Starting phenix.real_space_refine on Mon Feb 19 07:16:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m7i_23714/02_2024/7m7i_23714_updated.pdb" } resolution = 3.4 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= 0.010 sd= 0.123 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 87 5.16 5 C 14957 2.51 5 N 4299 2.21 5 O 4621 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 1411": "OE1" <-> "OE2" Residue "B ARG 1412": "NH1" <-> "NH2" Residue "B GLU 1413": "OE1" <-> "OE2" Residue "B GLU 1418": "OE1" <-> "OE2" Residue "B ARG 1435": "NH1" <-> "NH2" Residue "B GLU 1454": "OE1" <-> "OE2" Residue "B ARG 1458": "NH1" <-> "NH2" Residue "B ARG 1466": "NH1" <-> "NH2" Residue "B ASP 1474": "OD1" <-> "OD2" Residue "B ARG 1479": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23965 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7411 Classifications: {'peptide': 999} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 941} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1390, 10319 Classifications: {'peptide': 1390} Link IDs: {'PTRANS': 74, 'TRANS': 1315} Chain: "C" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "D" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "E" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 193} Chain breaks: 2 Chain: "F" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1568 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PN7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 13.33, per 1000 atoms: 0.56 Number of scatterers: 23965 At special positions: 0 Unit cell: (108, 180, 161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 P 1 15.00 O 4621 8.00 N 4299 7.00 C 14957 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 100 " distance=2.04 Simple disulfide: pdb=" SG CYS C 147 " - pdb=" SG CYS C 203 " distance=2.04 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 216 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.03 Simple disulfide: pdb=" SG CYS F 39 " - pdb=" SG CYS F 109 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 216 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.98 Conformation dependent library (CDL) restraints added in 4.5 seconds 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5806 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 28 sheets defined 26.6% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.11 Creating SS restraints... Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.914A pdb=" N ARG B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE B 27 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 121 through 135 removed outlier: 3.616A pdb=" N LEU B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU B 128 " --> pdb=" O ARG B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 178 No H-bonds generated for 'chain 'B' and resid 175 through 178' Processing helix chain 'B' and resid 181 through 191 removed outlier: 3.598A pdb=" N SER B 185 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ARG B 187 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE B 188 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 191 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 removed outlier: 5.838A pdb=" N SER B 208 " --> pdb=" O CYS B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 246 removed outlier: 3.502A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 313 through 327 Processing helix chain 'B' and resid 347 through 358 Processing helix chain 'B' and resid 372 through 376 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 386 through 397 Processing helix chain 'B' and resid 482 through 498 removed outlier: 3.567A pdb=" N ALA B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 492 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 512 Processing helix chain 'B' and resid 529 through 533 removed outlier: 3.593A pdb=" N LEU B 533 " --> pdb=" O GLU B 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 529 through 533' Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 586 through 595 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 612 through 616 removed outlier: 3.632A pdb=" N ASP B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 612 through 616' Processing helix chain 'B' and resid 624 through 644 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 658 through 665 Processing helix chain 'B' and resid 671 through 684 Processing helix chain 'B' and resid 701 through 707 removed outlier: 4.384A pdb=" N ALA B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 739 removed outlier: 3.896A pdb=" N VAL B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 769 removed outlier: 4.944A pdb=" N ASP B 765 " --> pdb=" O THR B 762 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU B 767 " --> pdb=" O ARG B 764 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 768 " --> pdb=" O ASP B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 838 through 846 removed outlier: 3.789A pdb=" N GLU B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 877 Processing helix chain 'B' and resid 884 through 887 No H-bonds generated for 'chain 'B' and resid 884 through 887' Processing helix chain 'B' and resid 1410 through 1427 Processing helix chain 'B' and resid 1449 through 1462 Processing helix chain 'B' and resid 1471 through 1474 No H-bonds generated for 'chain 'B' and resid 1471 through 1474' Processing helix chain 'B' and resid 1478 through 1487 Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.525A pdb=" N ARG A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 58 No H-bonds generated for 'chain 'A' and resid 55 through 58' Processing helix chain 'A' and resid 115 through 118 No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 121 through 135 removed outlier: 4.048A pdb=" N MET A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 182 through 191 removed outlier: 3.600A pdb=" N GLY A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 221 removed outlier: 4.846A pdb=" N SER A 208 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG A 220 " --> pdb=" O GLN A 217 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG A 221 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.636A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.996A pdb=" N VAL A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 497 removed outlier: 4.051A pdb=" N ARG A 486 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 529 through 541 removed outlier: 3.542A pdb=" N ARG A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 579 No H-bonds generated for 'chain 'A' and resid 576 through 579' Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.676A pdb=" N ALA A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) Proline residue: A 596 - end of helix Processing helix chain 'A' and resid 602 through 607 Processing helix chain 'A' and resid 624 through 644 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 658 through 666 Processing helix chain 'A' and resid 671 through 687 removed outlier: 4.925A pdb=" N THR A 687 " --> pdb=" O ARG A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 707 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 758 through 761 No H-bonds generated for 'chain 'A' and resid 758 through 761' Processing helix chain 'A' and resid 800 through 808 Processing helix chain 'A' and resid 813 through 822 Processing helix chain 'A' and resid 837 through 844 Processing helix chain 'A' and resid 865 through 878 Processing helix chain 'A' and resid 884 through 887 No H-bonds generated for 'chain 'A' and resid 884 through 887' Processing helix chain 'A' and resid 922 through 928 Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.956A pdb=" N ALA A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 997 Processing helix chain 'A' and resid 1018 through 1020 No H-bonds generated for 'chain 'A' and resid 1018 through 1020' Processing helix chain 'A' and resid 1022 through 1037 Processing helix chain 'A' and resid 1062 through 1076 removed outlier: 3.749A pdb=" N ALA A1066 " --> pdb=" O ALA A1062 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A1068 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A1076 " --> pdb=" O ARG A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1104 removed outlier: 5.659A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ALA A1102 " --> pdb=" O ARG A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 4.042A pdb=" N ILE A1156 " --> pdb=" O VAL A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1177 No H-bonds generated for 'chain 'A' and resid 1175 through 1177' Processing helix chain 'A' and resid 1181 through 1191 Processing helix chain 'A' and resid 1205 through 1214 Processing helix chain 'A' and resid 1236 through 1238 No H-bonds generated for 'chain 'A' and resid 1236 through 1238' Processing helix chain 'A' and resid 1241 through 1247 Processing helix chain 'A' and resid 1249 through 1264 removed outlier: 3.503A pdb=" N GLY A1254 " --> pdb=" O ALA A1250 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU A1264 " --> pdb=" O GLU A1260 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1304 Proline residue: A1290 - end of helix Processing helix chain 'A' and resid 1326 through 1331 Processing helix chain 'A' and resid 1341 through 1353 removed outlier: 4.466A pdb=" N ARG A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1373 removed outlier: 4.814A pdb=" N LEU A1371 " --> pdb=" O ASP A1367 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1372 " --> pdb=" O ARG A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1388 No H-bonds generated for 'chain 'A' and resid 1386 through 1388' Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing sheet with id= A, first strand: chain 'B' and resid 198 through 201 removed outlier: 7.750A pdb=" N ILE B 199 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL B 151 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 201 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL B 153 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU B 226 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N PHE B 152 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET B 228 " --> pdb=" O PHE B 152 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLY B 154 " --> pdb=" O MET B 228 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY B 230 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 39 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU B 278 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL B 37 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA B 292 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE B 453 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR B 297 " --> pdb=" O HIS B 451 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N HIS B 451 " --> pdb=" O THR B 297 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 299 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN B 449 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY B 439 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 337 " --> pdb=" O GLY B 439 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N SER B 441 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 367 through 369 Processing sheet with id= C, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.606A pdb=" N PHE B 524 " --> pdb=" O TRP B 475 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 652 through 654 removed outlier: 6.862A pdb=" N PHE B 560 " --> pdb=" O ILE B 653 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER B 853 " --> pdb=" O PHE B 828 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU B 830 " --> pdb=" O SER B 853 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE B 855 " --> pdb=" O GLU B 830 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 693 through 697 removed outlier: 3.654A pdb=" N VAL B 725 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA B 726 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE B 714 " --> pdb=" O ALA B 726 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 784 through 786 removed outlier: 4.959A pdb=" N PHE B 784 " --> pdb=" O THR B 793 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 793 " --> pdb=" O PHE B 784 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 198 through 201 removed outlier: 8.121A pdb=" N ILE A 199 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VAL A 151 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 201 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL A 153 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU A 226 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N PHE A 152 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N MET A 228 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY A 154 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLY A 230 " --> pdb=" O GLY A 154 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU A 278 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL A 37 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 292 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 453 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N THR A 297 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N HIS A 451 " --> pdb=" O THR A 297 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N VAL A 299 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN A 449 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N GLY A 439 " --> pdb=" O ASP A 335 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL A 337 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N SER A 441 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N HIS A 368 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 521 through 524 Processing sheet with id= I, first strand: chain 'A' and resid 828 through 830 removed outlier: 6.167A pdb=" N VAL A 559 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A 560 " --> pdb=" O ALA A 650 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 652 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE A 562 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 654 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 692 through 697 removed outlier: 3.545A pdb=" N GLY A 727 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ALA A 726 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ILE A 714 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASP A 728 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 712 " --> pdb=" O ASP A 728 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1359 through 1361 removed outlier: 3.629A pdb=" N ARG A1123 " --> pdb=" O GLN A1112 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLN A1112 " --> pdb=" O ARG A1123 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU A1113 " --> pdb=" O GLY A1083 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU A1085 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU A1115 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP A1087 " --> pdb=" O LEU A1115 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A1043 " --> pdb=" O GLY A1083 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU A1085 " --> pdb=" O LEU A1043 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N THR A1045 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP A1087 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N THR A1047 " --> pdb=" O ASP A1087 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 1168 through 1172 Processing sheet with id= M, first strand: chain 'C' and resid 5 through 9 Processing sheet with id= N, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.530A pdb=" N VAL C 97 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ARG C 40 " --> pdb=" O TRP C 49 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP C 49 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 144 through 148 Processing sheet with id= P, first strand: chain 'C' and resid 159 through 161 removed outlier: 3.949A pdb=" N SER C 160 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 204 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR C 201 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 21 through 23 Processing sheet with id= R, first strand: chain 'D' and resid 106 through 111 removed outlier: 6.452A pdb=" N LEU D 58 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU D 67 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.858A pdb=" N VAL D 154 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 201 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N CYS D 156 " --> pdb=" O SER D 199 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 199 " --> pdb=" O CYS D 156 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.577A pdb=" N GLU D 217 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 5 through 9 Processing sheet with id= V, first strand: chain 'E' and resid 114 through 116 removed outlier: 5.867A pdb=" N ARG E 40 " --> pdb=" O TRP E 49 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP E 49 " --> pdb=" O ARG E 40 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA E 42 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU E 47 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 144 through 148 removed outlier: 3.753A pdb=" N VAL E 188 " --> pdb=" O HIS E 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS E 171 " --> pdb=" O VAL E 188 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.951A pdb=" N SER E 160 " --> pdb=" O ASN E 204 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN E 204 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 21 through 23 Processing sheet with id= Z, first strand: chain 'F' and resid 124 through 126 removed outlier: 3.761A pdb=" N GLY F 105 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU F 58 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LEU F 67 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.889A pdb=" N VAL F 154 " --> pdb=" O LEU F 201 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU F 201 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS F 156 " --> pdb=" O SER F 199 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER F 199 " --> pdb=" O CYS F 156 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR F 195 " --> pdb=" O ASN F 160 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.577A pdb=" N GLU F 217 " --> pdb=" O GLN F 169 " (cutoff:3.500A) 704 hydrogen bonds defined for protein. 1905 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: 9.28 Time building geometry restraints manager: 10.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 15 1.20 - 1.35: 8229 1.35 - 1.51: 6470 1.51 - 1.66: 9604 1.66 - 1.81: 136 Bond restraints: 24454 Sorted by residual: bond pdb=" CG PRO B 519 " pdb=" CD PRO B 519 " ideal model delta sigma weight residual 1.503 1.040 0.463 3.40e-02 8.65e+02 1.85e+02 bond pdb=" CA SER B1449 " pdb=" CB SER B1449 " ideal model delta sigma weight residual 1.530 1.416 0.114 1.69e-02 3.50e+03 4.57e+01 bond pdb=" CA SER C 187 " pdb=" CB SER C 187 " ideal model delta sigma weight residual 1.530 1.438 0.092 1.55e-02 4.16e+03 3.52e+01 bond pdb=" N PRO B 519 " pdb=" CD PRO B 519 " ideal model delta sigma weight residual 1.473 1.543 -0.070 1.40e-02 5.10e+03 2.48e+01 bond pdb=" C LYS B 8 " pdb=" O LYS B 8 " ideal model delta sigma weight residual 1.235 1.164 0.071 1.43e-02 4.89e+03 2.46e+01 ... (remaining 24449 not shown) Histogram of bond angle deviations from ideal: 75.84 - 87.74: 3 87.74 - 99.64: 11 99.64 - 111.53: 11163 111.53 - 123.43: 20718 123.43 - 135.32: 1371 Bond angle restraints: 33266 Sorted by residual: angle pdb=" N PRO B 519 " pdb=" CD PRO B 519 " pdb=" CG PRO B 519 " ideal model delta sigma weight residual 103.20 75.84 27.36 1.50e+00 4.44e-01 3.33e+02 angle pdb=" C THR A 233 " pdb=" CA THR A 233 " pdb=" CB THR A 233 " ideal model delta sigma weight residual 110.62 83.19 27.43 1.51e+00 4.39e-01 3.30e+02 angle pdb=" CA PRO B 519 " pdb=" CB PRO B 519 " pdb=" CG PRO B 519 " ideal model delta sigma weight residual 104.50 82.91 21.59 1.90e+00 2.77e-01 1.29e+02 angle pdb=" C ARG A 221 " pdb=" CA ARG A 221 " pdb=" CB ARG A 221 " ideal model delta sigma weight residual 110.86 92.93 17.93 1.65e+00 3.67e-01 1.18e+02 angle pdb=" CA PRO B 519 " pdb=" N PRO B 519 " pdb=" CD PRO B 519 " ideal model delta sigma weight residual 112.00 99.75 12.25 1.40e+00 5.10e-01 7.65e+01 ... (remaining 33261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 13004 17.99 - 35.98: 1152 35.98 - 53.97: 334 53.97 - 71.96: 115 71.96 - 89.95: 26 Dihedral angle restraints: 14631 sinusoidal: 5563 harmonic: 9068 Sorted by residual: dihedral pdb=" CA THR D 115 " pdb=" C THR D 115 " pdb=" N PRO D 116 " pdb=" CA PRO D 116 " ideal model delta harmonic sigma weight residual 180.00 92.67 87.33 0 5.00e+00 4.00e-02 3.05e+02 dihedral pdb=" CA THR F 115 " pdb=" C THR F 115 " pdb=" N PRO F 116 " pdb=" CA PRO F 116 " ideal model delta harmonic sigma weight residual 180.00 92.70 87.30 0 5.00e+00 4.00e-02 3.05e+02 dihedral pdb=" C THR A 233 " pdb=" N THR A 233 " pdb=" CA THR A 233 " pdb=" CB THR A 233 " ideal model delta harmonic sigma weight residual -122.00 -88.31 -33.69 0 2.50e+00 1.60e-01 1.82e+02 ... (remaining 14628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3352 0.091 - 0.182: 337 0.182 - 0.273: 52 0.273 - 0.364: 8 0.364 - 0.455: 5 Chirality restraints: 3754 Sorted by residual: chirality pdb=" CA THR A1310 " pdb=" N THR A1310 " pdb=" C THR A1310 " pdb=" CB THR A1310 " both_signs ideal model delta sigma weight residual False 2.53 2.98 -0.46 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CA ARG A 221 " pdb=" N ARG A 221 " pdb=" C ARG A 221 " pdb=" CB ARG A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CA THR E 101 " pdb=" N THR E 101 " pdb=" C THR E 101 " pdb=" CB THR E 101 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 3751 not shown) Planarity restraints: 4401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 30 " 0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C LEU B 30 " -0.060 2.00e-02 2.50e+03 pdb=" O LEU B 30 " 0.022 2.00e-02 2.50e+03 pdb=" N GLU B 31 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 28 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C ARG A 28 " 0.050 2.00e-02 2.50e+03 pdb=" O ARG A 28 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 29 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 85 " -0.015 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C LEU E 85 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU E 85 " -0.018 2.00e-02 2.50e+03 pdb=" N GLN E 86 " -0.017 2.00e-02 2.50e+03 ... (remaining 4398 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 406 2.64 - 3.20: 21823 3.20 - 3.77: 39880 3.77 - 4.33: 55637 4.33 - 4.90: 88421 Nonbonded interactions: 206167 Sorted by model distance: nonbonded pdb=" O THR A 233 " pdb=" CB THR A 233 " model vdw 2.073 2.776 nonbonded pdb=" OG1 THR B 181 " pdb=" OD2 ASP A 202 " model vdw 2.135 2.440 nonbonded pdb=" OG SER B 182 " pdb=" OD1 ASP A 202 " model vdw 2.137 2.440 nonbonded pdb=" O LEU A 175 " pdb=" OG1 THR A 179 " model vdw 2.168 2.440 nonbonded pdb=" OG SER C 9 " pdb=" OG SER C 23 " model vdw 2.178 2.440 ... (remaining 206162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'D' and (resid 17 through 172 or resid 178 through 231)) selection = (chain 'F' and (resid 17 through 209 or resid 215 through 231)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 9.350 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 67.520 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.140 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:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 : 0.006 0.463 24454 Z= 0.453 Angle : 1.030 27.433 33266 Z= 0.672 Chirality : 0.060 0.455 3754 Planarity : 0.006 0.064 4401 Dihedral : 16.319 89.947 8801 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 6.90 % Allowed : 2.79 % Favored : 90.31 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 3181 helix: -1.54 (0.17), residues: 896 sheet: -1.37 (0.21), residues: 588 loop : -1.99 (0.14), residues: 1697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 569 HIS 0.005 0.001 HIS A1226 PHE 0.022 0.002 PHE C 52 TYR 0.023 0.002 TYR C 84 ARG 0.012 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 485 time to evaluate : 2.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 342 THR cc_start: 0.7918 (OUTLIER) cc_final: 0.7678 (p) REVERT: B 344 THR cc_start: 0.4693 (OUTLIER) cc_final: 0.3121 (m) REVERT: B 822 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: B 831 VAL cc_start: 0.6712 (m) cc_final: 0.6509 (m) REVERT: B 858 LEU cc_start: 0.6839 (mt) cc_final: 0.6633 (mt) REVERT: A 43 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7872 (mmt-90) REVERT: A 1240 THR cc_start: 0.6556 (OUTLIER) cc_final: 0.6249 (p) REVERT: D 84 SER cc_start: 0.7232 (t) cc_final: 0.6928 (p) REVERT: D 187 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6883 (tp30) REVERT: E 36 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7315 (mmt) REVERT: E 74 ILE cc_start: 0.7306 (mt) cc_final: 0.7014 (tp) REVERT: E 93 GLU cc_start: 0.8084 (mp0) cc_final: 0.7680 (mp0) REVERT: F 70 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7521 (p90) REVERT: F 99 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7558 (t) REVERT: F 114 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8236 (mp10) REVERT: F 157 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7023 (tt) outliers start: 171 outliers final: 26 residues processed: 612 average time/residue: 0.4867 time to fit residues: 426.5127 Evaluate side-chains 248 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 822 GLU Chi-restraints excluded: chain B residue 1435 ARG Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 279 ARG Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1244 ILE Chi-restraints excluded: chain A residue 1245 GLU Chi-restraints excluded: chain A residue 1249 ARG Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain E residue 36 MET Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 157 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 288 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 217 GLN ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B1423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 158 GLN A 322 GLN ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN C 41 GLN C 171 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN F 66 GLN F 182 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 24454 Z= 0.400 Angle : 0.736 8.675 33266 Z= 0.373 Chirality : 0.045 0.235 3754 Planarity : 0.006 0.059 4401 Dihedral : 7.556 64.926 3596 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.23 % Allowed : 11.75 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -2.31 (0.14), residues: 3181 helix: -1.09 (0.17), residues: 900 sheet: -1.47 (0.20), residues: 608 loop : -1.77 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 429 HIS 0.009 0.001 HIS A 288 PHE 0.022 0.002 PHE B 813 TYR 0.028 0.002 TYR C 109 ARG 0.015 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 194 time to evaluate : 2.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 MET cc_start: 0.2707 (OUTLIER) cc_final: 0.1789 (mpp) REVERT: A 40 MET cc_start: 0.8298 (mtm) cc_final: 0.8052 (mtp) REVERT: A 98 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6021 (mp) REVERT: A 240 MET cc_start: 0.8360 (tpt) cc_final: 0.8134 (mmt) REVERT: A 572 MET cc_start: 0.1920 (OUTLIER) cc_final: 0.1376 (tpp) REVERT: E 48 GLU cc_start: 0.6388 (tm-30) cc_final: 0.5854 (tm-30) REVERT: E 93 GLU cc_start: 0.8049 (mp0) cc_final: 0.7784 (mp0) REVERT: E 151 ASP cc_start: 0.6151 (t0) cc_final: 0.5889 (t0) REVERT: E 155 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 183 TYR cc_start: 0.8224 (m-10) cc_final: 0.7906 (m-10) outliers start: 80 outliers final: 41 residues processed: 255 average time/residue: 0.4013 time to fit residues: 157.8689 Evaluate side-chains 194 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1302 ARG Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 48 SER Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 164 ARG Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 160 optimal weight: 40.0000 chunk 89 optimal weight: 0.0870 chunk 240 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 79 optimal weight: 30.0000 chunk 289 optimal weight: 9.9990 chunk 312 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 286 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 232 optimal weight: 40.0000 overall best weight: 1.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B1423 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 122 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN E 8 GLN E 41 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 24454 Z= 0.265 Angle : 0.621 11.728 33266 Z= 0.313 Chirality : 0.042 0.175 3754 Planarity : 0.005 0.056 4401 Dihedral : 5.982 61.861 3530 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.03 % Allowed : 13.85 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -2.04 (0.14), residues: 3181 helix: -0.78 (0.17), residues: 915 sheet: -1.26 (0.20), residues: 610 loop : -1.70 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 429 HIS 0.010 0.001 HIS B 655 PHE 0.017 0.002 PHE B 813 TYR 0.026 0.002 TYR C 183 ARG 0.007 0.000 ARG F 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 165 time to evaluate : 2.704 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: B 126 MET cc_start: 0.8412 (mmm) cc_final: 0.7952 (mmm) REVERT: B 274 MET cc_start: 0.8431 (tpt) cc_final: 0.7820 (tpt) REVERT: B 477 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8091 (pp) REVERT: B 572 MET cc_start: 0.3144 (OUTLIER) cc_final: 0.2204 (mpp) REVERT: B 583 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: A 19 ASP cc_start: 0.7555 (m-30) cc_final: 0.7322 (m-30) REVERT: A 572 MET cc_start: 0.1778 (OUTLIER) cc_final: 0.1250 (tpp) REVERT: A 1322 MET cc_start: 0.5709 (tmm) cc_final: 0.5339 (tpt) REVERT: C 45 LYS cc_start: 0.6533 (OUTLIER) cc_final: 0.6088 (ptpp) REVERT: D 54 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8370 (tt) REVERT: D 201 LEU cc_start: 0.7797 (tp) cc_final: 0.7575 (tp) REVERT: E 48 GLU cc_start: 0.6424 (tm-30) cc_final: 0.5914 (tm-30) REVERT: E 93 GLU cc_start: 0.8111 (mp0) cc_final: 0.7840 (mp0) REVERT: E 109 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7404 (t80) REVERT: E 151 ASP cc_start: 0.6006 (t0) cc_final: 0.5785 (t0) REVERT: E 155 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7531 (mt-10) REVERT: E 183 TYR cc_start: 0.8294 (m-10) cc_final: 0.7870 (m-10) REVERT: F 75 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8403 (tpp80) REVERT: F 103 ASP cc_start: 0.7532 (m-30) cc_final: 0.7265 (m-30) REVERT: F 164 ARG cc_start: 0.8214 (ptm160) cc_final: 0.7400 (ttp-110) outliers start: 75 outliers final: 44 residues processed: 219 average time/residue: 0.3572 time to fit residues: 126.1496 Evaluate side-chains 198 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 146 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1413 GLU Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 285 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 290 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 82 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 HIS B 340 HIS B 555 GLN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN B1423 HIS A 122 GLN A 158 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 768 HIS ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 74 ASN ** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.132 24454 Z= 0.521 Angle : 0.754 9.559 33266 Z= 0.381 Chirality : 0.045 0.212 3754 Planarity : 0.006 0.097 4401 Dihedral : 6.093 69.029 3523 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.55 % Allowed : 14.82 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -2.06 (0.14), residues: 3181 helix: -0.72 (0.17), residues: 926 sheet: -1.54 (0.20), residues: 625 loop : -1.64 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 429 HIS 0.006 0.001 HIS A 495 PHE 0.022 0.002 PHE F 140 TYR 0.026 0.002 TYR C 183 ARG 0.006 0.001 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 156 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 274 MET cc_start: 0.8558 (tpt) cc_final: 0.7826 (tpt) REVERT: B 477 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8099 (pp) REVERT: B 556 GLN cc_start: 0.6421 (mm110) cc_final: 0.6129 (mp10) REVERT: B 583 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: A 572 MET cc_start: 0.2251 (OUTLIER) cc_final: 0.1613 (tpp) REVERT: A 1322 MET cc_start: 0.5820 (tmm) cc_final: 0.5591 (tpt) REVERT: C 45 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6718 (ptpp) REVERT: C 63 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7726 (mp0) REVERT: D 201 LEU cc_start: 0.7928 (tp) cc_final: 0.7606 (tp) REVERT: E 40 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7205 (ttm170) REVERT: E 41 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7934 (tp40) REVERT: E 48 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6167 (tm-30) REVERT: E 93 GLU cc_start: 0.8011 (mp0) cc_final: 0.7798 (mp0) REVERT: E 109 TYR cc_start: 0.8203 (OUTLIER) cc_final: 0.7923 (t80) REVERT: E 151 ASP cc_start: 0.6275 (t0) cc_final: 0.6035 (t0) REVERT: F 164 ARG cc_start: 0.8323 (ptm160) cc_final: 0.7828 (ptm-80) REVERT: F 187 GLU cc_start: 0.8045 (tp30) cc_final: 0.7704 (tp30) outliers start: 88 outliers final: 55 residues processed: 225 average time/residue: 0.3629 time to fit residues: 130.6822 Evaluate side-chains 201 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 139 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 255 optimal weight: 2.9990 chunk 174 optimal weight: 40.0000 chunk 4 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 212 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 0.0170 chunk 275 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 GLN F 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24454 Z= 0.260 Angle : 0.607 10.544 33266 Z= 0.304 Chirality : 0.042 0.171 3754 Planarity : 0.005 0.057 4401 Dihedral : 5.680 75.274 3514 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.43 % Allowed : 16.03 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.84 (0.15), residues: 3181 helix: -0.50 (0.17), residues: 932 sheet: -1.29 (0.20), residues: 637 loop : -1.59 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 55 HIS 0.004 0.001 HIS A1167 PHE 0.022 0.002 PHE A 868 TYR 0.025 0.002 TYR E 183 ARG 0.009 0.000 ARG B 681 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 152 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8250 (mp) REVERT: B 274 MET cc_start: 0.8449 (tpt) cc_final: 0.7826 (tpt) REVERT: B 477 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8176 (pp) REVERT: B 583 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6642 (m-80) REVERT: B 631 MET cc_start: 0.6225 (mmm) cc_final: 0.5824 (tpt) REVERT: A 572 MET cc_start: 0.2433 (OUTLIER) cc_final: 0.1690 (tpp) REVERT: A 838 THR cc_start: 0.5023 (OUTLIER) cc_final: 0.4392 (m) REVERT: C 63 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7625 (mp0) REVERT: D 183 GLU cc_start: 0.6923 (tp30) cc_final: 0.6715 (tp30) REVERT: D 201 LEU cc_start: 0.7835 (tp) cc_final: 0.7569 (tp) REVERT: E 48 GLU cc_start: 0.6411 (tm-30) cc_final: 0.6191 (tm-30) REVERT: E 109 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7619 (t80) REVERT: E 151 ASP cc_start: 0.6263 (t0) cc_final: 0.5999 (t0) REVERT: F 164 ARG cc_start: 0.8406 (ptm160) cc_final: 0.7762 (ttp-170) REVERT: F 187 GLU cc_start: 0.7977 (tp30) cc_final: 0.7665 (tp30) outliers start: 85 outliers final: 50 residues processed: 221 average time/residue: 0.3412 time to fit residues: 124.0544 Evaluate side-chains 197 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 141 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 103 optimal weight: 0.7980 chunk 276 optimal weight: 5.9990 chunk 60 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 307 optimal weight: 2.9990 chunk 255 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 161 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 217 GLN ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 GLN A 657 GLN E 41 GLN F 59 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24454 Z= 0.241 Angle : 0.586 12.230 33266 Z= 0.292 Chirality : 0.041 0.196 3754 Planarity : 0.005 0.056 4401 Dihedral : 5.494 79.149 3512 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.11 % Allowed : 16.43 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 2.21 % 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: -1.68 (0.15), residues: 3181 helix: -0.31 (0.17), residues: 935 sheet: -1.15 (0.20), residues: 625 loop : -1.55 (0.15), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 642 HIS 0.003 0.001 HIS A1334 PHE 0.017 0.001 PHE B 266 TYR 0.017 0.001 TYR D 70 ARG 0.006 0.000 ARG E 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 154 time to evaluate : 2.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8201 (mp) REVERT: B 274 MET cc_start: 0.8579 (tpt) cc_final: 0.7849 (tpt) REVERT: B 338 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7571 (tm-30) REVERT: B 477 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8074 (pp) REVERT: B 583 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: A 235 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.9002 (mtm) REVERT: A 556 GLN cc_start: 0.6605 (mm-40) cc_final: 0.5084 (mm-40) REVERT: A 572 MET cc_start: 0.2479 (OUTLIER) cc_final: 0.1697 (tpp) REVERT: A 838 THR cc_start: 0.5154 (OUTLIER) cc_final: 0.4524 (m) REVERT: C 63 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7598 (mp0) REVERT: C 84 TYR cc_start: 0.7112 (m-80) cc_final: 0.6823 (m-10) REVERT: D 81 ASP cc_start: 0.7928 (OUTLIER) cc_final: 0.7708 (t0) REVERT: D 201 LEU cc_start: 0.7816 (tp) cc_final: 0.7562 (tp) REVERT: E 48 GLU cc_start: 0.6411 (tm-30) cc_final: 0.6161 (tm-30) REVERT: E 76 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7389 (ptm160) REVERT: E 109 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: E 151 ASP cc_start: 0.6296 (t0) cc_final: 0.6024 (t0) REVERT: F 164 ARG cc_start: 0.8403 (ptm160) cc_final: 0.7787 (ttp-170) outliers start: 77 outliers final: 52 residues processed: 212 average time/residue: 0.3243 time to fit residues: 111.8127 Evaluate side-chains 203 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 142 time to evaluate : 2.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 476 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 836 ILE Chi-restraints excluded: chain B residue 1436 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 296 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 175 optimal weight: 0.0770 chunk 224 optimal weight: 6.9990 chunk 174 optimal weight: 30.0000 chunk 259 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 186 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 24454 Z= 0.344 Angle : 0.628 13.046 33266 Z= 0.312 Chirality : 0.042 0.210 3754 Planarity : 0.005 0.066 4401 Dihedral : 5.429 83.514 3509 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.15 % Allowed : 17.40 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -1.63 (0.15), residues: 3181 helix: -0.26 (0.17), residues: 938 sheet: -1.23 (0.20), residues: 628 loop : -1.47 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1159 HIS 0.004 0.001 HIS D 47 PHE 0.023 0.002 PHE A 266 TYR 0.018 0.002 TYR C 183 ARG 0.006 0.000 ARG D 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 150 time to evaluate : 2.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8239 (mp) REVERT: B 274 MET cc_start: 0.8462 (tpt) cc_final: 0.7826 (tpt) REVERT: B 338 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7596 (tm-30) REVERT: B 477 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8122 (pp) REVERT: B 583 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6485 (m-80) REVERT: A 235 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.9096 (mtm) REVERT: A 572 MET cc_start: 0.2690 (OUTLIER) cc_final: 0.1886 (tpp) REVERT: A 642 TRP cc_start: 0.7294 (OUTLIER) cc_final: 0.6798 (m-90) REVERT: C 63 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7565 (mp0) REVERT: D 201 LEU cc_start: 0.7832 (tp) cc_final: 0.7553 (tp) REVERT: E 48 GLU cc_start: 0.6623 (tm-30) cc_final: 0.6358 (tm-30) REVERT: E 109 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7710 (t80) REVERT: F 164 ARG cc_start: 0.8430 (ptm160) cc_final: 0.7831 (ttp-170) outliers start: 78 outliers final: 58 residues processed: 210 average time/residue: 0.3541 time to fit residues: 120.9399 Evaluate side-chains 208 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 143 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 583 PHE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 191 LYS Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 189 optimal weight: 0.2980 chunk 122 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 chunk 194 optimal weight: 0.0030 chunk 208 optimal weight: 20.0000 chunk 151 optimal weight: 0.0970 chunk 28 optimal weight: 0.7980 chunk 240 optimal weight: 9.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 556 GLN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN E 88 ASN ** E 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24454 Z= 0.158 Angle : 0.565 14.737 33266 Z= 0.278 Chirality : 0.041 0.161 3754 Planarity : 0.005 0.058 4401 Dihedral : 5.216 86.237 3508 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.58 % Allowed : 18.29 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -1.42 (0.15), residues: 3181 helix: -0.08 (0.18), residues: 932 sheet: -1.05 (0.20), residues: 616 loop : -1.38 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 642 HIS 0.003 0.001 HIS A1334 PHE 0.015 0.001 PHE B 266 TYR 0.018 0.001 TYR D 70 ARG 0.004 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 171 time to evaluate : 2.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 243 ASP cc_start: 0.7203 (m-30) cc_final: 0.6883 (m-30) REVERT: B 274 MET cc_start: 0.8546 (tpt) cc_final: 0.7970 (tpt) REVERT: B 477 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8034 (pp) REVERT: A 391 MET cc_start: 0.7062 (tpp) cc_final: 0.6686 (mmt) REVERT: A 572 MET cc_start: 0.2734 (OUTLIER) cc_final: 0.1908 (tpp) REVERT: A 642 TRP cc_start: 0.7187 (OUTLIER) cc_final: 0.6829 (m-90) REVERT: D 201 LEU cc_start: 0.7724 (tp) cc_final: 0.7487 (tp) REVERT: E 41 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: F 164 ARG cc_start: 0.8429 (ptm160) cc_final: 0.7800 (ttp80) outliers start: 64 outliers final: 43 residues processed: 220 average time/residue: 0.3525 time to fit residues: 126.7945 Evaluate side-chains 193 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1312 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 278 optimal weight: 7.9990 chunk 293 optimal weight: 0.0870 chunk 267 optimal weight: 3.9990 chunk 285 optimal weight: 8.9990 chunk 171 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 258 optimal weight: 0.0000 chunk 270 optimal weight: 0.3980 chunk 284 optimal weight: 6.9990 overall best weight: 1.0966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 GLN B 565 GLN B 628 GLN B 655 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24454 Z= 0.217 Angle : 0.572 14.753 33266 Z= 0.284 Chirality : 0.041 0.155 3754 Planarity : 0.005 0.059 4401 Dihedral : 5.154 87.924 3508 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 2.30 % Allowed : 18.49 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -1.33 (0.15), residues: 3181 helix: -0.03 (0.18), residues: 939 sheet: -1.06 (0.20), residues: 631 loop : -1.28 (0.16), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 642 HIS 0.004 0.001 HIS A 645 PHE 0.020 0.001 PHE C 173 TYR 0.019 0.001 TYR F 162 ARG 0.005 0.000 ARG B 557 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 147 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 274 MET cc_start: 0.8524 (tpt) cc_final: 0.7920 (tpt) REVERT: A 391 MET cc_start: 0.7164 (tpp) cc_final: 0.6881 (mmt) REVERT: A 572 MET cc_start: 0.2704 (OUTLIER) cc_final: 0.1863 (tpp) REVERT: A 635 MET cc_start: 0.6804 (mmm) cc_final: 0.5942 (mmm) REVERT: A 642 TRP cc_start: 0.7128 (OUTLIER) cc_final: 0.6723 (m-90) REVERT: C 183 TYR cc_start: 0.7091 (m-80) cc_final: 0.6704 (m-10) REVERT: D 201 LEU cc_start: 0.7734 (tp) cc_final: 0.7476 (tp) REVERT: E 36 MET cc_start: 0.8108 (mmm) cc_final: 0.7274 (mtt) REVERT: E 48 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6218 (tm-30) REVERT: F 140 PHE cc_start: 0.7301 (m-10) cc_final: 0.7070 (m-10) REVERT: F 164 ARG cc_start: 0.8436 (ptm160) cc_final: 0.7798 (ttp80) outliers start: 57 outliers final: 49 residues processed: 192 average time/residue: 0.3944 time to fit residues: 124.0308 Evaluate side-chains 192 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 140 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 556 GLN Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1312 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 187 optimal weight: 0.5980 chunk 302 optimal weight: 2.9990 chunk 184 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 316 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 252 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 194 optimal weight: 0.0170 chunk 154 optimal weight: 1.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24454 Z= 0.193 Angle : 0.574 15.093 33266 Z= 0.283 Chirality : 0.041 0.161 3754 Planarity : 0.005 0.058 4401 Dihedral : 5.133 89.382 3508 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.22 % Allowed : 18.69 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -1.26 (0.15), residues: 3181 helix: 0.03 (0.18), residues: 940 sheet: -0.97 (0.21), residues: 615 loop : -1.26 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A1159 HIS 0.016 0.001 HIS B 655 PHE 0.018 0.001 PHE A 868 TYR 0.019 0.001 TYR F 162 ARG 0.005 0.000 ARG D 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6362 Ramachandran restraints generated. 3181 Oldfield, 0 Emsley, 3181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 142 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 274 MET cc_start: 0.8409 (tpt) cc_final: 0.7865 (tpt) REVERT: B 477 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7992 (pp) REVERT: A 572 MET cc_start: 0.2729 (OUTLIER) cc_final: 0.1861 (tpp) REVERT: A 635 MET cc_start: 0.6874 (mmm) cc_final: 0.6094 (mmm) REVERT: A 642 TRP cc_start: 0.7200 (OUTLIER) cc_final: 0.6723 (m-90) REVERT: A 694 MET cc_start: -0.1958 (tmm) cc_final: -0.2198 (tmm) REVERT: C 183 TYR cc_start: 0.7112 (m-80) cc_final: 0.6690 (m-10) REVERT: D 201 LEU cc_start: 0.7729 (tp) cc_final: 0.7483 (tp) REVERT: E 36 MET cc_start: 0.8102 (mmm) cc_final: 0.7468 (mtt) REVERT: F 140 PHE cc_start: 0.7305 (m-10) cc_final: 0.7081 (m-10) REVERT: F 164 ARG cc_start: 0.8428 (ptm160) cc_final: 0.7798 (ttp80) outliers start: 55 outliers final: 46 residues processed: 188 average time/residue: 0.3596 time to fit residues: 110.0162 Evaluate side-chains 188 residues out of total 2478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 138 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 472 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 553 ARG Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 673 ASP Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1463 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 300 ASN Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain A residue 642 TRP Chi-restraints excluded: chain A residue 688 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 776 HIS Chi-restraints excluded: chain A residue 838 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 ASP Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1312 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 206 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 119 SER Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain F residue 75 ARG Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 231 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 200 optimal weight: 5.9990 chunk 268 optimal weight: 0.0040 chunk 77 optimal weight: 9.9990 chunk 232 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 252 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 259 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 556 GLN B 565 GLN B 628 GLN B 655 HIS ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.142040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.097735 restraints weight = 65292.068| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.17 r_work: 0.3552 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24454 Z= 0.191 Angle : 0.572 15.973 33266 Z= 0.281 Chirality : 0.041 0.167 3754 Planarity : 0.005 0.059 4401 Dihedral : 5.082 89.321 3507 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.26 % Allowed : 18.69 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.21 % Cis-general : 0.00 % Twisted Proline : 1.66 % 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: -1.17 (0.15), residues: 3181 helix: 0.14 (0.18), residues: 936 sheet: -0.95 (0.20), residues: 619 loop : -1.21 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 110 HIS 0.015 0.001 HIS B 655 PHE 0.017 0.001 PHE A 868 TYR 0.020 0.001 TYR F 162 ARG 0.005 0.000 ARG D 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5379.01 seconds wall clock time: 98 minutes 42.42 seconds (5922.42 seconds total)