3.889A pdb=" N VAL A 947 " --> pdb=" O GLU A 943 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 950 " --> pdb=" O VAL A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 976 removed outlier: 3.968A pdb=" N GLU A 976 " --> pdb=" O PRO A 972 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 972 through 976' Processing helix chain 'A' and resid 993 through 1000 Processing helix chain 'A' and resid 1035 through 1045 removed outlier: 3.772A pdb=" N TYR A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS A1042 " --> pdb=" O SER A1038 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1078 Processing helix chain 'A' and resid 1088 through 1091 No H-bonds generated for 'chain 'A' and resid 1088 through 1091' Processing helix chain 'A' and resid 1108 through 1119 removed outlier: 3.560A pdb=" N VAL A1114 " --> pdb=" O LYS A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1138 No H-bonds generated for 'chain 'A' and resid 1135 through 1138' Processing helix chain 'A' and resid 1166 through 1174 removed outlier: 4.194A pdb=" N ALA A1170 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL A1173 " --> pdb=" O ALA A1170 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A1174 " --> pdb=" O ARG A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1182 Processing helix chain 'A' and resid 1184 through 1196 removed outlier: 3.548A pdb=" N ILE A1188 " --> pdb=" O LEU A1184 " (cutoff:3.500A) Proline residue: A1189 - end of helix removed outlier: 3.567A pdb=" N PHE A1192 " --> pdb=" O ILE A1188 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET A1196 " --> pdb=" O PHE A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1238 Processing helix chain 'A' and resid 1248 through 1251 No H-bonds generated for 'chain 'A' and resid 1248 through 1251' Processing helix chain 'A' and resid 1253 through 1260 removed outlier: 3.549A pdb=" N ARG A1257 " --> pdb=" O GLN A1254 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1258 " --> pdb=" O LEU A1255 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A1260 " --> pdb=" O ARG A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1292 removed outlier: 4.046A pdb=" N TRP A1272 " --> pdb=" O ARG A1268 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A1282 " --> pdb=" O LEU A1278 " (cutoff:3.500A) Proline residue: A1288 - end of helix removed outlier: 3.784A pdb=" N VAL A1291 " --> pdb=" O PHE A1287 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A1292 " --> pdb=" O PRO A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1328 removed outlier: 3.653A pdb=" N ILE A1318 " --> pdb=" O TYR A1314 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS A1323 " --> pdb=" O ALA A1319 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1346 removed outlier: 3.601A pdb=" N ALA A1343 " --> pdb=" O GLY A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1349 through 1355 removed outlier: 3.536A pdb=" N THR A1353 " --> pdb=" O VAL A1349 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY A1354 " --> pdb=" O PHE A1350 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1373 removed outlier: 3.755A pdb=" N TYR A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1385 removed outlier: 3.679A pdb=" N PHE A1383 " --> pdb=" O TRP A1379 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1403 Proline residue: A1392 - end of helix removed outlier: 4.033A pdb=" N LYS A1401 " --> pdb=" O ASP A1397 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A1403 " --> pdb=" O PHE A1399 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1416 removed outlier: 3.566A pdb=" N GLN A1416 " --> pdb=" O ARG A1412 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 89 through 99 removed outlier: 4.297A pdb=" N LYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 190 No H-bonds generated for 'chain 'B' and resid 187 through 190' Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 267 through 269 No H-bonds generated for 'chain 'B' and resid 267 through 269' Processing helix chain 'B' and resid 309 through 312 No H-bonds generated for 'chain 'B' and resid 309 through 312' Processing helix chain 'B' and resid 373 through 394 removed outlier: 3.920A pdb=" N TYR B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 385 " --> pdb=" O GLY B 381 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 406 through 409 removed outlier: 3.631A pdb=" N GLY A 520 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 432 through 434 removed outlier: 4.102A pdb=" N TYR A 432 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 485 through 488 removed outlier: 4.146A pdb=" N MET A 485 " --> pdb=" O GLU A 498 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP A 487 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 496 " --> pdb=" O TRP A 487 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 682 through 684 Processing sheet with id= E, first strand: chain 'A' and resid 781 through 783 removed outlier: 3.555A pdb=" N ASP A 793 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 825 through 827 removed outlier: 3.648A pdb=" N ILE A 830 " --> pdb=" O MET A 827 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 848 through 851 removed outlier: 3.545A pdb=" N CYS A 851 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA A 914 " --> pdb=" O CYS A 870 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLN A 915 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU A 957 " --> pdb=" O GLN A 915 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 127 through 129 removed outlier: 6.512A pdb=" N TYR B 177 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU B 326 " --> pdb=" O TYR B 177 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 141 through 144 removed outlier: 3.557A pdb=" N ARG B 143 " --> pdb=" O GLN B 160 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 4.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1984 1.32 - 1.44: 3402 1.44 - 1.57: 6875 1.57 - 1.69: 6 1.69 - 1.82: 86 Bond restraints: 12353 Sorted by residual: bond pdb=" O3A ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.698 1.599 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O2B ACP A1601 " pdb=" PB ACP A1601 " ideal model delta sigma weight residual 1.507 1.606 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" N ILE B 214 " pdb=" CA ILE B 214 " ideal model delta sigma weight residual 1.460 1.406 0.054 1.10e-02 8.26e+03 2.40e+01 bond pdb=" C GLU A1028 " pdb=" N PRO A1029 " ideal model delta sigma weight residual 1.337 1.391 -0.054 1.24e-02 6.50e+03 1.92e+01 bond pdb=" C ILE B 214 " pdb=" O ILE B 214 " ideal model delta sigma weight residual 1.236 1.192 0.044 1.03e-02 9.43e+03 1.81e+01 ... (remaining 12348 not shown) Histogram of bond angle deviations from ideal: 98.90 - 106.29: 311 106.29 - 113.68: 6765 113.68 - 121.07: 6094 121.07 - 128.46: 3488 128.46 - 135.85: 103 Bond angle restraints: 16761 Sorted by residual: angle pdb=" C ILE B 214 " pdb=" CA ILE B 214 " pdb=" CB ILE B 214 " ideal model delta sigma weight residual 111.08 103.81 7.27 1.17e+00 7.31e-01 3.86e+01 angle pdb=" N VAL A1311 " pdb=" CA VAL A1311 " pdb=" C VAL A1311 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" C MET A1187 " pdb=" N ILE A1188 " pdb=" CA ILE A1188 " ideal model delta sigma weight residual 120.24 123.75 -3.51 6.30e-01 2.52e+00 3.10e+01 angle pdb=" C LYS A 668 " pdb=" N THR A 669 " pdb=" CA THR A 669 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C CYS A1102 " pdb=" N CYS A1103 " pdb=" CA CYS A1103 " ideal model delta sigma weight residual 123.47 131.75 -8.28 1.53e+00 4.27e-01 2.93e+01 ... (remaining 16756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.24: 7279 35.24 - 70.48: 82 70.48 - 105.72: 13 105.72 - 140.96: 0 140.96 - 176.20: 1 Dihedral angle restraints: 7375 sinusoidal: 3002 harmonic: 4373 Sorted by residual: dihedral pdb=" CA LEU A1101 " pdb=" C LEU A1101 " pdb=" N CYS A1102 " pdb=" CA CYS A1102 " ideal model delta harmonic sigma weight residual -180.00 -136.42 -43.58 0 5.00e+00 4.00e-02 7.60e+01 dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 159 " pdb=" CB CYS B 159 " ideal model delta sinusoidal sigma weight residual -86.00 -28.45 -57.55 1 1.00e+01 1.00e-02 4.45e+01 dihedral pdb=" CA PHE B 398 " pdb=" C PHE B 398 " pdb=" N GLY B 399 " pdb=" CA GLY B 399 " ideal model delta harmonic sigma weight residual 180.00 148.68 31.32 0 5.00e+00 4.00e-02 3.92e+01 ... (remaining 7372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1399 0.064 - 0.128: 390 0.128 - 0.192: 52 0.192 - 0.256: 18 0.256 - 0.320: 6 Chirality restraints: 1865 Sorted by residual: chirality pdb=" CB ILE A 836 " pdb=" CA ILE A 836 " pdb=" CG1 ILE A 836 " pdb=" CG2 ILE A 836 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA ASN A 675 " pdb=" N ASN A 675 " pdb=" C ASN A 675 " pdb=" CB ASN A 675 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A1072 " pdb=" CA ILE A1072 " pdb=" CG1 ILE A1072 " pdb=" CG2 ILE A1072 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 1862 not shown) Planarity restraints: 2124 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1408 " 0.031 2.00e-02 2.50e+03 5.98e-02 3.58e+01 pdb=" C VAL A1408 " -0.104 2.00e-02 2.50e+03 pdb=" O VAL A1408 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU A1409 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 398 " 0.029 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" C PHE B 398 " -0.099 2.00e-02 2.50e+03 pdb=" O PHE B 398 " 0.037 2.00e-02 2.50e+03 pdb=" N GLY B 399 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 986 " -0.023 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP A 986 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 986 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 986 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 986 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 986 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 986 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 986 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 986 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 986 " -0.006 2.00e-02 2.50e+03 ... (remaining 2121 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 226 2.66 - 3.22: 10944 3.22 - 3.78: 18703 3.78 - 4.34: 26106 4.34 - 4.90: 41500 Nonbonded interactions: 97479 Sorted by model distance: nonbonded pdb=" NE2 HIS B 209 " pdb=" OG SER B 220 " model vdw 2.099 2.520 nonbonded pdb=" N ASP B 210 " pdb=" OD1 ASP B 210 " model vdw 2.215 2.520 nonbonded pdb=" OH TYR A1193 " pdb=" OE1 GLN A1280 " model vdw 2.243 2.440 nonbonded pdb=" O THR A1353 " pdb=" OG SER A1357 " model vdw 2.250 2.440 nonbonded pdb=" O3G ACP A1601 " pdb="MG MG A1602 " model vdw 2.254 2.170 ... (remaining 97474 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.540 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: 0.010 Extract box with map and model: 7.990 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 34.140 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 0.007 0.099 12353 Z= 0.430 Angle : 1.085 13.725 16761 Z= 0.585 Chirality : 0.063 0.320 1865 Planarity : 0.007 0.070 2123 Dihedral : 12.541 176.197 4565 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.50 % Favored : 90.36 % Rotamer: Outliers : 0.46 % Allowed : 3.61 % Favored : 95.93 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.04 (0.14), residues: 1494 helix: -4.69 (0.09), residues: 536 sheet: -3.88 (0.36), residues: 128 loop : -3.64 (0.16), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP B 308 HIS 0.013 0.002 HIS A 216 PHE 0.030 0.003 PHE A1287 TYR 0.030 0.003 TYR A1217 ARG 0.006 0.001 ARG B 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASN cc_start: 0.7842 (t0) cc_final: 0.7468 (t0) REVERT: A 740 TYR cc_start: 0.6855 (p90) cc_final: 0.6138 (p90) REVERT: A 945 GLU cc_start: 0.7323 (tt0) cc_final: 0.6957 (tt0) REVERT: A 1097 CYS cc_start: 0.7329 (p) cc_final: 0.7069 (p) REVERT: A 1139 GLN cc_start: 0.6897 (mt0) cc_final: 0.6677 (pt0) REVERT: A 1296 MET cc_start: 0.8377 (mmm) cc_final: 0.8060 (mmt) REVERT: A 1306 ASP cc_start: 0.7188 (p0) cc_final: 0.6944 (t0) REVERT: A 1321 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7448 (mp) outliers start: 6 outliers final: 3 residues processed: 197 average time/residue: 0.2698 time to fit residues: 75.1486 Evaluate side-chains 110 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 106 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 1321 ILE Chi-restraints excluded: chain B residue 212 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 475 HIS A 484 ASN A 550 ASN A 736 ASN A 778 HIS A 831 GLN A1139 GLN A1307 HIS B 155 GLN B 172 ASN B 256 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12353 Z= 0.207 Angle : 0.676 9.917 16761 Z= 0.351 Chirality : 0.046 0.207 1865 Planarity : 0.005 0.043 2123 Dihedral : 10.344 174.060 1738 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 2.00 % Allowed : 7.37 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.17), residues: 1494 helix: -3.30 (0.16), residues: 544 sheet: -3.58 (0.36), residues: 136 loop : -3.33 (0.18), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1415 HIS 0.004 0.001 HIS A1307 PHE 0.037 0.002 PHE A 679 TYR 0.024 0.002 TYR A1040 ARG 0.009 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 200 LYS cc_start: 0.4628 (pttm) cc_final: 0.4413 (mtpt) REVERT: A 477 ASN cc_start: 0.7645 (t0) cc_final: 0.7111 (t0) REVERT: A 482 GLN cc_start: 0.6481 (pm20) cc_final: 0.6046 (mp10) REVERT: A 827 MET cc_start: 0.8327 (ppp) cc_final: 0.8059 (ppp) REVERT: A 942 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8016 (t0) REVERT: A 1006 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8328 (pp) REVERT: B 84 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8440 (p) outliers start: 26 outliers final: 13 residues processed: 136 average time/residue: 0.2301 time to fit residues: 47.1962 Evaluate side-chains 105 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 942 ASP Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 75 optimal weight: 0.0170 chunk 41 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 135 optimal weight: 0.0000 chunk 146 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 134 optimal weight: 0.0000 chunk 46 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.2426 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 831 GLN A 927 ASN A 998 ASN A1139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12353 Z= 0.144 Angle : 0.609 8.452 16761 Z= 0.315 Chirality : 0.044 0.178 1865 Planarity : 0.004 0.043 2123 Dihedral : 9.047 172.917 1735 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.50 % Favored : 92.44 % Rotamer: Outliers : 2.07 % Allowed : 9.98 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.19), residues: 1494 helix: -2.35 (0.19), residues: 548 sheet: -3.00 (0.38), residues: 147 loop : -3.09 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 517 HIS 0.003 0.001 HIS A 899 PHE 0.018 0.001 PHE A 679 TYR 0.028 0.001 TYR A1040 ARG 0.005 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 224 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7290 (tp) REVERT: A 267 VAL cc_start: 0.7180 (OUTLIER) cc_final: 0.6946 (t) REVERT: A 477 ASN cc_start: 0.7570 (t0) cc_final: 0.7069 (t0) REVERT: A 482 GLN cc_start: 0.6357 (pm20) cc_final: 0.6051 (mp10) REVERT: A 827 MET cc_start: 0.8319 (ppp) cc_final: 0.8041 (ppp) REVERT: A 852 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6856 (mt) REVERT: A 942 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8103 (t0) REVERT: A 1263 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7884 (tmtt) outliers start: 27 outliers final: 12 residues processed: 128 average time/residue: 0.2250 time to fit residues: 44.4051 Evaluate side-chains 106 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 942 ASP Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 133 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.0570 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 704 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12353 Z= 0.172 Angle : 0.588 6.916 16761 Z= 0.304 Chirality : 0.044 0.177 1865 Planarity : 0.003 0.044 2123 Dihedral : 8.619 172.495 1735 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.76 % Allowed : 10.60 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.20), residues: 1494 helix: -1.84 (0.21), residues: 544 sheet: -2.86 (0.39), residues: 147 loop : -2.96 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 348 HIS 0.004 0.001 HIS A 899 PHE 0.019 0.001 PHE A1399 TYR 0.025 0.001 TYR A1040 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 267 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7044 (t) REVERT: A 477 ASN cc_start: 0.7567 (t0) cc_final: 0.7004 (t0) REVERT: A 482 GLN cc_start: 0.6305 (pm20) cc_final: 0.5997 (mp10) REVERT: A 771 MET cc_start: 0.7967 (mmt) cc_final: 0.7597 (mmt) REVERT: A 827 MET cc_start: 0.8341 (ppp) cc_final: 0.8030 (ppp) REVERT: A 852 ILE cc_start: 0.7308 (OUTLIER) cc_final: 0.6712 (mt) REVERT: A 1306 ASP cc_start: 0.6688 (OUTLIER) cc_final: 0.6322 (p0) outliers start: 36 outliers final: 25 residues processed: 131 average time/residue: 0.2077 time to fit residues: 42.6451 Evaluate side-chains 120 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 92 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 119 optimal weight: 0.0570 chunk 81 optimal weight: 0.3980 chunk 2 optimal weight: 0.7980 chunk 107 optimal weight: 0.0570 chunk 59 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12353 Z= 0.181 Angle : 0.586 8.805 16761 Z= 0.299 Chirality : 0.044 0.181 1865 Planarity : 0.003 0.045 2123 Dihedral : 8.266 173.209 1733 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.43 % Favored : 92.50 % Rotamer: Outliers : 3.30 % Allowed : 10.45 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.20), residues: 1494 helix: -1.47 (0.22), residues: 543 sheet: -2.43 (0.42), residues: 137 loop : -2.87 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 986 HIS 0.004 0.001 HIS A 899 PHE 0.025 0.002 PHE A1382 TYR 0.025 0.002 TYR A1040 ARG 0.003 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 99 time to evaluate : 1.380 Fit side-chains REVERT: A 267 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.7061 (t) REVERT: A 477 ASN cc_start: 0.7575 (t0) cc_final: 0.6950 (t0) REVERT: A 482 GLN cc_start: 0.6326 (pm20) cc_final: 0.5986 (mp10) REVERT: A 827 MET cc_start: 0.8210 (ppp) cc_final: 0.7941 (ppp) REVERT: A 849 MET cc_start: 0.5115 (tpt) cc_final: 0.4734 (tpt) REVERT: A 852 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6775 (mt) REVERT: A 1306 ASP cc_start: 0.6625 (OUTLIER) cc_final: 0.6270 (p0) outliers start: 43 outliers final: 30 residues processed: 132 average time/residue: 0.1938 time to fit residues: 39.9983 Evaluate side-chains 121 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 88 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 119 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 0.0170 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12353 Z= 0.201 Angle : 0.589 8.721 16761 Z= 0.301 Chirality : 0.044 0.181 1865 Planarity : 0.003 0.045 2123 Dihedral : 8.227 173.349 1733 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.97 % Favored : 91.97 % Rotamer: Outliers : 3.00 % Allowed : 12.60 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.20), residues: 1494 helix: -1.30 (0.22), residues: 540 sheet: -2.28 (0.44), residues: 137 loop : -2.81 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 986 HIS 0.004 0.001 HIS A 899 PHE 0.026 0.002 PHE A1382 TYR 0.023 0.002 TYR A1040 ARG 0.003 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 95 time to evaluate : 1.318 Fit side-chains REVERT: A 246 PRO cc_start: 0.8152 (Cg_exo) cc_final: 0.7791 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7421 (OUTLIER) cc_final: 0.7108 (t) REVERT: A 477 ASN cc_start: 0.7561 (t0) cc_final: 0.6916 (t0) REVERT: A 482 GLN cc_start: 0.6294 (pm20) cc_final: 0.5976 (mp10) REVERT: A 771 MET cc_start: 0.7859 (mmt) cc_final: 0.7503 (mmt) REVERT: A 827 MET cc_start: 0.8191 (ppp) cc_final: 0.7853 (ppp) REVERT: A 849 MET cc_start: 0.5318 (tpt) cc_final: 0.5034 (tpt) REVERT: A 852 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6653 (mt) REVERT: A 1306 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6280 (p0) outliers start: 39 outliers final: 32 residues processed: 127 average time/residue: 0.2201 time to fit residues: 42.6953 Evaluate side-chains 123 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 88 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 567 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 138 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 143 optimal weight: 0.3980 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12353 Z= 0.166 Angle : 0.571 8.033 16761 Z= 0.292 Chirality : 0.043 0.170 1865 Planarity : 0.003 0.046 2123 Dihedral : 8.109 173.304 1733 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.63 % Favored : 92.30 % Rotamer: Outliers : 3.00 % Allowed : 12.75 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.21), residues: 1494 helix: -1.14 (0.23), residues: 542 sheet: -2.18 (0.45), residues: 137 loop : -2.73 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 314 HIS 0.004 0.001 HIS A 899 PHE 0.027 0.001 PHE A1382 TYR 0.023 0.001 TYR A1040 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 90 time to evaluate : 1.538 Fit side-chains REVERT: A 246 PRO cc_start: 0.8085 (Cg_exo) cc_final: 0.7737 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7190 (t) REVERT: A 477 ASN cc_start: 0.7479 (t0) cc_final: 0.6889 (t0) REVERT: A 771 MET cc_start: 0.7861 (mmt) cc_final: 0.7504 (mmt) REVERT: A 827 MET cc_start: 0.8186 (ppp) cc_final: 0.7981 (ppp) REVERT: A 852 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6709 (mt) REVERT: A 1306 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.6193 (p0) outliers start: 39 outliers final: 26 residues processed: 120 average time/residue: 0.2039 time to fit residues: 39.1936 Evaluate side-chains 114 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 351 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 88 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 85 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 71 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 660 GLN ** A1067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12353 Z= 0.168 Angle : 0.585 10.547 16761 Z= 0.294 Chirality : 0.043 0.169 1865 Planarity : 0.003 0.046 2123 Dihedral : 8.056 173.376 1733 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 3.38 % Allowed : 13.21 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.21), residues: 1494 helix: -1.01 (0.23), residues: 535 sheet: -2.16 (0.45), residues: 138 loop : -2.68 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 986 HIS 0.003 0.001 HIS A 899 PHE 0.026 0.001 PHE A1382 TYR 0.022 0.001 TYR A1040 ARG 0.002 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 90 time to evaluate : 1.398 Fit side-chains REVERT: A 246 PRO cc_start: 0.8020 (Cg_exo) cc_final: 0.7679 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7201 (t) REVERT: A 477 ASN cc_start: 0.7480 (t0) cc_final: 0.6909 (t0) REVERT: A 827 MET cc_start: 0.8144 (ppp) cc_final: 0.7938 (ppp) REVERT: A 852 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6632 (mt) REVERT: A 1306 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.6259 (p0) outliers start: 44 outliers final: 36 residues processed: 124 average time/residue: 0.2064 time to fit residues: 40.4397 Evaluate side-chains 124 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 130 optimal weight: 0.0470 chunk 137 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12353 Z= 0.188 Angle : 0.585 9.863 16761 Z= 0.295 Chirality : 0.044 0.170 1865 Planarity : 0.003 0.045 2123 Dihedral : 8.009 173.107 1733 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 3.30 % Allowed : 13.44 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.21), residues: 1494 helix: -0.92 (0.23), residues: 536 sheet: -2.16 (0.45), residues: 138 loop : -2.63 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 986 HIS 0.005 0.001 HIS A 899 PHE 0.024 0.002 PHE A1382 TYR 0.021 0.001 TYR A1040 ARG 0.005 0.000 ARG A1104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 85 time to evaluate : 1.250 Fit side-chains REVERT: A 246 PRO cc_start: 0.7993 (Cg_exo) cc_final: 0.7658 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7475 (OUTLIER) cc_final: 0.7169 (t) REVERT: A 477 ASN cc_start: 0.7489 (t0) cc_final: 0.6898 (t0) REVERT: A 771 MET cc_start: 0.7881 (mmt) cc_final: 0.7505 (mmt) REVERT: A 852 ILE cc_start: 0.7137 (OUTLIER) cc_final: 0.6655 (mt) REVERT: A 1006 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (pp) REVERT: A 1306 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6283 (p0) REVERT: B 343 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6696 (m-30) outliers start: 43 outliers final: 37 residues processed: 118 average time/residue: 0.1953 time to fit residues: 36.4712 Evaluate side-chains 126 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 84 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 989 THR Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1306 ASP Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1344 LEU Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 202 ASP Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 141 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 148 optimal weight: 0.0040 chunk 136 optimal weight: 0.0170 chunk 118 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 overall best weight: 0.3230 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12353 Z= 0.140 Angle : 0.561 8.881 16761 Z= 0.284 Chirality : 0.043 0.168 1865 Planarity : 0.003 0.047 2123 Dihedral : 7.825 173.470 1733 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.92 % Allowed : 13.98 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.21), residues: 1494 helix: -0.79 (0.23), residues: 543 sheet: -2.05 (0.46), residues: 138 loop : -2.59 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 517 HIS 0.004 0.001 HIS A 899 PHE 0.021 0.001 PHE A1382 TYR 0.023 0.001 TYR A1040 ARG 0.002 0.000 ARG A 909 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 92 time to evaluate : 1.424 Fit side-chains REVERT: A 246 PRO cc_start: 0.7884 (Cg_exo) cc_final: 0.7621 (Cg_endo) REVERT: A 267 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.7097 (t) REVERT: A 477 ASN cc_start: 0.7463 (t0) cc_final: 0.6875 (t0) REVERT: A 502 ILE cc_start: 0.6183 (tp) cc_final: 0.5868 (tp) REVERT: A 771 MET cc_start: 0.7928 (mmt) cc_final: 0.7577 (mmt) REVERT: A 827 MET cc_start: 0.8245 (ppp) cc_final: 0.7969 (ppp) REVERT: A 852 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6533 (mt) REVERT: A 1006 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8300 (pp) REVERT: B 343 ASP cc_start: 0.6951 (OUTLIER) cc_final: 0.6732 (m-30) outliers start: 38 outliers final: 31 residues processed: 119 average time/residue: 0.2170 time to fit residues: 40.8075 Evaluate side-chains 121 residues out of total 1302 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 963 ILE Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain A residue 995 THR Chi-restraints excluded: chain A residue 1006 LEU Chi-restraints excluded: chain A residue 1013 LEU Chi-restraints excluded: chain A residue 1126 LEU Chi-restraints excluded: chain A residue 1128 ILE Chi-restraints excluded: chain A residue 1163 ILE Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1381 VAL Chi-restraints excluded: chain A residue 1433 ASN Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 280 TYR Chi-restraints excluded: chain B residue 343 ASP Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 377 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 149 random chunks: chunk 125 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 ASN ** 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 = 0.3928 r_free = 0.3928 target = 0.131946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098739 restraints weight = 20085.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097370 restraints weight = 18561.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.098674 restraints weight = 16429.024| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12353 Z= 0.217 Angle : 0.608 9.345 16761 Z= 0.308 Chirality : 0.045 0.173 1865 Planarity : 0.003 0.047 2123 Dihedral : 7.946 173.562 1733 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 3.15 % Allowed : 13.98 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.21), residues: 1494 helix: -0.81 (0.23), residues: 549 sheet: -2.08 (0.46), residues: 138 loop : -2.63 (0.20), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 986 HIS 0.004 0.001 HIS A 899 PHE 0.021 0.002 PHE A1382 TYR 0.021 0.002 TYR A 689 ARG 0.005 0.000 ARG A 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2369.84 seconds wall clock time: 44 minutes 23.04 seconds (2663.04 seconds total)