Starting phenix.real_space_refine on Fri Mar 22 12:21:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1x_20614/03_2024/6u1x_20614.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1x_20614/03_2024/6u1x_20614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1x_20614/03_2024/6u1x_20614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1x_20614/03_2024/6u1x_20614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1x_20614/03_2024/6u1x_20614.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u1x_20614/03_2024/6u1x_20614.pdb" } resolution = 3.0 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= -0.004 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 92 5.16 5 C 10694 2.51 5 N 2907 2.21 5 O 3066 1.98 5 H 16768 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 595": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1275": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1295": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1360": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1504": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1569": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1621": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1781": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1797": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1816": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1882": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2057": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33529 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 33096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2059, 33096 Classifications: {'peptide': 2059} Link IDs: {'PTRANS': 97, 'TRANS': 1961} Chain breaks: 3 Chain: "P" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 431 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain breaks: 2 Chain: "A" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 17047 SG CYS A1081 67.106 70.840 82.524 1.00 67.09 S ATOM 20315 SG CYS A1299 67.893 67.213 81.956 1.00 71.67 S ATOM 20358 SG CYS A1302 65.606 68.756 79.521 1.00 71.70 S ATOM 17656 SG CYS A1120 66.119 51.227 72.920 1.00 74.28 S ATOM 17690 SG CYS A1123 62.607 50.900 73.847 1.00 75.85 S Time building chain proxies: 13.96, per 1000 atoms: 0.42 Number of scatterers: 33529 At special positions: 0 Unit cell: (124.16, 132.89, 100.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 92 16.00 O 3066 8.00 N 2907 7.00 C 10694 6.00 H 16768 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.25 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3000 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1299 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1081 " pdb="ZN ZN A3000 " - pdb=" SG CYS A1302 " pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1294 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1296 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1123 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1120 " Number of angles added : 2 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 12 sheets defined 52.7% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.00 Creating SS restraints... Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.522A pdb=" N LEU A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 68 removed outlier: 3.572A pdb=" N ASP A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 68' Processing helix chain 'A' and resid 71 through 80 Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.683A pdb=" N SER A 97 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 135 removed outlier: 3.598A pdb=" N ILE A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 Processing helix chain 'A' and resid 147 through 172 removed outlier: 4.247A pdb=" N ILE A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 227 through 247 removed outlier: 3.526A pdb=" N LEU A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.556A pdb=" N ILE A 261 " --> pdb=" O SER A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 288 through 302 removed outlier: 3.542A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 327 removed outlier: 4.401A pdb=" N GLU A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 340 removed outlier: 3.698A pdb=" N PHE A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 340 " --> pdb=" O HIS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 353 removed outlier: 3.883A pdb=" N THR A 348 " --> pdb=" O THR A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 377 Processing helix chain 'A' and resid 383 through 407 removed outlier: 3.749A pdb=" N ALA A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 428 Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.613A pdb=" N GLN A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 443 through 447 removed outlier: 3.562A pdb=" N LEU A 447 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 484 Processing helix chain 'A' and resid 494 through 501 Processing helix chain 'A' and resid 505 through 517 Processing helix chain 'A' and resid 545 through 563 Processing helix chain 'A' and resid 564 through 567 Processing helix chain 'A' and resid 575 through 587 Processing helix chain 'A' and resid 614 through 629 Proline residue: A 620 - end of helix removed outlier: 3.714A pdb=" N MET A 625 " --> pdb=" O VAL A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 643 Processing helix chain 'A' and resid 684 through 704 Processing helix chain 'A' and resid 729 through 759 removed outlier: 3.636A pdb=" N LEU A 733 " --> pdb=" O ASN A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 removed outlier: 3.968A pdb=" N ARG A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 825 removed outlier: 3.687A pdb=" N SER A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 815 " --> pdb=" O ILE A 811 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 850 removed outlier: 3.745A pdb=" N HIS A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 880 removed outlier: 3.985A pdb=" N LEU A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 896 removed outlier: 3.540A pdb=" N ARG A 894 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 918 removed outlier: 3.548A pdb=" N LEU A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.616A pdb=" N LYS A 924 " --> pdb=" O SER A 920 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 926 " --> pdb=" O HIS A 922 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY A 931 " --> pdb=" O SER A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.507A pdb=" N LEU A 946 " --> pdb=" O HIS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 976 Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 1006 removed outlier: 3.612A pdb=" N SER A1001 " --> pdb=" O ASP A 997 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A1006 " --> pdb=" O PHE A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1020 Processing helix chain 'A' and resid 1023 through 1031 removed outlier: 3.810A pdb=" N LEU A1029 " --> pdb=" O VAL A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1043 Processing helix chain 'A' and resid 1045 through 1069 removed outlier: 4.106A pdb=" N ARG A1049 " --> pdb=" O LYS A1045 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A1051 " --> pdb=" O TYR A1047 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP A1052 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASP A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU A1054 " --> pdb=" O GLU A1050 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A1059 " --> pdb=" O ILE A1055 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N HIS A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1105 through 1110 Processing helix chain 'A' and resid 1121 through 1126 removed outlier: 4.080A pdb=" N THR A1125 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1121 through 1126' Processing helix chain 'A' and resid 1174 through 1181 Processing helix chain 'A' and resid 1182 through 1186 Processing helix chain 'A' and resid 1196 through 1208 removed outlier: 3.617A pdb=" N ILE A1204 " --> pdb=" O ILE A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1243 through 1248 removed outlier: 4.187A pdb=" N LEU A1247 " --> pdb=" O SER A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1263 removed outlier: 3.835A pdb=" N ASP A1262 " --> pdb=" O ASP A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1268 through 1284 removed outlier: 3.535A pdb=" N THR A1272 " --> pdb=" O LEU A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1377 Processing helix chain 'A' and resid 1379 through 1383 Processing helix chain 'A' and resid 1388 through 1392 removed outlier: 3.829A pdb=" N ILE A1391 " --> pdb=" O PRO A1388 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A1392 " --> pdb=" O LEU A1389 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1388 through 1392' Processing helix chain 'A' and resid 1396 through 1417 removed outlier: 3.529A pdb=" N PHE A1400 " --> pdb=" O ARG A1396 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE A1417 " --> pdb=" O CYS A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1427 through 1444 removed outlier: 3.737A pdb=" N ALA A1431 " --> pdb=" O ARG A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1451 Processing helix chain 'A' and resid 1456 through 1463 Processing helix chain 'A' and resid 1476 through 1493 removed outlier: 3.633A pdb=" N ILE A1483 " --> pdb=" O ASP A1479 " (cutoff:3.500A) Processing helix chain 'A' and resid 1510 through 1514 Processing helix chain 'A' and resid 1515 through 1534 Proline residue: A1521 - end of helix removed outlier: 4.568A pdb=" N THR A1526 " --> pdb=" O PHE A1522 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR A1527 " --> pdb=" O SER A1523 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A1528 " --> pdb=" O ILE A1524 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN A1530 " --> pdb=" O THR A1526 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS A1534 " --> pdb=" O GLN A1530 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1557 Processing helix chain 'A' and resid 1564 through 1568 removed outlier: 4.004A pdb=" N LYS A1567 " --> pdb=" O ILE A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1583 removed outlier: 3.520A pdb=" N HIS A1582 " --> pdb=" O GLU A1579 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A1583 " --> pdb=" O ILE A1580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1579 through 1583' Processing helix chain 'A' and resid 1634 through 1640 Processing helix chain 'A' and resid 1648 through 1659 Processing helix chain 'A' and resid 1674 through 1684 Processing helix chain 'A' and resid 1710 through 1716 removed outlier: 3.529A pdb=" N LEU A1713 " --> pdb=" O PRO A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1719 through 1723 removed outlier: 3.636A pdb=" N ARG A1722 " --> pdb=" O ASP A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1753 removed outlier: 4.076A pdb=" N TRP A1742 " --> pdb=" O ASP A1738 " (cutoff:3.500A) Processing helix chain 'A' and resid 1767 through 1780 removed outlier: 3.535A pdb=" N SER A1771 " --> pdb=" O ASP A1767 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A1780 " --> pdb=" O THR A1776 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1786 Processing helix chain 'A' and resid 1798 through 1804 Processing helix chain 'A' and resid 1807 through 1815 Proline residue: A1814 - end of helix Processing helix chain 'A' and resid 1851 through 1854 Processing helix chain 'A' and resid 1855 through 1860 removed outlier: 4.322A pdb=" N LYS A1860 " --> pdb=" O ASN A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1867 through 1880 removed outlier: 3.503A pdb=" N GLU A1871 " --> pdb=" O SER A1867 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A1874 " --> pdb=" O GLN A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1892 removed outlier: 3.547A pdb=" N PHE A1891 " --> pdb=" O PRO A1888 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A1892 " --> pdb=" O SER A1889 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1888 through 1892' Processing helix chain 'A' and resid 1894 through 1906 removed outlier: 3.514A pdb=" N GLU A1900 " --> pdb=" O PHE A1896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1909 through 1923 removed outlier: 3.619A pdb=" N SER A1920 " --> pdb=" O ALA A1916 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A1921 " --> pdb=" O ALA A1917 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A1923 " --> pdb=" O LYS A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1943 Processing helix chain 'A' and resid 1961 through 1980 removed outlier: 3.744A pdb=" N TRP A1974 " --> pdb=" O GLY A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1994 Processing helix chain 'A' and resid 2029 through 2045 removed outlier: 3.769A pdb=" N ILE A2033 " --> pdb=" O SER A2029 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A2037 " --> pdb=" O ILE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2053 through 2063 removed outlier: 3.688A pdb=" N THR A2063 " --> pdb=" O GLN A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2071 through 2076 removed outlier: 3.836A pdb=" N ARG A2075 " --> pdb=" O SER A2071 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A2076 " --> pdb=" O ASN A2072 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2071 through 2076' Processing helix chain 'A' and resid 2078 through 2084 Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 Processing sheet with id=AA2, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA3, first strand: chain 'A' and resid 524 through 525 Processing sheet with id=AA4, first strand: chain 'A' and resid 707 through 711 removed outlier: 4.411A pdb=" N GLN A 716 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 770 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 707 through 711 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 Processing sheet with id=AA7, first strand: chain 'A' and resid 773 through 775 Processing sheet with id=AA8, first strand: chain 'A' and resid 1114 through 1115 removed outlier: 3.726A pdb=" N SER A1132 " --> pdb=" O THR A1253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1151 through 1155 removed outlier: 5.333A pdb=" N TYR A1152 " --> pdb=" O TRP A2107 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASP A2109 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY A1154 " --> pdb=" O ASP A2109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1346 through 1347 removed outlier: 6.973A pdb=" N LEU A1346 " --> pdb=" O LEU A1575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1609 through 1613 removed outlier: 7.033A pdb=" N GLY A1840 " --> pdb=" O LYS A1817 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL A1819 " --> pdb=" O CYS A1838 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N CYS A1838 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A1821 " --> pdb=" O MET A1836 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET A1836 " --> pdb=" O LEU A1821 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLN A1823 " --> pdb=" O VAL A1834 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N VAL A1834 " --> pdb=" O GLN A1823 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU A1667 " --> pdb=" O VAL A1760 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2010 through 2014 733 hydrogen bonds defined for protein. 2106 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: 13.75 Time building geometry restraints manager: 26.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16739 1.03 - 1.23: 29 1.23 - 1.42: 7198 1.42 - 1.62: 9807 1.62 - 1.81: 150 Bond restraints: 33923 Sorted by residual: bond pdb=" C ASN A1633 " pdb=" N PRO A1634 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.38e+00 bond pdb=" C LEU A1644 " pdb=" N PRO A1645 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.03e+00 bond pdb=" C LYS A1534 " pdb=" N PRO A1535 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.30e-02 5.92e+03 1.07e+00 bond pdb=" CG PRO A1106 " pdb=" CD PRO A1106 " ideal model delta sigma weight residual 1.503 1.470 0.033 3.40e-02 8.65e+02 9.69e-01 bond pdb=" CB PRO A1645 " pdb=" CG PRO A1645 " ideal model delta sigma weight residual 1.492 1.448 0.044 5.00e-02 4.00e+02 7.72e-01 ... (remaining 33918 not shown) Histogram of bond angle deviations from ideal: 98.35 - 105.49: 345 105.49 - 112.64: 39382 112.64 - 119.78: 9001 119.78 - 126.92: 12333 126.92 - 134.07: 274 Bond angle restraints: 61335 Sorted by residual: angle pdb=" N TYR A1473 " pdb=" CA TYR A1473 " pdb=" C TYR A1473 " ideal model delta sigma weight residual 109.41 104.09 5.32 1.53e+00 4.27e-01 1.21e+01 angle pdb=" N LEU A1644 " pdb=" CA LEU A1644 " pdb=" C LEU A1644 " ideal model delta sigma weight residual 109.87 104.87 5.00 1.62e+00 3.81e-01 9.53e+00 angle pdb=" C GLY A1753 " pdb=" N LEU A1754 " pdb=" CA LEU A1754 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.00e+00 angle pdb=" CA TYR A1473 " pdb=" C TYR A1473 " pdb=" N PRO A1474 " ideal model delta sigma weight residual 117.69 120.32 -2.63 9.30e-01 1.16e+00 7.99e+00 angle pdb=" N GLY A2007 " pdb=" CA GLY A2007 " pdb=" C GLY A2007 " ideal model delta sigma weight residual 113.18 108.13 5.05 2.37e+00 1.78e-01 4.55e+00 ... (remaining 61330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 14604 16.91 - 33.81: 1005 33.81 - 50.72: 218 50.72 - 67.62: 103 67.62 - 84.53: 5 Dihedral angle restraints: 15935 sinusoidal: 8694 harmonic: 7241 Sorted by residual: dihedral pdb=" CA TYR A1473 " pdb=" C TYR A1473 " pdb=" N PRO A1474 " pdb=" CA PRO A1474 " ideal model delta harmonic sigma weight residual -180.00 -132.20 -47.80 0 5.00e+00 4.00e-02 9.14e+01 dihedral pdb=" CA GLN A1643 " pdb=" C GLN A1643 " pdb=" N LEU A1644 " pdb=" CA LEU A1644 " ideal model delta harmonic sigma weight residual 180.00 151.31 28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO A1474 " pdb=" C PRO A1474 " pdb=" N THR A1475 " pdb=" CA THR A1475 " ideal model delta harmonic sigma weight residual -180.00 -156.94 -23.06 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 15932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1486 0.028 - 0.056: 749 0.056 - 0.084: 191 0.084 - 0.111: 92 0.111 - 0.139: 43 Chirality restraints: 2561 Sorted by residual: chirality pdb=" CA ILE A1469 " pdb=" N ILE A1469 " pdb=" C ILE A1469 " pdb=" CB ILE A1469 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE A1465 " pdb=" N ILE A1465 " pdb=" C ILE A1465 " pdb=" CB ILE A1465 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE A 455 " pdb=" N ILE A 455 " pdb=" C ILE A 455 " pdb=" CB ILE A 455 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2558 not shown) Planarity restraints: 4933 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1473 " -0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A1474 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A1474 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A1474 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A1060 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C VAL A1060 " 0.038 2.00e-02 2.50e+03 pdb=" O VAL A1060 " -0.014 2.00e-02 2.50e+03 pdb=" N SER A1061 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1058 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C SER A1058 " -0.028 2.00e-02 2.50e+03 pdb=" O SER A1058 " 0.011 2.00e-02 2.50e+03 pdb=" N GLU A1059 " 0.009 2.00e-02 2.50e+03 ... (remaining 4930 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 4119 2.26 - 2.84: 76858 2.84 - 3.43: 84709 3.43 - 4.01: 119679 4.01 - 4.60: 188665 Nonbonded interactions: 474030 Sorted by model distance: nonbonded pdb=" O LYS A 528 " pdb=" H PHE A 541 " model vdw 1.670 1.850 nonbonded pdb=" O SER A 814 " pdb="HD22 ASN A 818 " model vdw 1.673 1.850 nonbonded pdb=" OE1 GLU A 827 " pdb=" H GLU A 827 " model vdw 1.682 1.850 nonbonded pdb=" O GLN A 685 " pdb=" HG1 THR A 689 " model vdw 1.688 1.850 nonbonded pdb=" O ASN A1780 " pdb="HH21 ARG A1784 " model vdw 1.689 1.850 ... (remaining 474025 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 0.490 Extract box with map and model: 15.340 Check model and map are aligned: 0.470 Set scattering table: 0.260 Process input model: 111.870 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 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 : 0.004 0.044 17155 Z= 0.276 Angle : 0.548 5.466 23213 Z= 0.290 Chirality : 0.039 0.139 2561 Planarity : 0.004 0.096 2951 Dihedral : 10.379 84.529 6403 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -3.08 (0.16), residues: 2073 helix: -1.39 (0.14), residues: 1000 sheet: -2.69 (0.36), residues: 135 loop : -2.64 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 609 HIS 0.004 0.001 HIS A1296 PHE 0.012 0.001 PHE A1973 TYR 0.009 0.001 TYR A1744 ARG 0.003 0.000 ARG A 787 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 2.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 821 THR cc_start: 0.9159 (m) cc_final: 0.8955 (m) REVERT: A 973 LEU cc_start: 0.8470 (mp) cc_final: 0.8214 (mt) REVERT: A 1139 ILE cc_start: 0.8657 (mm) cc_final: 0.8451 (mp) REVERT: A 1172 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8089 (mmmt) REVERT: A 1755 GLN cc_start: 0.7314 (mp10) cc_final: 0.6859 (mm-40) REVERT: A 2006 LYS cc_start: 0.7893 (mttm) cc_final: 0.7526 (mppt) REVERT: A 2081 GLU cc_start: 0.7180 (tt0) cc_final: 0.6669 (tt0) outliers start: 2 outliers final: 1 residues processed: 349 average time/residue: 2.6134 time to fit residues: 1027.2001 Evaluate side-chains 207 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1624 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 406 HIS A 590 GLN A 613 GLN A 685 GLN A1264 ASN A1866 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17155 Z= 0.274 Angle : 0.516 5.152 23213 Z= 0.271 Chirality : 0.040 0.142 2561 Planarity : 0.004 0.093 2951 Dihedral : 4.351 45.722 2274 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 1.61 % Allowed : 11.08 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % 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: -2.00 (0.18), residues: 2073 helix: -0.38 (0.16), residues: 1016 sheet: -2.28 (0.36), residues: 137 loop : -2.25 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A2013 HIS 0.006 0.001 HIS A 603 PHE 0.011 0.001 PHE A 842 TYR 0.014 0.001 TYR A 875 ARG 0.006 0.000 ARG A 670 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 2.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.7488 (mtt) cc_final: 0.6909 (mtt) REVERT: A 539 ARG cc_start: 0.8098 (mpp80) cc_final: 0.7799 (mtp85) REVERT: A 890 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.7366 (ppp) REVERT: A 973 LEU cc_start: 0.8418 (mp) cc_final: 0.8191 (mt) REVERT: A 1165 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: A 1172 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8073 (mmmt) REVERT: A 1376 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7756 (mtp180) REVERT: A 1603 ARG cc_start: 0.7176 (ttt-90) cc_final: 0.6864 (ttt90) REVERT: A 1870 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.6527 (tt0) REVERT: A 2006 LYS cc_start: 0.7978 (mttm) cc_final: 0.7616 (mppt) REVERT: P 83 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7700 (mp10) outliers start: 30 outliers final: 16 residues processed: 227 average time/residue: 2.5143 time to fit residues: 650.1455 Evaluate side-chains 207 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 2.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 808 CYS Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 890 MET Chi-restraints excluded: chain A residue 1055 ILE Chi-restraints excluded: chain A residue 1165 GLN Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1540 LYS Chi-restraints excluded: chain A residue 1584 CYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1767 ASP Chi-restraints excluded: chain A residue 1870 GLN Chi-restraints excluded: chain A residue 1976 SER Chi-restraints excluded: chain A residue 2066 ASN Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 932 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17155 Z= 0.214 Angle : 0.482 5.108 23213 Z= 0.252 Chirality : 0.039 0.140 2561 Planarity : 0.004 0.086 2951 Dihedral : 4.160 43.424 2271 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.61 % Allowed : 12.04 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2073 helix: 0.31 (0.16), residues: 1012 sheet: -1.87 (0.37), residues: 137 loop : -1.98 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.003 0.001 HIS A 373 PHE 0.011 0.001 PHE A 842 TYR 0.011 0.001 TYR A1941 ARG 0.003 0.000 ARG A 670 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.7527 (mtt) cc_final: 0.6963 (mtt) REVERT: A 973 LEU cc_start: 0.8448 (mp) cc_final: 0.8209 (mt) REVERT: A 1050 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: A 1165 GLN cc_start: 0.7914 (mp10) cc_final: 0.7635 (mm-40) REVERT: A 1172 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8071 (mmmt) REVERT: A 1376 ARG cc_start: 0.7988 (mtp85) cc_final: 0.7777 (mtp180) REVERT: A 1540 LYS cc_start: 0.7079 (pmmt) cc_final: 0.6512 (pptt) REVERT: A 1763 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7144 (ptp) REVERT: A 2006 LYS cc_start: 0.7939 (mttm) cc_final: 0.7617 (mppt) REVERT: P 83 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7707 (mp10) outliers start: 30 outliers final: 16 residues processed: 217 average time/residue: 2.4704 time to fit residues: 611.2294 Evaluate side-chains 203 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 1050 GLU Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1291 CYS Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1584 CYS Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1802 CYS Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 97 optimal weight: 0.2980 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17155 Z= 0.184 Angle : 0.464 5.468 23213 Z= 0.241 Chirality : 0.038 0.142 2561 Planarity : 0.004 0.085 2951 Dihedral : 4.014 41.107 2271 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.09 % Allowed : 11.94 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.19), residues: 2073 helix: 0.71 (0.17), residues: 1017 sheet: -1.58 (0.39), residues: 137 loop : -1.76 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 94 HIS 0.003 0.001 HIS A 603 PHE 0.009 0.001 PHE A 842 TYR 0.013 0.001 TYR A1941 ARG 0.003 0.000 ARG A 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7081 (tt0) REVERT: A 530 LYS cc_start: 0.8370 (mtpt) cc_final: 0.7707 (mttt) REVERT: A 535 LYS cc_start: 0.8438 (mtpp) cc_final: 0.8059 (mtpm) REVERT: A 978 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: A 1165 GLN cc_start: 0.7919 (mp10) cc_final: 0.7665 (mm-40) REVERT: A 1172 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8063 (mmmt) REVERT: A 1376 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7658 (mtp180) REVERT: A 1763 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7010 (ptp) REVERT: A 1870 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: A 2006 LYS cc_start: 0.7927 (mttm) cc_final: 0.7644 (mppt) REVERT: P 83 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7738 (mp10) outliers start: 39 outliers final: 16 residues processed: 224 average time/residue: 2.4123 time to fit residues: 616.6434 Evaluate side-chains 204 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1291 CYS Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1870 GLN Chi-restraints excluded: chain A residue 1976 SER Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 1.9990 chunk 113 optimal weight: 0.1980 chunk 2 optimal weight: 0.0970 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17155 Z= 0.151 Angle : 0.451 5.589 23213 Z= 0.233 Chirality : 0.038 0.142 2561 Planarity : 0.004 0.084 2951 Dihedral : 3.942 42.050 2271 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.93 % Allowed : 12.47 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 2073 helix: 0.97 (0.17), residues: 1018 sheet: -1.42 (0.40), residues: 139 loop : -1.63 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.003 0.000 HIS A1296 PHE 0.008 0.001 PHE A 842 TYR 0.012 0.001 TYR A1941 ARG 0.003 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 2.672 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: A 483 MET cc_start: 0.7373 (mtt) cc_final: 0.6891 (mtt) REVERT: A 496 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: A 502 LYS cc_start: 0.8394 (pttt) cc_final: 0.8005 (ttmt) REVERT: A 530 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7695 (mttt) REVERT: A 535 LYS cc_start: 0.8433 (mtpp) cc_final: 0.8066 (mtpm) REVERT: A 978 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: A 1165 GLN cc_start: 0.7910 (mp10) cc_final: 0.7660 (mm-40) REVERT: A 1172 LYS cc_start: 0.8528 (mmtm) cc_final: 0.8046 (mmmt) REVERT: A 1376 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7693 (mtp180) REVERT: A 1763 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.6979 (ptp) REVERT: A 2006 LYS cc_start: 0.7897 (mttm) cc_final: 0.7613 (mppt) REVERT: A 2046 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: A 2103 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: P 83 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7735 (mp10) outliers start: 36 outliers final: 14 residues processed: 217 average time/residue: 2.3124 time to fit residues: 576.3536 Evaluate side-chains 197 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 177 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1512 ASP Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain A residue 2046 GLN Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17155 Z= 0.317 Angle : 0.527 6.082 23213 Z= 0.278 Chirality : 0.040 0.142 2561 Planarity : 0.004 0.086 2951 Dihedral : 4.267 44.632 2271 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.25 % Allowed : 12.63 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 2073 helix: 0.87 (0.17), residues: 1011 sheet: -1.35 (0.41), residues: 139 loop : -1.68 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.006 0.001 HIS A1296 PHE 0.013 0.001 PHE A1143 TYR 0.023 0.001 TYR A1941 ARG 0.003 0.000 ARG A2048 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 483 MET cc_start: 0.7476 (mtt) cc_final: 0.7032 (mtt) REVERT: A 502 LYS cc_start: 0.8445 (pttt) cc_final: 0.8048 (ttmt) REVERT: A 530 LYS cc_start: 0.8381 (mtpt) cc_final: 0.7741 (mttp) REVERT: A 535 LYS cc_start: 0.8466 (mtpp) cc_final: 0.8092 (mtpm) REVERT: A 835 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7844 (mt0) REVERT: A 978 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7158 (mt0) REVERT: A 1078 MET cc_start: 0.7957 (tpt) cc_final: 0.7724 (tpt) REVERT: A 1165 GLN cc_start: 0.7852 (mp10) cc_final: 0.7645 (mm-40) REVERT: A 1172 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8052 (mmmt) REVERT: A 1376 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7710 (mtp180) REVERT: A 1636 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7610 (mp) REVERT: A 1960 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 2006 LYS cc_start: 0.8011 (mttm) cc_final: 0.7789 (mppt) REVERT: P 83 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7763 (mp10) outliers start: 42 outliers final: 22 residues processed: 211 average time/residue: 2.3873 time to fit residues: 575.5519 Evaluate side-chains 207 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 835 GLN Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1243 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1291 CYS Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1584 CYS Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1960 ILE Chi-restraints excluded: chain A residue 1976 SER Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17155 Z= 0.212 Angle : 0.481 5.867 23213 Z= 0.251 Chirality : 0.039 0.143 2561 Planarity : 0.004 0.085 2951 Dihedral : 4.171 44.086 2271 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.87 % Allowed : 13.65 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 2073 helix: 1.01 (0.17), residues: 1012 sheet: -1.26 (0.41), residues: 139 loop : -1.57 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.003 0.001 HIS A 603 PHE 0.010 0.001 PHE A 842 TYR 0.022 0.001 TYR A1941 ARG 0.003 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 181 time to evaluate : 2.934 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: A 496 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: A 502 LYS cc_start: 0.8421 (pttt) cc_final: 0.8064 (ttmt) REVERT: A 530 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7737 (mttp) REVERT: A 535 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8095 (mtpm) REVERT: A 978 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7176 (mt0) REVERT: A 1078 MET cc_start: 0.7985 (tpt) cc_final: 0.7753 (tpt) REVERT: A 1172 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8037 (mmmt) REVERT: A 1376 ARG cc_start: 0.7974 (mtp85) cc_final: 0.7716 (mtp180) REVERT: A 1636 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 1702 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7760 (mtt) REVERT: A 1870 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6342 (tt0) REVERT: A 1923 ARG cc_start: 0.8496 (ptp-170) cc_final: 0.8198 (ptp-170) REVERT: A 1960 ILE cc_start: 0.7936 (mt) cc_final: 0.7580 (mp) REVERT: A 2006 LYS cc_start: 0.7974 (mttm) cc_final: 0.7749 (mppt) REVERT: P 83 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7766 (mp10) outliers start: 35 outliers final: 19 residues processed: 204 average time/residue: 2.4440 time to fit residues: 570.3345 Evaluate side-chains 201 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1584 CYS Chi-restraints excluded: chain A residue 1636 LEU Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1870 GLN Chi-restraints excluded: chain A residue 1902 MET Chi-restraints excluded: chain A residue 1976 SER Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 53 TYR Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17155 Z= 0.155 Angle : 0.465 5.652 23213 Z= 0.241 Chirality : 0.038 0.144 2561 Planarity : 0.004 0.084 2951 Dihedral : 4.047 42.661 2271 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.55 % Allowed : 13.97 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.19), residues: 2073 helix: 1.16 (0.17), residues: 1012 sheet: -1.18 (0.42), residues: 139 loop : -1.47 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.002 0.000 HIS A 92 PHE 0.008 0.001 PHE A 842 TYR 0.017 0.001 TYR A1941 ARG 0.003 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7010 (tt0) REVERT: A 502 LYS cc_start: 0.8393 (pttt) cc_final: 0.8053 (ttmt) REVERT: A 530 LYS cc_start: 0.8371 (mtpt) cc_final: 0.7733 (mttp) REVERT: A 535 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8095 (mtpm) REVERT: A 978 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7154 (mt0) REVERT: A 1078 MET cc_start: 0.7940 (tpt) cc_final: 0.7710 (tpt) REVERT: A 1172 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8028 (mmmt) REVERT: A 1376 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7706 (mtp180) REVERT: A 1421 SER cc_start: 0.8605 (OUTLIER) cc_final: 0.8249 (p) REVERT: A 1702 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7722 (mtt) REVERT: A 1923 ARG cc_start: 0.8480 (ptp-170) cc_final: 0.8168 (ptp-170) REVERT: A 2006 LYS cc_start: 0.7942 (mttm) cc_final: 0.7704 (mppt) REVERT: A 2103 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: P 83 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7732 (mp10) outliers start: 29 outliers final: 16 residues processed: 205 average time/residue: 2.3905 time to fit residues: 560.9455 Evaluate side-chains 200 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 178 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1976 SER Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 185 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1870 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17155 Z= 0.246 Angle : 0.492 5.835 23213 Z= 0.257 Chirality : 0.039 0.140 2561 Planarity : 0.004 0.085 2951 Dihedral : 4.147 44.014 2271 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.71 % Allowed : 13.97 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.19), residues: 2073 helix: 1.14 (0.17), residues: 1005 sheet: -1.13 (0.42), residues: 140 loop : -1.37 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.004 0.001 HIS A1296 PHE 0.010 0.001 PHE A 842 TYR 0.019 0.001 TYR A1941 ARG 0.003 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 181 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: A 502 LYS cc_start: 0.8410 (pttt) cc_final: 0.8079 (ttmt) REVERT: A 530 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7667 (mttp) REVERT: A 539 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7331 (mtp85) REVERT: A 877 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8274 (tpt) REVERT: A 978 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7158 (mt0) REVERT: A 1172 LYS cc_start: 0.8555 (mmtm) cc_final: 0.8016 (mmmt) REVERT: A 1376 ARG cc_start: 0.7969 (mtp85) cc_final: 0.7725 (mtp180) REVERT: A 1421 SER cc_start: 0.8604 (OUTLIER) cc_final: 0.8229 (p) REVERT: A 1702 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: A 1923 ARG cc_start: 0.8510 (ptp-170) cc_final: 0.8191 (ptp-170) REVERT: A 2006 LYS cc_start: 0.8012 (mttm) cc_final: 0.7747 (mppt) REVERT: P 83 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7787 (mp10) outliers start: 32 outliers final: 16 residues processed: 199 average time/residue: 2.4071 time to fit residues: 547.5243 Evaluate side-chains 198 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 877 MET Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1141 ASP Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1584 CYS Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1976 SER Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2072 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17155 Z= 0.235 Angle : 0.493 5.738 23213 Z= 0.258 Chirality : 0.039 0.142 2561 Planarity : 0.004 0.085 2951 Dihedral : 4.175 44.538 2271 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.39 % Allowed : 14.45 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2073 helix: 1.13 (0.17), residues: 1007 sheet: -1.08 (0.43), residues: 140 loop : -1.31 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 94 HIS 0.004 0.001 HIS A1296 PHE 0.010 0.001 PHE A 842 TYR 0.023 0.001 TYR A1941 ARG 0.003 0.000 ARG A1766 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4146 Ramachandran restraints generated. 2073 Oldfield, 0 Emsley, 2073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 2.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: A 530 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7668 (mttp) REVERT: A 539 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7285 (mtp85) REVERT: A 978 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7128 (mt0) REVERT: A 1172 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8018 (mmmt) REVERT: A 1376 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7720 (mtp180) REVERT: A 1421 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 1702 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7672 (mtt) REVERT: A 1923 ARG cc_start: 0.8506 (ptp-170) cc_final: 0.8195 (ptp-170) REVERT: A 2006 LYS cc_start: 0.8025 (mttm) cc_final: 0.7748 (mppt) REVERT: P 83 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7792 (mp10) outliers start: 26 outliers final: 14 residues processed: 193 average time/residue: 2.4566 time to fit residues: 541.4882 Evaluate side-chains 194 residues out of total 1868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 539 ARG Chi-restraints excluded: chain A residue 755 THR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 978 GLN Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1250 LEU Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1421 SER Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1584 CYS Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1763 MET Chi-restraints excluded: chain A residue 1820 ASP Chi-restraints excluded: chain A residue 1976 SER Chi-restraints excluded: chain A residue 2043 VAL Chi-restraints excluded: chain P residue 83 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 164 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 144 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1264 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 = 0.3477 r_free = 0.3477 target = 0.112648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101462 restraints weight = 83375.603| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.03 r_work: 0.3223 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17155 Z= 0.167 Angle : 0.466 5.523 23213 Z= 0.242 Chirality : 0.038 0.143 2561 Planarity : 0.004 0.084 2951 Dihedral : 4.049 42.849 2271 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.18 % Allowed : 14.67 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.02 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.19), residues: 2073 helix: 1.28 (0.17), residues: 1009 sheet: -1.07 (0.43), residues: 140 loop : -1.22 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 94 HIS 0.003 0.000 HIS A 92 PHE 0.008 0.001 PHE A 362 TYR 0.020 0.001 TYR A1941 ARG 0.003 0.000 ARG A 684 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10849.29 seconds wall clock time: 190 minutes 14.67 seconds (11414.67 seconds total)