Starting phenix.real_space_refine on Fri Mar 15 06:34:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/03_2024/8hw2_35049_updated.pdb" } resolution = 3.65 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= 0.003 sd= 0.059 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7063 2.51 5 N 1812 2.21 5 O 1921 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 518": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A ASP 564": "OD1" <-> "OD2" Residue "A GLU 734": "OE1" <-> "OE2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A ARG 1011": "NH1" <-> "NH2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1054": "NH1" <-> "NH2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1067": "NH1" <-> "NH2" Residue "A TYR 1122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1138": "NH1" <-> "NH2" Residue "A ARG 1144": "NH1" <-> "NH2" Residue "A GLU 1153": "OE1" <-> "OE2" Residue "A ARG 1162": "NH1" <-> "NH2" Residue "A ARG 1166": "NH1" <-> "NH2" Residue "A ARG 1168": "NH1" <-> "NH2" Residue "A ASP 1175": "OD1" <-> "OD2" Residue "A ASP 1179": "OD1" <-> "OD2" Residue "A ARG 1193": "NH1" <-> "NH2" Residue "A GLU 1251": "OE1" <-> "OE2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A GLU 1288": "OE1" <-> "OE2" Residue "A TYR 1294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1421": "OE1" <-> "OE2" Residue "A TYR 1490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1517": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10853 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1377, 10853 Unusual residues: {'U38': 2} Inner-chain residues flagged as termini: ['pdbres="ALA A1527 "'] Classifications: {'peptide': 1375, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1313, None: 2} Not linked: pdbres="ALA A1527 " pdbres="U38 A1601 " Not linked: pdbres="U38 A1601 " pdbres="U38 A1602 " Chain breaks: 2 Time building chain proxies: 6.10, per 1000 atoms: 0.56 Number of scatterers: 10853 At special positions: 0 Unit cell: (78.11, 109.14, 149.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1921 8.00 N 1812 7.00 C 7063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.66 Conformation dependent library (CDL) restraints added in 2.2 seconds 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 5 sheets defined 55.3% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.33 Creating SS restraints... Processing helix chain 'A' and resid 35 through 58 removed outlier: 4.011A pdb=" N TRP A 39 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Proline residue: A 41 - end of helix removed outlier: 5.327A pdb=" N LEU A 49 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Proline residue: A 50 - end of helix removed outlier: 3.510A pdb=" N LEU A 54 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS A 58 " --> pdb=" O TYR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 95 removed outlier: 3.681A pdb=" N GLY A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 108 through 128 removed outlier: 3.697A pdb=" N VAL A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.800A pdb=" N VAL A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Proline residue: A 151 - end of helix Processing helix chain 'A' and resid 168 through 188 Processing helix chain 'A' and resid 221 through 227 removed outlier: 4.006A pdb=" N LYS A 225 " --> pdb=" O TRP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 299 through 306 removed outlier: 3.612A pdb=" N THR A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 318 through 340 removed outlier: 3.915A pdb=" N PHE A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) Proline residue: A 329 - end of helix removed outlier: 4.350A pdb=" N SER A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 361 removed outlier: 3.661A pdb=" N LEU A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 385 removed outlier: 3.789A pdb=" N THR A 377 " --> pdb=" O TYR A 373 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY A 378 " --> pdb=" O ILE A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.741A pdb=" N LYS A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 424 through 435 removed outlier: 3.881A pdb=" N ASN A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU A 429 " --> pdb=" O PRO A 425 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N TRP A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 441 through 447 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.667A pdb=" N MET A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) Proline residue: A 464 - end of helix removed outlier: 4.649A pdb=" N VAL A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 470 " --> pdb=" O ASN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 482 through 495 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 507 through 527 removed outlier: 4.213A pdb=" N ILE A 517 " --> pdb=" O GLN A 513 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR A 527 " --> pdb=" O GLN A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 535 through 555 removed outlier: 3.899A pdb=" N TRP A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) Proline residue: A 543 - end of helix Processing helix chain 'A' and resid 565 through 578 removed outlier: 4.909A pdb=" N VAL A 570 " --> pdb=" O GLU A 566 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN A 576 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 583 No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 585 through 606 removed outlier: 3.799A pdb=" N THR A 593 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N SER A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 674 removed outlier: 4.142A pdb=" N VAL A 671 " --> pdb=" O LYS A 667 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N SER A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 710 Processing helix chain 'A' and resid 717 through 726 Processing helix chain 'A' and resid 729 through 735 removed outlier: 4.205A pdb=" N MET A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 741 No H-bonds generated for 'chain 'A' and resid 739 through 741' Processing helix chain 'A' and resid 753 through 766 removed outlier: 4.285A pdb=" N ARG A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 792 removed outlier: 3.975A pdb=" N HIS A 788 " --> pdb=" O HIS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 removed outlier: 3.952A pdb=" N ARG A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 851 removed outlier: 4.164A pdb=" N PHE A 848 " --> pdb=" O SER A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 966 Processing helix chain 'A' and resid 968 through 971 No H-bonds generated for 'chain 'A' and resid 968 through 971' Processing helix chain 'A' and resid 975 through 1000 removed outlier: 3.934A pdb=" N ASP A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA A 999 " --> pdb=" O TRP A 995 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N MET A1000 " --> pdb=" O THR A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1019 removed outlier: 4.223A pdb=" N ARG A1011 " --> pdb=" O THR A1008 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N LEU A1012 " --> pdb=" O SER A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1052 removed outlier: 3.895A pdb=" N ALA A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1066 through 1070 Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1084 through 1107 removed outlier: 3.729A pdb=" N PHE A1095 " --> pdb=" O LEU A1091 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A1100 " --> pdb=" O ASN A1096 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A1105 " --> pdb=" O LEU A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1150 removed outlier: 4.592A pdb=" N TYR A1122 " --> pdb=" O LEU A1118 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A1134 " --> pdb=" O ALA A1130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) Proline residue: A1146 - end of helix Processing helix chain 'A' and resid 1158 through 1161 No H-bonds generated for 'chain 'A' and resid 1158 through 1161' Processing helix chain 'A' and resid 1168 through 1184 removed outlier: 4.506A pdb=" N ILE A1172 " --> pdb=" O ARG A1168 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A1176 " --> pdb=" O ILE A1172 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A1181 " --> pdb=" O LYS A1177 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER A1184 " --> pdb=" O ALA A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1189 No H-bonds generated for 'chain 'A' and resid 1186 through 1189' Processing helix chain 'A' and resid 1194 through 1197 No H-bonds generated for 'chain 'A' and resid 1194 through 1197' Processing helix chain 'A' and resid 1202 through 1216 removed outlier: 4.436A pdb=" N VAL A1207 " --> pdb=" O GLY A1203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE A1213 " --> pdb=" O PHE A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1220 No H-bonds generated for 'chain 'A' and resid 1218 through 1220' Processing helix chain 'A' and resid 1223 through 1231 Processing helix chain 'A' and resid 1236 through 1239 No H-bonds generated for 'chain 'A' and resid 1236 through 1239' Processing helix chain 'A' and resid 1250 through 1252 No H-bonds generated for 'chain 'A' and resid 1250 through 1252' Processing helix chain 'A' and resid 1254 through 1262 Processing helix chain 'A' and resid 1275 through 1277 No H-bonds generated for 'chain 'A' and resid 1275 through 1277' Processing helix chain 'A' and resid 1329 through 1336 Processing helix chain 'A' and resid 1359 through 1365 removed outlier: 3.735A pdb=" N GLN A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1385 Processing helix chain 'A' and resid 1392 through 1401 Processing helix chain 'A' and resid 1405 through 1410 Processing helix chain 'A' and resid 1414 through 1416 No H-bonds generated for 'chain 'A' and resid 1414 through 1416' Processing helix chain 'A' and resid 1428 through 1442 removed outlier: 3.731A pdb=" N ARG A1442 " --> pdb=" O ARG A1438 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1471 removed outlier: 3.959A pdb=" N LEU A1463 " --> pdb=" O GLU A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1507 through 1513 removed outlier: 3.775A pdb=" N ALA A1512 " --> pdb=" O ALA A1508 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1523 Processing sheet with id= A, first strand: chain 'A' and resid 684 through 687 removed outlier: 3.621A pdb=" N THR A 628 " --> pdb=" O HIS A 686 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 651 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR A 628 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE A 649 " --> pdb=" O THR A 628 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 828 through 833 removed outlier: 3.990A pdb=" N SER A 830 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL A 823 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N MET A 832 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 821 " --> pdb=" O MET A 832 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 822 " --> pdb=" O LEU A 656 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA A 658 " --> pdb=" O ILE A 822 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU A 824 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL A 660 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG A 805 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL A 659 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 807 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA A 692 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ASP A 775 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A 694 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1289 through 1292 Processing sheet with id= D, first strand: chain 'A' and resid 1500 through 1505 removed outlier: 6.559A pdb=" N VAL A1495 " --> pdb=" O ALA A1502 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE A1504 " --> pdb=" O VAL A1493 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A1493 " --> pdb=" O PHE A1504 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 633 through 635 removed outlier: 4.118A pdb=" N GLU A 682 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR A 635 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS A 680 " --> pdb=" O THR A 635 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 5.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1711 1.32 - 1.44: 2999 1.44 - 1.57: 6300 1.57 - 1.69: 12 1.69 - 1.82: 91 Bond restraints: 11113 Sorted by residual: bond pdb=" C11 U38 A1602 " pdb=" C12 U38 A1602 " ideal model delta sigma weight residual 1.762 1.384 0.378 2.00e-02 2.50e+03 3.56e+02 bond pdb=" C11 U38 A1601 " pdb=" C12 U38 A1601 " ideal model delta sigma weight residual 1.762 1.386 0.376 2.00e-02 2.50e+03 3.54e+02 bond pdb=" C8 U38 A1601 " pdb=" C9 U38 A1601 " ideal model delta sigma weight residual 1.441 1.196 0.245 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C8 U38 A1602 " pdb=" C9 U38 A1602 " ideal model delta sigma weight residual 1.441 1.196 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C10 U38 A1602 " pdb=" C11 U38 A1602 " ideal model delta sigma weight residual 1.376 1.604 -0.228 2.00e-02 2.50e+03 1.30e+02 ... (remaining 11108 not shown) Histogram of bond angle deviations from ideal: 98.24 - 105.40: 242 105.40 - 112.57: 5840 112.57 - 119.73: 3666 119.73 - 126.89: 5211 126.89 - 134.05: 169 Bond angle restraints: 15128 Sorted by residual: angle pdb=" N VAL A1026 " pdb=" CA VAL A1026 " pdb=" C VAL A1026 " ideal model delta sigma weight residual 113.71 107.72 5.99 9.50e-01 1.11e+00 3.98e+01 angle pdb=" N VAL A 114 " pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 112.96 107.58 5.38 1.00e+00 1.00e+00 2.89e+01 angle pdb=" C PHE A 420 " pdb=" N MET A 421 " pdb=" CA MET A 421 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C20 U38 A1601 " pdb=" C21 U38 A1601 " pdb=" C22 U38 A1601 " ideal model delta sigma weight residual 111.68 124.91 -13.23 3.00e+00 1.11e-01 1.95e+01 angle pdb=" C20 U38 A1602 " pdb=" C21 U38 A1602 " pdb=" C22 U38 A1602 " ideal model delta sigma weight residual 111.68 124.67 -12.99 3.00e+00 1.11e-01 1.87e+01 ... (remaining 15123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.49: 6091 22.49 - 44.99: 441 44.99 - 67.48: 49 67.48 - 89.97: 8 89.97 - 112.47: 1 Dihedral angle restraints: 6590 sinusoidal: 2596 harmonic: 3994 Sorted by residual: dihedral pdb=" CD ARG A1245 " pdb=" NE ARG A1245 " pdb=" CZ ARG A1245 " pdb=" NH1 ARG A1245 " ideal model delta sinusoidal sigma weight residual 0.00 -66.78 66.78 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CA TRP A1283 " pdb=" C TRP A1283 " pdb=" N PRO A1284 " pdb=" CA PRO A1284 " ideal model delta harmonic sigma weight residual 180.00 147.73 32.27 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 6587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1616 0.080 - 0.160: 141 0.160 - 0.240: 7 0.240 - 0.320: 2 0.320 - 0.400: 2 Chirality restraints: 1768 Sorted by residual: chirality pdb=" C15 U38 A1601 " pdb=" C14 U38 A1601 " pdb=" C16 U38 A1601 " pdb=" C19 U38 A1601 " both_signs ideal model delta sigma weight residual False 2.49 2.89 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C5 U38 A1601 " pdb=" C4 U38 A1601 " pdb=" O1 U38 A1601 " pdb=" O4 U38 A1601 " both_signs ideal model delta sigma weight residual False -2.35 -1.97 -0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" C22 U38 A1602 " pdb=" C14 U38 A1602 " pdb=" C21 U38 A1602 " pdb=" C23 U38 A1602 " both_signs ideal model delta sigma weight residual False 2.61 2.92 -0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1765 not shown) Planarity restraints: 1883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1245 " -1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG A1245 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A1245 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A1245 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1245 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A1283 " -0.065 5.00e-02 4.00e+02 9.87e-02 1.56e+01 pdb=" N PRO A1284 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO A1284 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1284 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 205 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 206 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.026 5.00e-02 4.00e+02 ... (remaining 1880 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 396 2.70 - 3.25: 12081 3.25 - 3.80: 17646 3.80 - 4.35: 22196 4.35 - 4.90: 34978 Nonbonded interactions: 87297 Sorted by model distance: nonbonded pdb=" OG SER A 364 " pdb=" OE1 GLU A1200 " model vdw 2.154 2.440 nonbonded pdb=" OD1 ASP A 416 " pdb=" OG SER A 598 " model vdw 2.184 2.440 nonbonded pdb=" OG1 THR A 383 " pdb=" OE1 GLN A1182 " model vdw 2.184 2.440 nonbonded pdb=" O SER A 844 " pdb=" ND2 ASN A 847 " model vdw 2.188 2.520 nonbonded pdb=" O HIS A1050 " pdb=" NH1 ARG A1054 " model vdw 2.196 2.520 ... (remaining 87292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 4.090 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 32.940 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.378 11113 Z= 0.669 Angle : 0.860 13.234 15128 Z= 0.442 Chirality : 0.049 0.400 1768 Planarity : 0.012 0.451 1883 Dihedral : 14.861 112.467 4010 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -2.33 (0.22), residues: 1369 helix: -1.37 (0.18), residues: 812 sheet: -0.87 (0.62), residues: 76 loop : -1.68 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 431 HIS 0.004 0.001 HIS A 177 PHE 0.028 0.002 PHE A 89 TYR 0.017 0.002 TYR A 90 ARG 0.007 0.001 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 459 MET cc_start: 0.7916 (mmt) cc_final: 0.7294 (mmt) REVERT: A 493 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 496 ASN cc_start: 0.8682 (m-40) cc_final: 0.8352 (m-40) REVERT: A 504 TYR cc_start: 0.8447 (p90) cc_final: 0.7900 (p90) REVERT: A 540 MET cc_start: 0.8023 (mmm) cc_final: 0.7004 (mmm) REVERT: A 820 PHE cc_start: 0.7268 (t80) cc_final: 0.6325 (t80) REVERT: A 835 TYR cc_start: 0.7405 (t80) cc_final: 0.7157 (t80) REVERT: A 1294 TYR cc_start: 0.7911 (t80) cc_final: 0.7051 (t80) REVERT: A 1472 PHE cc_start: 0.7862 (m-80) cc_final: 0.7625 (m-80) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.1928 time to fit residues: 55.7306 Evaluate side-chains 146 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 145 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1245 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.0470 chunk 70 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 79 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN A1241 ASN A1430 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11113 Z= 0.183 Angle : 0.694 10.568 15128 Z= 0.345 Chirality : 0.044 0.213 1768 Planarity : 0.005 0.097 1883 Dihedral : 7.126 101.743 1525 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.19 % Allowed : 11.39 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.96 (0.23), residues: 1369 helix: -0.96 (0.18), residues: 818 sheet: -0.50 (0.67), residues: 65 loop : -1.79 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1242 HIS 0.005 0.001 HIS A1050 PHE 0.027 0.002 PHE A1111 TYR 0.012 0.001 TYR A 90 ARG 0.018 0.000 ARG A1245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 178 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8013 (t80) cc_final: 0.7664 (t80) REVERT: A 493 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7691 (tm-30) REVERT: A 496 ASN cc_start: 0.8658 (m-40) cc_final: 0.8309 (m-40) REVERT: A 504 TYR cc_start: 0.8356 (p90) cc_final: 0.7810 (p90) REVERT: A 1094 PHE cc_start: 0.8618 (t80) cc_final: 0.8172 (t80) REVERT: A 1105 MET cc_start: 0.8144 (mmm) cc_final: 0.7887 (mmm) REVERT: A 1472 PHE cc_start: 0.7848 (m-80) cc_final: 0.7564 (m-80) outliers start: 14 outliers final: 8 residues processed: 183 average time/residue: 0.1931 time to fit residues: 53.2771 Evaluate side-chains 158 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1098 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN A1312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11113 Z= 0.226 Angle : 0.667 9.803 15128 Z= 0.332 Chirality : 0.044 0.166 1768 Planarity : 0.005 0.095 1883 Dihedral : 6.938 102.316 1521 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 2.30 % Allowed : 15.22 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.74 (0.23), residues: 1369 helix: -0.80 (0.18), residues: 813 sheet: -0.26 (0.68), residues: 65 loop : -1.68 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 960 HIS 0.005 0.001 HIS A1050 PHE 0.018 0.002 PHE A 544 TYR 0.016 0.001 TYR A 835 ARG 0.004 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8015 (t80) cc_final: 0.7706 (t80) REVERT: A 496 ASN cc_start: 0.8684 (m-40) cc_final: 0.8319 (m-40) REVERT: A 504 TYR cc_start: 0.8403 (p90) cc_final: 0.7789 (p90) REVERT: A 678 MET cc_start: 0.8358 (ttt) cc_final: 0.7797 (mtp) REVERT: A 820 PHE cc_start: 0.7262 (t80) cc_final: 0.7028 (t80) REVERT: A 1052 LYS cc_start: 0.8909 (tppt) cc_final: 0.8702 (tppt) REVERT: A 1094 PHE cc_start: 0.8648 (t80) cc_final: 0.8210 (t80) REVERT: A 1105 MET cc_start: 0.8148 (mmm) cc_final: 0.7885 (mmm) REVERT: A 1110 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7891 (tt) REVERT: A 1195 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8148 (tp) REVERT: A 1472 PHE cc_start: 0.7792 (m-80) cc_final: 0.7563 (m-80) outliers start: 27 outliers final: 18 residues processed: 180 average time/residue: 0.1839 time to fit residues: 50.9008 Evaluate side-chains 176 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 156 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 564 ASP Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1371 GLN Chi-restraints excluded: chain A residue 1495 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 0.0270 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.0010 chunk 35 optimal weight: 4.9990 overall best weight: 0.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11113 Z= 0.173 Angle : 0.652 10.389 15128 Z= 0.318 Chirality : 0.043 0.169 1768 Planarity : 0.004 0.095 1883 Dihedral : 6.667 100.481 1521 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.64 % Allowed : 18.11 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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: -1.54 (0.23), residues: 1369 helix: -0.65 (0.18), residues: 813 sheet: 0.02 (0.69), residues: 65 loop : -1.62 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.005 0.001 HIS A1050 PHE 0.016 0.001 PHE A 820 TYR 0.016 0.001 TYR A 835 ARG 0.005 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 176 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.6079 (ttt) cc_final: 0.5872 (ttp) REVERT: A 171 PHE cc_start: 0.8112 (t80) cc_final: 0.7878 (t80) REVERT: A 496 ASN cc_start: 0.8658 (m-40) cc_final: 0.8286 (m-40) REVERT: A 504 TYR cc_start: 0.8394 (p90) cc_final: 0.7803 (p90) REVERT: A 551 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9220 (mm) REVERT: A 820 PHE cc_start: 0.7172 (t80) cc_final: 0.6775 (t80) REVERT: A 1094 PHE cc_start: 0.8640 (t80) cc_final: 0.8237 (t80) REVERT: A 1110 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7704 (tt) REVERT: A 1145 SER cc_start: 0.9017 (m) cc_final: 0.8722 (p) REVERT: A 1195 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8166 (tp) REVERT: A 1232 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7180 (m-10) outliers start: 31 outliers final: 16 residues processed: 190 average time/residue: 0.1881 time to fit residues: 55.2682 Evaluate side-chains 179 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 118 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11113 Z= 0.187 Angle : 0.644 10.720 15128 Z= 0.317 Chirality : 0.042 0.157 1768 Planarity : 0.004 0.093 1883 Dihedral : 6.589 101.614 1521 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.23 % Allowed : 19.64 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1369 helix: -0.54 (0.19), residues: 814 sheet: 0.16 (0.68), residues: 65 loop : -1.58 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 960 HIS 0.004 0.001 HIS A1050 PHE 0.018 0.001 PHE A 820 TYR 0.012 0.001 TYR A 231 ARG 0.004 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 PHE cc_start: 0.8133 (t80) cc_final: 0.7907 (t80) REVERT: A 421 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7963 (ptm) REVERT: A 496 ASN cc_start: 0.8666 (m-40) cc_final: 0.8296 (m-40) REVERT: A 504 TYR cc_start: 0.8409 (p90) cc_final: 0.7808 (p90) REVERT: A 635 THR cc_start: 0.7956 (m) cc_final: 0.7501 (m) REVERT: A 1094 PHE cc_start: 0.8675 (t80) cc_final: 0.8205 (t80) REVERT: A 1110 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7604 (tt) REVERT: A 1145 SER cc_start: 0.8975 (m) cc_final: 0.8691 (p) REVERT: A 1195 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8187 (tp) REVERT: A 1232 TYR cc_start: 0.8240 (OUTLIER) cc_final: 0.7274 (m-10) outliers start: 38 outliers final: 24 residues processed: 188 average time/residue: 0.1750 time to fit residues: 51.4633 Evaluate side-chains 189 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 161 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1165 ASN Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 110 optimal weight: 0.0030 chunk 61 optimal weight: 0.0060 chunk 11 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11113 Z= 0.161 Angle : 0.646 11.595 15128 Z= 0.313 Chirality : 0.042 0.159 1768 Planarity : 0.004 0.093 1883 Dihedral : 6.440 100.347 1521 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 3.32 % Allowed : 20.32 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1369 helix: -0.51 (0.18), residues: 826 sheet: 0.26 (0.68), residues: 65 loop : -1.68 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 241 HIS 0.005 0.001 HIS A1050 PHE 0.015 0.001 PHE A 196 TYR 0.012 0.001 TYR A 231 ARG 0.003 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 177 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 CYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7836 (p) REVERT: A 171 PHE cc_start: 0.8146 (t80) cc_final: 0.7929 (t80) REVERT: A 421 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7851 (ptm) REVERT: A 496 ASN cc_start: 0.8660 (m-40) cc_final: 0.8281 (m-40) REVERT: A 504 TYR cc_start: 0.8360 (p90) cc_final: 0.7759 (p90) REVERT: A 551 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9228 (mm) REVERT: A 1094 PHE cc_start: 0.8680 (t80) cc_final: 0.8232 (t80) REVERT: A 1110 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7555 (tt) REVERT: A 1145 SER cc_start: 0.8916 (m) cc_final: 0.8627 (p) REVERT: A 1195 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8146 (tp) REVERT: A 1232 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7267 (m-10) outliers start: 39 outliers final: 23 residues processed: 197 average time/residue: 0.1910 time to fit residues: 58.2546 Evaluate side-chains 195 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 166 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 111 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11113 Z= 0.173 Angle : 0.644 11.341 15128 Z= 0.313 Chirality : 0.042 0.166 1768 Planarity : 0.004 0.092 1883 Dihedral : 6.357 98.174 1521 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.49 % Allowed : 21.26 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.23), residues: 1369 helix: -0.50 (0.19), residues: 828 sheet: 0.28 (0.68), residues: 65 loop : -1.61 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1242 HIS 0.004 0.001 HIS A1050 PHE 0.028 0.001 PHE A 569 TYR 0.015 0.001 TYR A 231 ARG 0.004 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 173 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 CYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8129 (t) REVERT: A 421 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7948 (ptm) REVERT: A 496 ASN cc_start: 0.8686 (m-40) cc_final: 0.8287 (m-40) REVERT: A 504 TYR cc_start: 0.8368 (p90) cc_final: 0.7772 (p90) REVERT: A 551 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9248 (mm) REVERT: A 1094 PHE cc_start: 0.8672 (t80) cc_final: 0.8239 (t80) REVERT: A 1145 SER cc_start: 0.8876 (m) cc_final: 0.8568 (p) REVERT: A 1195 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8169 (tp) REVERT: A 1232 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7196 (m-10) outliers start: 41 outliers final: 23 residues processed: 197 average time/residue: 0.1833 time to fit residues: 55.9971 Evaluate side-chains 188 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 TYR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 421 MET Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 12 optimal weight: 0.0870 chunk 103 optimal weight: 0.3980 chunk 120 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 981 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1022 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11113 Z= 0.163 Angle : 0.657 12.532 15128 Z= 0.315 Chirality : 0.042 0.159 1768 Planarity : 0.004 0.089 1883 Dihedral : 6.183 95.745 1521 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.64 % Allowed : 22.62 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1369 helix: -0.41 (0.19), residues: 828 sheet: 0.39 (0.66), residues: 65 loop : -1.67 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 81 HIS 0.004 0.001 HIS A1050 PHE 0.030 0.001 PHE A1059 TYR 0.015 0.001 TYR A 231 ARG 0.005 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 CYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8118 (t) REVERT: A 493 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 496 ASN cc_start: 0.8670 (m-40) cc_final: 0.8270 (m-40) REVERT: A 504 TYR cc_start: 0.8319 (p90) cc_final: 0.7743 (p90) REVERT: A 551 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9276 (mm) REVERT: A 1094 PHE cc_start: 0.8729 (t80) cc_final: 0.8291 (t80) REVERT: A 1145 SER cc_start: 0.8764 (m) cc_final: 0.8488 (p) REVERT: A 1195 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8176 (tp) REVERT: A 1232 TYR cc_start: 0.8114 (OUTLIER) cc_final: 0.7174 (m-10) REVERT: A 1278 ARG cc_start: 0.8190 (mmp-170) cc_final: 0.7373 (mmp80) outliers start: 31 outliers final: 20 residues processed: 195 average time/residue: 0.2013 time to fit residues: 61.1453 Evaluate side-chains 185 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11113 Z= 0.233 Angle : 0.682 13.060 15128 Z= 0.327 Chirality : 0.043 0.159 1768 Planarity : 0.004 0.087 1883 Dihedral : 6.247 95.115 1521 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.47 % Allowed : 23.81 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.23), residues: 1369 helix: -0.39 (0.19), residues: 826 sheet: 0.43 (0.67), residues: 65 loop : -1.81 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 431 HIS 0.005 0.001 HIS A1050 PHE 0.026 0.002 PHE A1059 TYR 0.020 0.001 TYR A1294 ARG 0.004 0.000 ARG A1144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.5933 (ttp) cc_final: 0.4791 (mmt) REVERT: A 359 CYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8106 (t) REVERT: A 474 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7473 (mtm180) REVERT: A 493 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7895 (tm-30) REVERT: A 496 ASN cc_start: 0.8673 (m-40) cc_final: 0.8268 (m-40) REVERT: A 504 TYR cc_start: 0.8415 (p90) cc_final: 0.7805 (p90) REVERT: A 551 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9348 (mm) REVERT: A 1145 SER cc_start: 0.8896 (m) cc_final: 0.8571 (p) REVERT: A 1195 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8201 (tp) REVERT: A 1232 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7318 (m-10) REVERT: A 1449 LEU cc_start: 0.8674 (tt) cc_final: 0.8050 (mp) outliers start: 29 outliers final: 23 residues processed: 179 average time/residue: 0.1837 time to fit residues: 50.8061 Evaluate side-chains 184 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 157 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 82 CYS Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1077 TYR Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11113 Z= 0.194 Angle : 0.687 13.094 15128 Z= 0.326 Chirality : 0.043 0.192 1768 Planarity : 0.004 0.088 1883 Dihedral : 6.200 94.356 1521 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 2.47 % Allowed : 23.89 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.23), residues: 1369 helix: -0.33 (0.19), residues: 826 sheet: 0.44 (0.67), residues: 65 loop : -1.81 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 431 HIS 0.005 0.001 HIS A1050 PHE 0.031 0.002 PHE A 569 TYR 0.019 0.001 TYR A1294 ARG 0.004 0.000 ARG A1144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2738 Ramachandran restraints generated. 1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 MET cc_start: 0.5921 (ttp) cc_final: 0.4774 (mmt) REVERT: A 359 CYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8093 (t) REVERT: A 493 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 496 ASN cc_start: 0.8661 (m-40) cc_final: 0.8264 (m-40) REVERT: A 504 TYR cc_start: 0.8363 (p90) cc_final: 0.7764 (p90) REVERT: A 551 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9324 (mm) REVERT: A 1145 SER cc_start: 0.8880 (m) cc_final: 0.8552 (p) REVERT: A 1195 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8158 (tp) REVERT: A 1232 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.7305 (m-10) REVERT: A 1278 ARG cc_start: 0.8184 (mmp-170) cc_final: 0.7457 (mmp80) REVERT: A 1449 LEU cc_start: 0.8653 (tt) cc_final: 0.8023 (mp) outliers start: 29 outliers final: 23 residues processed: 178 average time/residue: 0.1867 time to fit residues: 51.0496 Evaluate side-chains 180 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 544 PHE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 606 LEU Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain A residue 1008 THR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1077 TYR Chi-restraints excluded: chain A residue 1110 LEU Chi-restraints excluded: chain A residue 1112 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1232 TYR Chi-restraints excluded: chain A residue 1336 LEU Chi-restraints excluded: chain A residue 1371 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 16 optimal weight: 30.0000 chunk 30 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 111 optimal weight: 0.0010 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 0.0670 chunk 95 optimal weight: 0.9990 overall best weight: 0.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN ** A 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.157207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.111818 restraints weight = 17904.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.111235 restraints weight = 9777.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.112220 restraints weight = 7765.060| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11113 Z= 0.184 Angle : 0.684 13.179 15128 Z= 0.324 Chirality : 0.042 0.167 1768 Planarity : 0.004 0.087 1883 Dihedral : 6.127 95.025 1521 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.72 % Allowed : 23.89 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1369 helix: -0.27 (0.19), residues: 833 sheet: 0.46 (0.67), residues: 65 loop : -1.77 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 431 HIS 0.004 0.001 HIS A1050 PHE 0.024 0.002 PHE A1059 TYR 0.019 0.001 TYR A1294 ARG 0.004 0.000 ARG A1144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.86 seconds wall clock time: 41 minutes 10.69 seconds (2470.69 seconds total)