Starting phenix.real_space_refine on Sat Dec 9 11:04:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_35049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_35049.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_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_35049/12_2023/8hw2_35049_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_35049_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_35049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_35049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_35049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hw2_35049/12_2023/8hw2_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.69, per 1000 atoms: 0.52 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: 4.11 Conformation dependent library (CDL) restraints added in 2.0 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: 3.49 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: 4.15 Time building geometry restraints manager: 4.49 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.170 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.820 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.460 ------------------------------------------------------------------------------- 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 : 1.230 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.2007 time to fit residues: 58.1500 Evaluate side-chains 142 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6289 time to fit residues: 2.4884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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: 0.7881 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11113 Z= 0.191 Angle : 0.695 10.448 15128 Z= 0.347 Chirality : 0.044 0.197 1768 Planarity : 0.005 0.097 1883 Dihedral : 7.133 102.962 1521 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 1.28 % Allowed : 10.88 % Favored : 87.84 % 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: -2.00 (0.23), residues: 1369 helix: -0.99 (0.18), residues: 820 sheet: -0.52 (0.67), residues: 65 loop : -1.80 (0.28), residues: 484 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 A1294 ARG 0.005 0.000 ARG A1144 *********************** 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 185 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 170 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 175 average time/residue: 0.1959 time to fit residues: 52.0320 Evaluate side-chains 158 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 149 time to evaluate : 1.259 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1011 time to fit residues: 3.4094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7919 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11113 Z= 0.239 Angle : 0.675 9.560 15128 Z= 0.337 Chirality : 0.044 0.175 1768 Planarity : 0.005 0.095 1883 Dihedral : 6.966 102.752 1521 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.53 % Allowed : 15.56 % Favored : 82.91 % 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: -1.78 (0.23), residues: 1369 helix: -0.84 (0.18), residues: 816 sheet: -0.29 (0.68), residues: 65 loop : -1.69 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 960 HIS 0.005 0.001 HIS A1050 PHE 0.022 0.002 PHE A1094 TYR 0.015 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 185 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 177 average time/residue: 0.1897 time to fit residues: 52.2627 Evaluate side-chains 166 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1111 time to fit residues: 3.7845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 7.9990 chunk 93 optimal weight: 0.0060 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11113 Z= 0.215 Angle : 0.668 10.779 15128 Z= 0.327 Chirality : 0.043 0.167 1768 Planarity : 0.004 0.095 1883 Dihedral : 6.758 101.277 1521 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 1.53 % Allowed : 18.96 % Favored : 79.51 % 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: -1.68 (0.23), residues: 1369 helix: -0.76 (0.18), residues: 819 sheet: -0.13 (0.68), residues: 65 loop : -1.67 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 960 HIS 0.005 0.001 HIS A1050 PHE 0.017 0.002 PHE A 544 TYR 0.022 0.001 TYR A 835 ARG 0.003 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 189 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 178 average time/residue: 0.1783 time to fit residues: 49.3994 Evaluate side-chains 167 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 159 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1045 time to fit residues: 3.2526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 0.0470 chunk 75 optimal weight: 0.0980 chunk 1 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 0.0470 chunk 91 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 overall best weight: 0.3176 ------------------------------------------------------------------------------- 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 989 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: 0.7846 moved from start: 0.1930 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= 0.162 Angle : 0.656 11.247 15128 Z= 0.322 Chirality : 0.042 0.161 1768 Planarity : 0.004 0.095 1883 Dihedral : 6.530 102.135 1521 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 1.45 % Allowed : 20.75 % Favored : 77.81 % 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: -1.48 (0.23), residues: 1369 helix: -0.60 (0.19), residues: 814 sheet: 0.13 (0.69), residues: 65 loop : -1.61 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 241 HIS 0.005 0.001 HIS A1050 PHE 0.018 0.001 PHE A1094 TYR 0.018 0.001 TYR A 835 ARG 0.004 0.000 ARG A 474 *********************** 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 197 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 8 residues processed: 186 average time/residue: 0.1897 time to fit residues: 54.2450 Evaluate side-chains 165 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 157 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1118 time to fit residues: 3.2917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 26 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** A1165 ASN A1314 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11113 Z= 0.242 Angle : 0.677 10.839 15128 Z= 0.332 Chirality : 0.044 0.176 1768 Planarity : 0.004 0.092 1883 Dihedral : 6.579 101.309 1521 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.38 % Allowed : 21.94 % Favored : 75.68 % 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: -1.54 (0.23), residues: 1369 helix: -0.62 (0.18), residues: 823 sheet: 0.11 (0.69), residues: 65 loop : -1.72 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 960 HIS 0.006 0.001 HIS A1050 PHE 0.014 0.001 PHE A 196 TYR 0.018 0.001 TYR A 835 ARG 0.004 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 197 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 169 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 14 residues processed: 185 average time/residue: 0.1879 time to fit residues: 53.7317 Evaluate side-chains 172 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1035 time to fit residues: 4.2993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2201 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= 0.189 Angle : 0.665 12.421 15128 Z= 0.323 Chirality : 0.043 0.180 1768 Planarity : 0.004 0.093 1883 Dihedral : 6.465 101.245 1521 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 1.53 % Allowed : 22.96 % Favored : 75.51 % 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: -1.45 (0.23), residues: 1369 helix: -0.56 (0.18), residues: 822 sheet: 0.17 (0.68), residues: 65 loop : -1.65 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 241 HIS 0.005 0.001 HIS A1050 PHE 0.017 0.001 PHE A1094 TYR 0.020 0.001 TYR A 835 ARG 0.008 0.000 ARG A1054 *********************** 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 190 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 7 residues processed: 180 average time/residue: 0.1884 time to fit residues: 52.6820 Evaluate side-chains 162 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 155 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1126 time to fit residues: 3.0403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.0040 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11113 Z= 0.187 Angle : 0.671 13.129 15128 Z= 0.326 Chirality : 0.043 0.273 1768 Planarity : 0.004 0.089 1883 Dihedral : 6.372 100.497 1521 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.11 % Allowed : 24.06 % Favored : 74.83 % 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: -1.39 (0.23), residues: 1369 helix: -0.51 (0.19), residues: 824 sheet: 0.18 (0.68), residues: 65 loop : -1.65 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 241 HIS 0.004 0.001 HIS A1050 PHE 0.015 0.001 PHE A 196 TYR 0.019 0.001 TYR A 835 ARG 0.005 0.000 ARG A1054 *********************** 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 178 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 171 average time/residue: 0.1825 time to fit residues: 48.7100 Evaluate side-chains 163 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 156 time to evaluate : 1.217 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1032 time to fit residues: 3.1172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 126 optimal weight: 6.9990 chunk 74 optimal weight: 0.0050 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.0870 chunk 37 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.4772 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11113 Z= 0.174 Angle : 0.677 13.318 15128 Z= 0.325 Chirality : 0.043 0.248 1768 Planarity : 0.004 0.089 1883 Dihedral : 6.250 99.356 1521 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.68 % Allowed : 24.74 % Favored : 74.57 % 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: -1.31 (0.23), residues: 1369 helix: -0.41 (0.19), residues: 825 sheet: 0.29 (0.68), residues: 65 loop : -1.69 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1242 HIS 0.004 0.001 HIS A1050 PHE 0.018 0.001 PHE A1094 TYR 0.020 0.001 TYR A 835 ARG 0.003 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 189 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 185 average time/residue: 0.1910 time to fit residues: 53.9524 Evaluate side-chains 165 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 160 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1156 time to fit residues: 2.7371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 90 optimal weight: 0.0570 chunk 136 optimal weight: 20.0000 chunk 125 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6902 ------------------------------------------------------------------------------- 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: 0.7843 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 11113 Z= 0.203 Angle : 0.713 13.315 15128 Z= 0.343 Chirality : 0.044 0.260 1768 Planarity : 0.005 0.088 1883 Dihedral : 6.269 98.058 1521 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.13 % Rotamer: Outliers : 0.51 % Allowed : 26.19 % Favored : 73.30 % 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: -1.36 (0.23), residues: 1369 helix: -0.42 (0.19), residues: 824 sheet: 0.36 (0.68), residues: 65 loop : -1.77 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 431 HIS 0.004 0.001 HIS A1050 PHE 0.020 0.001 PHE A 105 TYR 0.020 0.001 TYR A 835 ARG 0.006 0.000 ARG A1278 ********************** 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 164 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.542 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 162 average time/residue: 0.2073 time to fit residues: 53.2455 Evaluate side-chains 157 residues out of total 1176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 156 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1030 time to fit residues: 1.8916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.0170 chunk 16 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 0.0570 chunk 95 optimal weight: 0.5980 overall best weight: 0.1914 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.159178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114427 restraints weight = 18014.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.114506 restraints weight = 10688.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.114778 restraints weight = 8105.548| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11113 Z= 0.176 Angle : 0.710 13.314 15128 Z= 0.337 Chirality : 0.043 0.249 1768 Planarity : 0.004 0.087 1883 Dihedral : 6.070 95.754 1521 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.51 % Allowed : 26.53 % Favored : 72.96 % 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: -1.28 (0.23), residues: 1369 helix: -0.33 (0.19), residues: 821 sheet: 0.39 (0.67), residues: 65 loop : -1.79 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 431 HIS 0.004 0.001 HIS A 93 PHE 0.023 0.001 PHE A 89 TYR 0.018 0.001 TYR A 835 ARG 0.010 0.000 ARG A1278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.19 seconds wall clock time: 41 minutes 17.77 seconds (2477.77 seconds total)