Starting phenix.real_space_refine on Wed May 21 02:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhk_36271/05_2025/8jhk_36271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhk_36271/05_2025/8jhk_36271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jhk_36271/05_2025/8jhk_36271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhk_36271/05_2025/8jhk_36271.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhk_36271/05_2025/8jhk_36271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhk_36271/05_2025/8jhk_36271.cif" } resolution = 4.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 116 5.16 5 C 13112 2.51 5 N 3470 2.21 5 O 3814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20512 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5879 Classifications: {'peptide': 727} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 693} Chain: "B" Number of atoms: 13436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1642, 13436 Classifications: {'peptide': 1642} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1583} Chain: "E" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1197 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 2, 'TRANS': 137} Time building chain proxies: 11.61, per 1000 atoms: 0.57 Number of scatterers: 20512 At special positions: 0 Unit cell: (176.89, 135.66, 159.6, 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 116 16.00 O 3814 8.00 N 3470 7.00 C 13112 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.7 seconds 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4818 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 14 sheets defined 60.5% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 31 through 41 removed outlier: 3.870A pdb=" N TRP A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 64 through 69 removed outlier: 3.926A pdb=" N ASN A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 Processing helix chain 'A' and resid 96 through 111 Processing helix chain 'A' and resid 114 through 123 Processing helix chain 'A' and resid 124 through 140 removed outlier: 4.003A pdb=" N LEU A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 167 removed outlier: 4.434A pdb=" N ILE A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Proline residue: A 149 - end of helix Processing helix chain 'A' and resid 177 through 189 Processing helix chain 'A' and resid 194 through 212 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.756A pdb=" N LEU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.865A pdb=" N LYS A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 270 Processing helix chain 'A' and resid 270 through 279 Processing helix chain 'A' and resid 287 through 310 removed outlier: 4.562A pdb=" N ARG A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 333 Processing helix chain 'A' and resid 344 through 358 Processing helix chain 'A' and resid 366 through 372 removed outlier: 4.351A pdb=" N ASP A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 372 " --> pdb=" O MET A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 391 Processing helix chain 'A' and resid 391 through 402 Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 442 through 446 Processing helix chain 'A' and resid 450 through 471 Processing helix chain 'A' and resid 476 through 494 Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 510 through 521 removed outlier: 3.560A pdb=" N ILE A 514 " --> pdb=" O SER A 510 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 517 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 4.205A pdb=" N SER A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 559 removed outlier: 3.518A pdb=" N LEU A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 541 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Proline residue: A 542 - end of helix removed outlier: 4.094A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 627 removed outlier: 4.180A pdb=" N GLU A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 640 Processing helix chain 'A' and resid 659 through 672 Processing helix chain 'A' and resid 679 through 698 removed outlier: 4.880A pdb=" N ASP A 687 " --> pdb=" O ARG A 683 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR A 688 " --> pdb=" O ASN A 684 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 689 " --> pdb=" O ASP A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 701 No H-bonds generated for 'chain 'A' and resid 699 through 701' Processing helix chain 'B' and resid 8 through 11 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 83 through 104 removed outlier: 4.279A pdb=" N LEU B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 133 Processing helix chain 'B' and resid 137 through 159 removed outlier: 3.607A pdb=" N LEU B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 207 removed outlier: 3.739A pdb=" N GLN B 206 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN B 207 " --> pdb=" O SER B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 4.311A pdb=" N ILE B 219 " --> pdb=" O ILE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 378 through 389 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.561A pdb=" N LEU B 588 " --> pdb=" O TYR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 Processing helix chain 'B' and resid 634 through 642 removed outlier: 3.584A pdb=" N ASN B 642 " --> pdb=" O LEU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 647 removed outlier: 3.739A pdb=" N ASN B 646 " --> pdb=" O ASN B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 658 removed outlier: 4.324A pdb=" N MET B 658 " --> pdb=" O LEU B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 668 removed outlier: 3.518A pdb=" N ILE B 665 " --> pdb=" O ASP B 661 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 683 Processing helix chain 'B' and resid 686 through 705 Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 712 through 724 Processing helix chain 'B' and resid 728 through 743 Processing helix chain 'B' and resid 746 through 758 removed outlier: 4.202A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 779 removed outlier: 3.729A pdb=" N LEU B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 802 Processing helix chain 'B' and resid 803 through 804 No H-bonds generated for 'chain 'B' and resid 803 through 804' Processing helix chain 'B' and resid 805 through 808 Processing helix chain 'B' and resid 809 through 820 Processing helix chain 'B' and resid 823 through 828 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 832 through 846 removed outlier: 3.902A pdb=" N SER B 846 " --> pdb=" O LYS B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 866 removed outlier: 3.976A pdb=" N SER B 866 " --> pdb=" O LYS B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 891 removed outlier: 4.000A pdb=" N CYS B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Proline residue: B 880 - end of helix removed outlier: 4.464A pdb=" N ASP B 891 " --> pdb=" O SER B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 915 removed outlier: 4.417A pdb=" N GLU B 900 " --> pdb=" O LYS B 896 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG B 915 " --> pdb=" O GLU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 943 removed outlier: 6.743A pdb=" N ARG B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ARG B 935 " --> pdb=" O ARG B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 964 removed outlier: 4.114A pdb=" N PHE B 953 " --> pdb=" O HIS B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 972 Processing helix chain 'B' and resid 978 through 998 removed outlier: 3.543A pdb=" N GLY B 998 " --> pdb=" O LYS B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1032 Processing helix chain 'B' and resid 1033 through 1037 Processing helix chain 'B' and resid 1042 through 1055 Processing helix chain 'B' and resid 1058 through 1064 Processing helix chain 'B' and resid 1065 through 1077 Processing helix chain 'B' and resid 1078 through 1095 removed outlier: 4.463A pdb=" N GLU B1082 " --> pdb=" O ASP B1078 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B1095 " --> pdb=" O TRP B1091 " (cutoff:3.500A) Processing helix chain 'B' and resid 1097 through 1100 Processing helix chain 'B' and resid 1101 through 1114 removed outlier: 5.261A pdb=" N GLY B1107 " --> pdb=" O PRO B1103 " (cutoff:3.500A) Proline residue: B1108 - end of helix removed outlier: 4.525A pdb=" N GLU B1111 " --> pdb=" O GLY B1107 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B1112 " --> pdb=" O PRO B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1118 through 1125 Processing helix chain 'B' and resid 1125 through 1138 removed outlier: 3.989A pdb=" N PHE B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1162 removed outlier: 5.668A pdb=" N GLU B1150 " --> pdb=" O MET B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1165 through 1181 Processing helix chain 'B' and resid 1185 through 1215 removed outlier: 3.905A pdb=" N MET B1212 " --> pdb=" O ARG B1208 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN B1213 " --> pdb=" O THR B1209 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASP B1214 " --> pdb=" O ILE B1210 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B1215 " --> pdb=" O ILE B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1216 through 1234 Processing helix chain 'B' and resid 1236 through 1255 Processing helix chain 'B' and resid 1257 through 1269 Processing helix chain 'B' and resid 1292 through 1311 removed outlier: 3.773A pdb=" N LEU B1296 " --> pdb=" O THR B1292 " (cutoff:3.500A) Processing helix chain 'B' and resid 1314 through 1332 Processing helix chain 'B' and resid 1334 through 1355 Processing helix chain 'B' and resid 1373 through 1377 Processing helix chain 'B' and resid 1390 through 1401 Processing helix chain 'B' and resid 1447 through 1457 removed outlier: 3.721A pdb=" N LEU B1451 " --> pdb=" O PRO B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1513 through 1537 Processing helix chain 'B' and resid 1544 through 1556 Processing helix chain 'B' and resid 1560 through 1568 removed outlier: 3.733A pdb=" N ASN B1565 " --> pdb=" O GLY B1561 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR B1566 " --> pdb=" O GLY B1562 " (cutoff:3.500A) Processing helix chain 'B' and resid 1573 through 1578 Processing helix chain 'B' and resid 1583 through 1611 removed outlier: 4.170A pdb=" N GLU B1587 " --> pdb=" O GLN B1583 " (cutoff:3.500A) Proline residue: B1598 - end of helix Processing helix chain 'B' and resid 1614 through 1635 removed outlier: 3.996A pdb=" N LEU B1618 " --> pdb=" O GLN B1614 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1235 Processing helix chain 'E' and resid 1236 through 1255 Processing helix chain 'E' and resid 1257 through 1271 Processing helix chain 'E' and resid 1292 through 1312 Processing helix chain 'E' and resid 1314 through 1331 removed outlier: 3.715A pdb=" N GLU E1323 " --> pdb=" O LYS E1319 " (cutoff:3.500A) Processing helix chain 'E' and resid 1334 through 1354 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 9 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 51 Processing sheet with id=AA3, first strand: chain 'A' and resid 561 through 563 Processing sheet with id=AA4, first strand: chain 'A' and resid 616 through 617 removed outlier: 3.751A pdb=" N ILE A 644 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 232 removed outlier: 3.895A pdb=" N VAL B 401 " --> pdb=" O HIS B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 259 through 261 removed outlier: 3.909A pdb=" N TYR B 246 " --> pdb=" O SER B 295 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER B 295 " --> pdb=" O TYR B 246 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET B 327 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 323 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ARG B 302 " --> pdb=" O PRO B 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 279 through 282 removed outlier: 6.823A pdb=" N VAL B 280 " --> pdb=" O ALA B 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.193A pdb=" N ILE B 451 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU B 511 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR B 449 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 513 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR B 447 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 515 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP B 445 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 449 " --> pdb=" O ALA B 623 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 451 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLN B 621 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B 620 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 484 through 485 removed outlier: 6.193A pdb=" N ILE B 451 " --> pdb=" O TRP B 509 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU B 511 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR B 449 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL B 513 " --> pdb=" O TYR B 447 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR B 447 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL B 515 " --> pdb=" O ASP B 445 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ASP B 445 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP B 445 " --> pdb=" O CYS B 627 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 466 through 472 removed outlier: 3.813A pdb=" N ARG B 532 " --> pdb=" O GLU B 467 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS B 533 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA B 546 " --> pdb=" O HIS B 533 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1379 through 1384 removed outlier: 3.681A pdb=" N PHE B1363 " --> pdb=" O TYR B1383 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR B1362 " --> pdb=" O VAL B1431 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B1427 " --> pdb=" O GLY B1366 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1379 through 1384 removed outlier: 3.681A pdb=" N PHE B1363 " --> pdb=" O TYR B1383 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR B1362 " --> pdb=" O VAL B1431 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN B1427 " --> pdb=" O GLY B1366 " (cutoff:3.500A) 1110 hydrogen bonds defined for protein. 3222 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: 7.67 Time building geometry restraints manager: 5.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6656 1.34 - 1.46: 4501 1.46 - 1.58: 9582 1.58 - 1.70: 0 1.70 - 1.82: 198 Bond restraints: 20937 Sorted by residual: bond pdb=" CA ASP B 849 " pdb=" C ASP B 849 " ideal model delta sigma weight residual 1.523 1.498 0.026 1.34e-02 5.57e+03 3.67e+00 bond pdb=" C TYR A 18 " pdb=" N PRO A 19 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.01e-02 9.80e+03 2.52e+00 bond pdb=" CB GLN B 885 " pdb=" CG GLN B 885 " ideal model delta sigma weight residual 1.520 1.475 0.045 3.00e-02 1.11e+03 2.26e+00 bond pdb=" CG PRO A 376 " pdb=" CD PRO A 376 " ideal model delta sigma weight residual 1.512 1.472 0.040 2.70e-02 1.37e+03 2.23e+00 bond pdb=" CG GLN B 885 " pdb=" CD GLN B 885 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.23e+00 ... (remaining 20932 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.87: 27718 2.87 - 5.73: 466 5.73 - 8.60: 53 8.60 - 11.46: 7 11.46 - 14.33: 3 Bond angle restraints: 28247 Sorted by residual: angle pdb=" C LYS B1423 " pdb=" N GLN B1424 " pdb=" CA GLN B1424 " ideal model delta sigma weight residual 121.26 129.47 -8.21 1.59e+00 3.96e-01 2.67e+01 angle pdb=" N GLN B1424 " pdb=" CA GLN B1424 " pdb=" C GLN B1424 " ideal model delta sigma weight residual 110.30 116.60 -6.30 1.50e+00 4.44e-01 1.76e+01 angle pdb=" N VAL E1279 " pdb=" CA VAL E1279 " pdb=" C VAL E1279 " ideal model delta sigma weight residual 107.76 111.98 -4.22 1.01e+00 9.80e-01 1.74e+01 angle pdb=" CA LEU B 753 " pdb=" CB LEU B 753 " pdb=" CG LEU B 753 " ideal model delta sigma weight residual 116.30 101.97 14.33 3.50e+00 8.16e-02 1.68e+01 angle pdb=" C GLN B1302 " pdb=" N GLU B1303 " pdb=" CA GLU B1303 " ideal model delta sigma weight residual 120.31 114.29 6.02 1.52e+00 4.33e-01 1.57e+01 ... (remaining 28242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 11321 17.80 - 35.61: 1262 35.61 - 53.41: 179 53.41 - 71.21: 43 71.21 - 89.02: 14 Dihedral angle restraints: 12819 sinusoidal: 5394 harmonic: 7425 Sorted by residual: dihedral pdb=" CA SER A 643 " pdb=" C SER A 643 " pdb=" N ILE A 644 " pdb=" CA ILE A 644 " ideal model delta harmonic sigma weight residual 180.00 148.42 31.58 0 5.00e+00 4.00e-02 3.99e+01 dihedral pdb=" CA PHE B1064 " pdb=" C PHE B1064 " pdb=" N SER B1065 " pdb=" CA SER B1065 " ideal model delta harmonic sigma weight residual 180.00 148.93 31.07 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA TYR B1288 " pdb=" C TYR B1288 " pdb=" N TYR B1289 " pdb=" CA TYR B1289 " ideal model delta harmonic sigma weight residual 180.00 149.59 30.41 0 5.00e+00 4.00e-02 3.70e+01 ... (remaining 12816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2095 0.046 - 0.092: 794 0.092 - 0.138: 189 0.138 - 0.184: 32 0.184 - 0.230: 8 Chirality restraints: 3118 Sorted by residual: chirality pdb=" CA GLU B1458 " pdb=" N GLU B1458 " pdb=" C GLU B1458 " pdb=" CB GLU B1458 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU B1338 " pdb=" CB LEU B1338 " pdb=" CD1 LEU B1338 " pdb=" CD2 LEU B1338 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA GLU B1323 " pdb=" N GLU B1323 " pdb=" C GLU B1323 " pdb=" CB GLU B1323 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3115 not shown) Planarity restraints: 3616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 375 " -0.065 5.00e-02 4.00e+02 9.95e-02 1.58e+01 pdb=" N PRO A 376 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO A 376 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 376 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 174 " -0.057 5.00e-02 4.00e+02 8.54e-02 1.17e+01 pdb=" N PRO B 175 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 656 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.31e+00 pdb=" N PRO A 657 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 657 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 657 " 0.042 5.00e-02 4.00e+02 ... (remaining 3613 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 496 2.61 - 3.18: 21868 3.18 - 3.76: 35692 3.76 - 4.33: 49325 4.33 - 4.90: 72389 Nonbonded interactions: 179770 Sorted by model distance: nonbonded pdb=" O GLU A 238 " pdb=" OG1 THR A 241 " model vdw 2.041 3.040 nonbonded pdb=" OE1 GLU B1573 " pdb=" NE2 GLN B1577 " model vdw 2.054 3.120 nonbonded pdb=" O PHE B 216 " pdb=" OH TYR B 222 " model vdw 2.056 3.040 nonbonded pdb=" O ARG B1357 " pdb=" NE2 GLN B1359 " model vdw 2.079 3.120 nonbonded pdb=" O LEU B1059 " pdb=" OG1 THR B1063 " model vdw 2.087 3.040 ... (remaining 179765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.770 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 45.270 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 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: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20937 Z= 0.273 Angle : 0.940 14.329 28247 Z= 0.513 Chirality : 0.051 0.230 3118 Planarity : 0.006 0.100 3616 Dihedral : 14.925 89.016 8001 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 36.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.79 % Favored : 88.21 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.15), residues: 2503 helix: -1.32 (0.13), residues: 1313 sheet: -2.59 (0.33), residues: 193 loop : -2.75 (0.18), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 41 HIS 0.011 0.002 HIS B 154 PHE 0.020 0.002 PHE B 798 TYR 0.027 0.003 TYR A 588 ARG 0.010 0.001 ARG A 258 Details of bonding type rmsd hydrogen bonds : bond 0.17088 ( 1092) hydrogen bonds : angle 7.92875 ( 3222) covalent geometry : bond 0.00569 (20937) covalent geometry : angle 0.94031 (28247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TRP cc_start: 0.3536 (m-90) cc_final: 0.3256 (m-90) REVERT: A 132 MET cc_start: 0.8163 (ppp) cc_final: 0.7886 (ppp) REVERT: A 290 MET cc_start: 0.7225 (mmp) cc_final: 0.6884 (mmt) REVERT: A 309 MET cc_start: 0.6785 (ppp) cc_final: 0.5908 (ppp) REVERT: A 310 MET cc_start: 0.8584 (mpp) cc_final: 0.8085 (mpp) REVERT: A 369 MET cc_start: 0.6587 (mmp) cc_final: 0.6353 (mmm) REVERT: B 283 ASP cc_start: 0.7035 (m-30) cc_final: 0.6555 (t70) REVERT: B 306 MET cc_start: -0.2201 (mtt) cc_final: -0.2604 (mtt) REVERT: B 680 MET cc_start: 0.8806 (ppp) cc_final: 0.8599 (ppp) REVERT: B 683 MET cc_start: 0.7090 (tmm) cc_final: 0.6713 (tmm) REVERT: B 694 PHE cc_start: 0.9222 (t80) cc_final: 0.8684 (t80) REVERT: B 798 PHE cc_start: 0.9563 (m-80) cc_final: 0.9282 (m-80) REVERT: B 1007 MET cc_start: 0.8175 (ppp) cc_final: 0.7686 (ppp) REVERT: B 1008 VAL cc_start: 0.8881 (t) cc_final: 0.8294 (t) REVERT: B 1011 MET cc_start: 0.8991 (mpp) cc_final: 0.8479 (mpp) REVERT: B 1101 PHE cc_start: 0.8935 (m-80) cc_final: 0.8468 (m-80) REVERT: E 1228 LEU cc_start: 0.9497 (mt) cc_final: 0.9271 (mt) REVERT: E 1240 TYR cc_start: 0.8783 (t80) cc_final: 0.8558 (t80) REVERT: E 1303 GLU cc_start: 0.9524 (mp0) cc_final: 0.9308 (mp0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2942 time to fit residues: 90.2684 Evaluate side-chains 149 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 2.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 127 optimal weight: 0.0070 chunk 101 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 HIS ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 GLN B 265 ASN B 526 HIS B 556 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS B1293 GLN ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 ASN B1534 GLN ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.059599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037046 restraints weight = 147733.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.038631 restraints weight = 87498.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.039737 restraints weight = 60899.755| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20937 Z= 0.163 Angle : 0.751 11.397 28247 Z= 0.393 Chirality : 0.046 0.164 3118 Planarity : 0.006 0.090 3616 Dihedral : 6.667 51.810 2731 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 21.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.26 % Allowed : 7.30 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.25 (0.16), residues: 2503 helix: -0.63 (0.13), residues: 1360 sheet: -2.04 (0.34), residues: 208 loop : -2.58 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 PHE 0.018 0.002 PHE B 114 TYR 0.028 0.002 TYR B 969 ARG 0.005 0.001 ARG B1242 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 1092) hydrogen bonds : angle 6.13397 ( 3222) covalent geometry : bond 0.00346 (20937) covalent geometry : angle 0.75058 (28247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 225 time to evaluate : 2.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7694 (ppp) cc_final: 0.7439 (ppp) REVERT: A 290 MET cc_start: 0.7326 (mmp) cc_final: 0.7044 (mmt) REVERT: A 309 MET cc_start: 0.6855 (ppp) cc_final: 0.6351 (ppp) REVERT: B 120 MET cc_start: 0.9090 (mmp) cc_final: 0.8862 (mmm) REVERT: B 283 ASP cc_start: 0.7149 (m-30) cc_final: 0.6672 (t0) REVERT: B 306 MET cc_start: -0.2461 (mtt) cc_final: -0.2883 (mtt) REVERT: B 470 MET cc_start: 0.6510 (ppp) cc_final: 0.6267 (ppp) REVERT: B 680 MET cc_start: 0.8878 (ppp) cc_final: 0.8658 (ppp) REVERT: B 683 MET cc_start: 0.7108 (tmm) cc_final: 0.6771 (tmm) REVERT: B 694 PHE cc_start: 0.9330 (t80) cc_final: 0.8875 (t80) REVERT: B 787 PHE cc_start: 0.9425 (t80) cc_final: 0.8998 (t80) REVERT: B 798 PHE cc_start: 0.9520 (m-80) cc_final: 0.9205 (m-80) REVERT: B 800 MET cc_start: 0.9207 (tmm) cc_final: 0.8800 (tmm) REVERT: B 964 MET cc_start: 0.6873 (ptm) cc_final: 0.6502 (ptm) REVERT: B 1007 MET cc_start: 0.8408 (ppp) cc_final: 0.7848 (ppp) REVERT: B 1008 VAL cc_start: 0.9027 (t) cc_final: 0.8475 (t) REVERT: B 1011 MET cc_start: 0.9152 (mpp) cc_final: 0.8451 (mpp) REVERT: B 1038 PHE cc_start: 0.7207 (p90) cc_final: 0.6906 (t80) REVERT: B 1101 PHE cc_start: 0.8848 (m-80) cc_final: 0.8397 (m-80) REVERT: B 1313 MET cc_start: 0.8434 (tmm) cc_final: 0.8192 (tmm) REVERT: B 1328 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.8042 (m-80) REVERT: B 1348 PHE cc_start: 0.8680 (m-10) cc_final: 0.8332 (m-10) outliers start: 6 outliers final: 2 residues processed: 230 average time/residue: 0.3170 time to fit residues: 116.8819 Evaluate side-chains 168 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 2.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 217 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 170 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 246 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 465 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 GLN ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1535 GLN ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1577 GLN ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.059015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.036637 restraints weight = 149155.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.038169 restraints weight = 88808.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.039231 restraints weight = 62155.295| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20937 Z= 0.192 Angle : 0.751 11.711 28247 Z= 0.394 Chirality : 0.046 0.188 3118 Planarity : 0.006 0.085 3616 Dihedral : 6.527 45.002 2731 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.26 % Allowed : 6.03 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.12 (0.16), residues: 2503 helix: -0.53 (0.13), residues: 1362 sheet: -2.05 (0.35), residues: 207 loop : -2.49 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 102 HIS 0.007 0.001 HIS A 89 PHE 0.017 0.002 PHE A 574 TYR 0.025 0.002 TYR A 588 ARG 0.006 0.001 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.05228 ( 1092) hydrogen bonds : angle 6.02020 ( 3222) covalent geometry : bond 0.00409 (20937) covalent geometry : angle 0.75055 (28247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 214 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.7937 (ppp) cc_final: 0.7737 (ppp) REVERT: A 208 MET cc_start: 0.8612 (tmm) cc_final: 0.8183 (tmm) REVERT: A 309 MET cc_start: 0.7165 (ppp) cc_final: 0.6652 (ppp) REVERT: B 283 ASP cc_start: 0.7176 (m-30) cc_final: 0.6730 (t70) REVERT: B 306 MET cc_start: -0.2594 (mtt) cc_final: -0.2968 (mtt) REVERT: B 680 MET cc_start: 0.8706 (ppp) cc_final: 0.8449 (ppp) REVERT: B 683 MET cc_start: 0.6973 (tmm) cc_final: 0.6613 (tmm) REVERT: B 694 PHE cc_start: 0.9458 (t80) cc_final: 0.9029 (t80) REVERT: B 785 ASP cc_start: 0.8620 (m-30) cc_final: 0.8355 (p0) REVERT: B 798 PHE cc_start: 0.9550 (m-80) cc_final: 0.9223 (m-80) REVERT: B 800 MET cc_start: 0.9304 (tmm) cc_final: 0.8891 (tmm) REVERT: B 964 MET cc_start: 0.6816 (ptm) cc_final: 0.6576 (ptm) REVERT: B 1007 MET cc_start: 0.8529 (ppp) cc_final: 0.7961 (ppp) REVERT: B 1008 VAL cc_start: 0.9143 (t) cc_final: 0.8478 (t) REVERT: B 1011 MET cc_start: 0.8939 (mpp) cc_final: 0.8325 (mpp) REVERT: B 1090 MET cc_start: 0.8681 (tpt) cc_final: 0.8437 (mtp) REVERT: B 1101 PHE cc_start: 0.8759 (m-80) cc_final: 0.8396 (m-80) REVERT: B 1265 LEU cc_start: 0.9311 (mp) cc_final: 0.9102 (mp) REVERT: B 1302 GLN cc_start: 0.8622 (mt0) cc_final: 0.8420 (mt0) REVERT: E 1228 LEU cc_start: 0.9427 (mt) cc_final: 0.9214 (mt) outliers start: 6 outliers final: 1 residues processed: 219 average time/residue: 0.2944 time to fit residues: 103.8521 Evaluate side-chains 162 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 41 optimal weight: 0.0370 chunk 115 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 213 optimal weight: 0.0570 chunk 69 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 ASN B1203 ASN B1293 GLN ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.061184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.038464 restraints weight = 143100.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040108 restraints weight = 85100.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.041245 restraints weight = 59109.110| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 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 0.074 20937 Z= 0.140 Angle : 0.696 8.895 28247 Z= 0.363 Chirality : 0.044 0.187 3118 Planarity : 0.005 0.082 3616 Dihedral : 6.042 37.448 2731 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.62 (0.17), residues: 2503 helix: -0.13 (0.14), residues: 1353 sheet: -2.00 (0.33), residues: 227 loop : -2.17 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 102 HIS 0.012 0.001 HIS A 89 PHE 0.017 0.001 PHE B 114 TYR 0.049 0.002 TYR E1328 ARG 0.009 0.000 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 1092) hydrogen bonds : angle 5.57613 ( 3222) covalent geometry : bond 0.00297 (20937) covalent geometry : angle 0.69624 (28247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 252 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7966 (mp0) cc_final: 0.7610 (mp0) REVERT: A 132 MET cc_start: 0.7891 (ppp) cc_final: 0.7687 (ppp) REVERT: A 180 PHE cc_start: 0.8400 (t80) cc_final: 0.8166 (t80) REVERT: A 208 MET cc_start: 0.8567 (tmm) cc_final: 0.8167 (tmm) REVERT: A 290 MET cc_start: 0.8002 (mmm) cc_final: 0.7711 (mmt) REVERT: A 309 MET cc_start: 0.6850 (ppp) cc_final: 0.6448 (ppp) REVERT: B 106 TYR cc_start: 0.6179 (p90) cc_final: 0.5955 (p90) REVERT: B 283 ASP cc_start: 0.8060 (m-30) cc_final: 0.7672 (t70) REVERT: B 465 ASN cc_start: 0.7152 (t0) cc_final: 0.6935 (t0) REVERT: B 551 PHE cc_start: 0.7209 (p90) cc_final: 0.6980 (p90) REVERT: B 683 MET cc_start: 0.7008 (tmm) cc_final: 0.6753 (tmm) REVERT: B 694 PHE cc_start: 0.9373 (t80) cc_final: 0.8869 (t80) REVERT: B 722 LYS cc_start: 0.8895 (mmpt) cc_final: 0.8547 (pttm) REVERT: B 785 ASP cc_start: 0.8489 (m-30) cc_final: 0.8276 (p0) REVERT: B 787 PHE cc_start: 0.9359 (t80) cc_final: 0.8921 (t80) REVERT: B 798 PHE cc_start: 0.9521 (m-80) cc_final: 0.9138 (m-80) REVERT: B 800 MET cc_start: 0.9235 (tmm) cc_final: 0.8999 (tpt) REVERT: B 908 ASN cc_start: 0.8739 (m-40) cc_final: 0.8527 (m110) REVERT: B 943 MET cc_start: 0.8069 (mtt) cc_final: 0.7718 (mtp) REVERT: B 964 MET cc_start: 0.7219 (ptm) cc_final: 0.6938 (ptm) REVERT: B 1008 VAL cc_start: 0.9115 (t) cc_final: 0.8575 (t) REVERT: B 1033 MET cc_start: 0.8895 (mmm) cc_final: 0.8235 (mmm) REVERT: B 1101 PHE cc_start: 0.8681 (m-80) cc_final: 0.8360 (m-80) REVERT: B 1247 LEU cc_start: 0.9137 (mm) cc_final: 0.8862 (mt) REVERT: B 1265 LEU cc_start: 0.9235 (mp) cc_final: 0.9025 (mp) REVERT: B 1313 MET cc_start: 0.8463 (tmm) cc_final: 0.8235 (tmm) REVERT: B 1348 PHE cc_start: 0.8649 (m-10) cc_final: 0.8435 (m-10) REVERT: B 1489 TYR cc_start: 0.8296 (m-80) cc_final: 0.7967 (m-80) REVERT: E 1228 LEU cc_start: 0.9321 (mt) cc_final: 0.9110 (mt) REVERT: E 1238 ASP cc_start: 0.9369 (p0) cc_final: 0.9074 (p0) REVERT: E 1303 GLU cc_start: 0.9367 (mp0) cc_final: 0.9165 (tp30) outliers start: 4 outliers final: 2 residues processed: 255 average time/residue: 0.3053 time to fit residues: 124.3245 Evaluate side-chains 187 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 141 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 GLN ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1293 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.059110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.036520 restraints weight = 153843.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038087 restraints weight = 90388.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.039136 restraints weight = 63046.666| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20937 Z= 0.216 Angle : 0.776 15.188 28247 Z= 0.405 Chirality : 0.047 0.206 3118 Planarity : 0.006 0.081 3616 Dihedral : 6.280 31.706 2731 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.78 (0.16), residues: 2503 helix: -0.28 (0.14), residues: 1342 sheet: -2.13 (0.34), residues: 217 loop : -2.17 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1043 HIS 0.008 0.001 HIS B 949 PHE 0.017 0.002 PHE B1193 TYR 0.025 0.002 TYR E1231 ARG 0.007 0.001 ARG B 935 Details of bonding type rmsd hydrogen bonds : bond 0.05041 ( 1092) hydrogen bonds : angle 5.86154 ( 3222) covalent geometry : bond 0.00465 (20937) covalent geometry : angle 0.77571 (28247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7890 (mp0) cc_final: 0.7579 (mp0) REVERT: A 132 MET cc_start: 0.7890 (ppp) cc_final: 0.7662 (ppp) REVERT: A 208 MET cc_start: 0.8627 (tmm) cc_final: 0.8217 (tmm) REVERT: A 309 MET cc_start: 0.6445 (ppp) cc_final: 0.5537 (ppp) REVERT: A 310 MET cc_start: 0.8271 (mpp) cc_final: 0.7755 (mpp) REVERT: A 692 MET cc_start: 0.8812 (mmp) cc_final: 0.8507 (mmm) REVERT: B 283 ASP cc_start: 0.7632 (m-30) cc_final: 0.7253 (t70) REVERT: B 465 ASN cc_start: 0.7226 (t0) cc_final: 0.6986 (t0) REVERT: B 680 MET cc_start: 0.8714 (ppp) cc_final: 0.8452 (ppp) REVERT: B 683 MET cc_start: 0.7060 (tmm) cc_final: 0.6768 (tmm) REVERT: B 694 PHE cc_start: 0.9354 (t80) cc_final: 0.8925 (t80) REVERT: B 785 ASP cc_start: 0.8616 (m-30) cc_final: 0.8357 (p0) REVERT: B 798 PHE cc_start: 0.9547 (m-80) cc_final: 0.9243 (m-80) REVERT: B 943 MET cc_start: 0.8322 (mtt) cc_final: 0.7960 (mtp) REVERT: B 1007 MET cc_start: 0.8413 (ppp) cc_final: 0.7903 (ppp) REVERT: B 1008 VAL cc_start: 0.9086 (t) cc_final: 0.8371 (t) REVERT: B 1011 MET cc_start: 0.8910 (mpp) cc_final: 0.8446 (mpp) REVERT: B 1033 MET cc_start: 0.9060 (mmm) cc_final: 0.8810 (mmm) REVERT: B 1064 PHE cc_start: 0.7452 (m-10) cc_final: 0.7145 (m-10) REVERT: B 1090 MET cc_start: 0.8698 (tpt) cc_final: 0.8427 (mtp) REVERT: B 1101 PHE cc_start: 0.8749 (m-80) cc_final: 0.8455 (m-80) REVERT: B 1313 MET cc_start: 0.8546 (tmm) cc_final: 0.8319 (tmm) REVERT: B 1344 LYS cc_start: 0.9024 (mttp) cc_final: 0.8496 (mttm) REVERT: B 1348 PHE cc_start: 0.8736 (m-10) cc_final: 0.8477 (m-10) REVERT: E 1228 LEU cc_start: 0.9428 (mt) cc_final: 0.9137 (mt) outliers start: 2 outliers final: 0 residues processed: 225 average time/residue: 0.2919 time to fit residues: 105.5240 Evaluate side-chains 160 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 176 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 132 optimal weight: 0.0010 chunk 110 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 199 optimal weight: 0.7980 chunk 144 optimal weight: 9.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.062364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.038902 restraints weight = 146557.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040604 restraints weight = 86290.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.041726 restraints weight = 60011.860| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20937 Z= 0.139 Angle : 0.715 9.774 28247 Z= 0.368 Chirality : 0.045 0.206 3118 Planarity : 0.005 0.077 3616 Dihedral : 5.866 31.494 2731 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.17), residues: 2503 helix: -0.06 (0.14), residues: 1376 sheet: -1.84 (0.34), residues: 213 loop : -2.13 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1043 HIS 0.013 0.001 HIS A 89 PHE 0.028 0.002 PHE B 993 TYR 0.035 0.002 TYR B1328 ARG 0.007 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.04494 ( 1092) hydrogen bonds : angle 5.51160 ( 3222) covalent geometry : bond 0.00293 (20937) covalent geometry : angle 0.71469 (28247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8489 (pmm) cc_final: 0.7993 (pmm) REVERT: A 23 GLU cc_start: 0.8116 (mp0) cc_final: 0.7848 (mp0) REVERT: A 290 MET cc_start: 0.7718 (mmm) cc_final: 0.7462 (mmt) REVERT: A 309 MET cc_start: 0.6537 (ppp) cc_final: 0.5944 (ppp) REVERT: A 692 MET cc_start: 0.8777 (mmp) cc_final: 0.8563 (mmm) REVERT: A 726 CYS cc_start: 0.7542 (m) cc_final: 0.7077 (p) REVERT: A 727 ASN cc_start: 0.6697 (t0) cc_final: 0.6272 (t0) REVERT: B 283 ASP cc_start: 0.7792 (m-30) cc_final: 0.7365 (t70) REVERT: B 551 PHE cc_start: 0.7396 (p90) cc_final: 0.7057 (p90) REVERT: B 680 MET cc_start: 0.8716 (ppp) cc_final: 0.8294 (ppp) REVERT: B 681 MET cc_start: 0.7553 (mmt) cc_final: 0.7324 (mmt) REVERT: B 683 MET cc_start: 0.7031 (tmm) cc_final: 0.6787 (tmm) REVERT: B 694 PHE cc_start: 0.9403 (t80) cc_final: 0.9050 (t80) REVERT: B 722 LYS cc_start: 0.8919 (mmpt) cc_final: 0.8527 (pttm) REVERT: B 787 PHE cc_start: 0.9334 (t80) cc_final: 0.8877 (t80) REVERT: B 798 PHE cc_start: 0.9499 (m-80) cc_final: 0.9145 (m-80) REVERT: B 878 LEU cc_start: 0.9274 (mp) cc_final: 0.9055 (mp) REVERT: B 908 ASN cc_start: 0.8716 (m-40) cc_final: 0.8496 (m110) REVERT: B 943 MET cc_start: 0.8247 (mtt) cc_final: 0.7623 (mtp) REVERT: B 961 LEU cc_start: 0.8728 (pp) cc_final: 0.8500 (pp) REVERT: B 969 TYR cc_start: 0.8968 (m-80) cc_final: 0.8672 (m-80) REVERT: B 1008 VAL cc_start: 0.9080 (t) cc_final: 0.8596 (t) REVERT: B 1101 PHE cc_start: 0.8606 (m-80) cc_final: 0.8356 (m-80) REVERT: B 1212 MET cc_start: 0.8879 (pmm) cc_final: 0.8667 (pmm) REVERT: B 1247 LEU cc_start: 0.9157 (mm) cc_final: 0.8841 (mt) REVERT: B 1275 ASP cc_start: 0.7501 (p0) cc_final: 0.7235 (p0) REVERT: B 1313 MET cc_start: 0.8540 (tmm) cc_final: 0.8236 (tmm) REVERT: B 1348 PHE cc_start: 0.8678 (m-10) cc_final: 0.8427 (m-10) REVERT: E 1231 TYR cc_start: 0.8955 (m-80) cc_final: 0.8644 (m-80) REVERT: E 1238 ASP cc_start: 0.9111 (p0) cc_final: 0.8907 (p0) REVERT: E 1242 ARG cc_start: 0.8389 (ptt180) cc_final: 0.7690 (ptm160) REVERT: E 1243 TYR cc_start: 0.8287 (m-80) cc_final: 0.7479 (m-80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.3006 time to fit residues: 120.1725 Evaluate side-chains 186 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 49 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 17 optimal weight: 0.1980 chunk 73 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 173 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 ASN B 108 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS B 926 GLN ** B1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1302 GLN ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.036695 restraints weight = 147903.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.038222 restraints weight = 89004.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.039281 restraints weight = 62694.270| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20937 Z= 0.219 Angle : 0.791 13.613 28247 Z= 0.413 Chirality : 0.047 0.244 3118 Planarity : 0.006 0.074 3616 Dihedral : 6.175 34.447 2731 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.66 (0.17), residues: 2503 helix: -0.24 (0.13), residues: 1359 sheet: -1.94 (0.34), residues: 216 loop : -2.09 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 41 HIS 0.012 0.002 HIS A 89 PHE 0.020 0.002 PHE E1348 TYR 0.029 0.002 TYR B 969 ARG 0.015 0.001 ARG B 935 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 1092) hydrogen bonds : angle 5.81496 ( 3222) covalent geometry : bond 0.00466 (20937) covalent geometry : angle 0.79082 (28247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7952 (mp0) cc_final: 0.7635 (mp0) REVERT: A 132 MET cc_start: 0.7632 (ppp) cc_final: 0.7316 (ppp) REVERT: A 208 MET cc_start: 0.8543 (tmm) cc_final: 0.8209 (tmm) REVERT: A 290 MET cc_start: 0.8027 (mmm) cc_final: 0.7736 (mmt) REVERT: A 309 MET cc_start: 0.6703 (ppp) cc_final: 0.5972 (ppp) REVERT: A 310 MET cc_start: 0.8313 (mpp) cc_final: 0.7817 (mpp) REVERT: A 692 MET cc_start: 0.8882 (mmp) cc_final: 0.8614 (mmm) REVERT: B 45 TYR cc_start: 0.7885 (m-10) cc_final: 0.7587 (m-80) REVERT: B 158 MET cc_start: 0.8778 (mtp) cc_final: 0.8512 (mmp) REVERT: B 283 ASP cc_start: 0.7370 (m-30) cc_final: 0.6909 (t70) REVERT: B 551 PHE cc_start: 0.7515 (p90) cc_final: 0.7227 (p90) REVERT: B 683 MET cc_start: 0.7018 (tmm) cc_final: 0.6784 (tmm) REVERT: B 694 PHE cc_start: 0.9310 (t80) cc_final: 0.8919 (t80) REVERT: B 798 PHE cc_start: 0.9537 (m-80) cc_final: 0.9247 (m-80) REVERT: B 961 LEU cc_start: 0.8844 (pp) cc_final: 0.8541 (pp) REVERT: B 1007 MET cc_start: 0.8430 (ppp) cc_final: 0.7817 (ppp) REVERT: B 1011 MET cc_start: 0.8997 (mpp) cc_final: 0.8514 (mpp) REVERT: B 1101 PHE cc_start: 0.8732 (m-80) cc_final: 0.8499 (m-80) REVERT: B 1158 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8703 (tp30) REVERT: B 1169 LYS cc_start: 0.9433 (ttpp) cc_final: 0.8952 (tttt) REVERT: B 1173 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9102 (mm-30) REVERT: B 1348 PHE cc_start: 0.8753 (m-10) cc_final: 0.8472 (m-10) REVERT: E 1228 LEU cc_start: 0.9478 (mt) cc_final: 0.9189 (mt) REVERT: E 1238 ASP cc_start: 0.9151 (p0) cc_final: 0.8892 (p0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2940 time to fit residues: 104.8871 Evaluate side-chains 166 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 78 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 224 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 104 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 129 optimal weight: 0.0470 chunk 89 optimal weight: 0.8980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** 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 = 0.3531 r_free = 0.3531 target = 0.062067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.038658 restraints weight = 149339.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.040354 restraints weight = 87733.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.041521 restraints weight = 61164.402| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20937 Z= 0.139 Angle : 0.722 9.794 28247 Z= 0.372 Chirality : 0.045 0.215 3118 Planarity : 0.005 0.071 3616 Dihedral : 5.825 31.554 2731 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.38 (0.17), residues: 2503 helix: 0.04 (0.14), residues: 1366 sheet: -1.80 (0.36), residues: 197 loop : -2.08 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 41 HIS 0.013 0.001 HIS A 89 PHE 0.015 0.001 PHE B 114 TYR 0.028 0.002 TYR B 969 ARG 0.007 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 1092) hydrogen bonds : angle 5.51777 ( 3222) covalent geometry : bond 0.00299 (20937) covalent geometry : angle 0.72160 (28247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8645 (pmm) cc_final: 0.8265 (pmm) REVERT: A 23 GLU cc_start: 0.8043 (mp0) cc_final: 0.7798 (mp0) REVERT: A 132 MET cc_start: 0.7745 (ppp) cc_final: 0.7389 (ppp) REVERT: A 290 MET cc_start: 0.7823 (mmm) cc_final: 0.7482 (mmt) REVERT: A 309 MET cc_start: 0.6740 (ppp) cc_final: 0.6013 (ppp) REVERT: A 310 MET cc_start: 0.8327 (mpp) cc_final: 0.7814 (mpp) REVERT: A 726 CYS cc_start: 0.7823 (m) cc_final: 0.7515 (p) REVERT: B 283 ASP cc_start: 0.7471 (m-30) cc_final: 0.6970 (t70) REVERT: B 551 PHE cc_start: 0.7415 (p90) cc_final: 0.7115 (p90) REVERT: B 579 MET cc_start: 0.2595 (mtt) cc_final: 0.2150 (mtt) REVERT: B 683 MET cc_start: 0.7341 (tmm) cc_final: 0.7141 (tmm) REVERT: B 694 PHE cc_start: 0.9366 (t80) cc_final: 0.8949 (t80) REVERT: B 722 LYS cc_start: 0.8914 (mmpt) cc_final: 0.8526 (pttp) REVERT: B 787 PHE cc_start: 0.9374 (t80) cc_final: 0.8939 (t80) REVERT: B 798 PHE cc_start: 0.9517 (m-80) cc_final: 0.9185 (m-80) REVERT: B 961 LEU cc_start: 0.8714 (pp) cc_final: 0.8416 (pp) REVERT: B 1008 VAL cc_start: 0.9034 (t) cc_final: 0.8576 (t) REVERT: B 1009 MET cc_start: 0.9302 (mmt) cc_final: 0.8998 (mmt) REVERT: B 1090 MET cc_start: 0.8671 (tpt) cc_final: 0.8378 (mtp) REVERT: B 1169 LYS cc_start: 0.9541 (ttpp) cc_final: 0.9264 (tttm) REVERT: B 1191 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7850 (mt-10) REVERT: B 1247 LEU cc_start: 0.9195 (mm) cc_final: 0.8949 (mp) REVERT: B 1348 PHE cc_start: 0.8697 (m-10) cc_final: 0.8443 (m-10) REVERT: E 1231 TYR cc_start: 0.9009 (m-80) cc_final: 0.8647 (m-80) REVERT: E 1238 ASP cc_start: 0.9087 (p0) cc_final: 0.8824 (p0) REVERT: E 1243 TYR cc_start: 0.8326 (m-80) cc_final: 0.7571 (m-80) REVERT: E 1303 GLU cc_start: 0.9506 (mp0) cc_final: 0.9280 (mp0) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2873 time to fit residues: 113.1336 Evaluate side-chains 186 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1213 GLN ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.061047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038003 restraints weight = 144053.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.039594 restraints weight = 87376.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040697 restraints weight = 61771.129| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20937 Z= 0.159 Angle : 0.738 10.863 28247 Z= 0.382 Chirality : 0.046 0.201 3118 Planarity : 0.005 0.070 3616 Dihedral : 5.807 41.091 2731 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.42 (0.17), residues: 2503 helix: 0.01 (0.14), residues: 1370 sheet: -1.85 (0.36), residues: 203 loop : -2.10 (0.21), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 41 HIS 0.010 0.001 HIS A 89 PHE 0.017 0.001 PHE B 976 TYR 0.028 0.002 TYR B1328 ARG 0.006 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 1092) hydrogen bonds : angle 5.59349 ( 3222) covalent geometry : bond 0.00345 (20937) covalent geometry : angle 0.73766 (28247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8616 (pmm) cc_final: 0.8231 (pmm) REVERT: A 23 GLU cc_start: 0.8062 (mp0) cc_final: 0.7812 (mp0) REVERT: A 132 MET cc_start: 0.7734 (ppp) cc_final: 0.7465 (ppp) REVERT: A 147 MET cc_start: 0.3011 (ppp) cc_final: 0.1585 (mmm) REVERT: A 208 MET cc_start: 0.8519 (tmm) cc_final: 0.8175 (tmm) REVERT: A 290 MET cc_start: 0.8040 (mmm) cc_final: 0.7702 (mmt) REVERT: A 309 MET cc_start: 0.6809 (ppp) cc_final: 0.6108 (ppp) REVERT: A 310 MET cc_start: 0.8232 (mpp) cc_final: 0.7735 (mpp) REVERT: A 726 CYS cc_start: 0.7871 (m) cc_final: 0.7461 (p) REVERT: A 727 ASN cc_start: 0.6559 (t0) cc_final: 0.5996 (m-40) REVERT: B 283 ASP cc_start: 0.7411 (m-30) cc_final: 0.6900 (t70) REVERT: B 287 MET cc_start: 0.8667 (tpt) cc_final: 0.8363 (mpp) REVERT: B 551 PHE cc_start: 0.7366 (p90) cc_final: 0.7136 (p90) REVERT: B 579 MET cc_start: 0.2474 (mtt) cc_final: 0.2052 (mtt) REVERT: B 694 PHE cc_start: 0.9362 (t80) cc_final: 0.8872 (t80) REVERT: B 722 LYS cc_start: 0.8887 (mmpt) cc_final: 0.8484 (pttp) REVERT: B 787 PHE cc_start: 0.9370 (t80) cc_final: 0.8936 (t80) REVERT: B 798 PHE cc_start: 0.9535 (m-80) cc_final: 0.9211 (m-80) REVERT: B 961 LEU cc_start: 0.8732 (pp) cc_final: 0.8383 (pp) REVERT: B 1101 PHE cc_start: 0.8876 (m-80) cc_final: 0.8561 (m-80) REVERT: B 1169 LYS cc_start: 0.9517 (ttpp) cc_final: 0.9173 (ttmm) REVERT: B 1247 LEU cc_start: 0.9161 (mm) cc_final: 0.8907 (mt) REVERT: B 1348 PHE cc_start: 0.8706 (m-10) cc_final: 0.8443 (m-10) REVERT: E 1231 TYR cc_start: 0.9031 (m-80) cc_final: 0.8645 (m-80) REVERT: E 1238 ASP cc_start: 0.9117 (p0) cc_final: 0.8826 (p0) REVERT: E 1242 ARG cc_start: 0.8588 (ptt180) cc_final: 0.8134 (ptt180) REVERT: E 1243 TYR cc_start: 0.8328 (m-80) cc_final: 0.7590 (m-80) REVERT: E 1303 GLU cc_start: 0.9511 (mp0) cc_final: 0.9269 (mp0) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2985 time to fit residues: 112.1539 Evaluate side-chains 180 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 120 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 111 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 52 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.035571 restraints weight = 151941.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.037054 restraints weight = 91363.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.038074 restraints weight = 64337.867| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 20937 Z= 0.323 Angle : 0.945 15.102 28247 Z= 0.491 Chirality : 0.052 0.246 3118 Planarity : 0.007 0.069 3616 Dihedral : 6.698 38.238 2731 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.15 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.15 (0.16), residues: 2503 helix: -0.65 (0.13), residues: 1366 sheet: -2.37 (0.35), residues: 197 loop : -2.26 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 173 HIS 0.011 0.002 HIS B 949 PHE 0.022 0.003 PHE A 441 TYR 0.036 0.004 TYR E1328 ARG 0.007 0.001 ARG B1466 Details of bonding type rmsd hydrogen bonds : bond 0.05833 ( 1092) hydrogen bonds : angle 6.22693 ( 3222) covalent geometry : bond 0.00677 (20937) covalent geometry : angle 0.94543 (28247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5006 Ramachandran restraints generated. 2503 Oldfield, 0 Emsley, 2503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7966 (mp0) cc_final: 0.7761 (mp0) REVERT: A 208 MET cc_start: 0.8584 (tmm) cc_final: 0.8132 (tmm) REVERT: A 290 MET cc_start: 0.8151 (mmm) cc_final: 0.7793 (mmt) REVERT: A 309 MET cc_start: 0.7043 (ppp) cc_final: 0.6630 (ppp) REVERT: A 378 MET cc_start: 0.2979 (mpp) cc_final: 0.2755 (mpp) REVERT: B 158 MET cc_start: 0.8884 (mtp) cc_final: 0.8546 (mmp) REVERT: B 551 PHE cc_start: 0.7541 (p90) cc_final: 0.7275 (p90) REVERT: B 579 MET cc_start: 0.4151 (mtt) cc_final: 0.3891 (mtt) REVERT: B 694 PHE cc_start: 0.9253 (t80) cc_final: 0.8828 (t80) REVERT: B 798 PHE cc_start: 0.9528 (m-80) cc_final: 0.9264 (m-80) REVERT: B 961 LEU cc_start: 0.8893 (pp) cc_final: 0.8496 (pp) REVERT: B 1101 PHE cc_start: 0.8885 (m-80) cc_final: 0.8503 (m-80) REVERT: B 1158 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8658 (tp30) REVERT: B 1169 LYS cc_start: 0.9411 (ttpp) cc_final: 0.9184 (tttt) REVERT: B 1348 PHE cc_start: 0.8779 (m-10) cc_final: 0.8498 (m-10) REVERT: E 1228 LEU cc_start: 0.9526 (mt) cc_final: 0.9233 (mt) REVERT: E 1231 TYR cc_start: 0.9055 (m-80) cc_final: 0.8742 (m-80) REVERT: E 1238 ASP cc_start: 0.9142 (p0) cc_final: 0.8810 (p0) REVERT: E 1243 TYR cc_start: 0.8388 (m-80) cc_final: 0.7845 (m-80) REVERT: E 1303 GLU cc_start: 0.9478 (mp0) cc_final: 0.9254 (mp0) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2807 time to fit residues: 94.6456 Evaluate side-chains 158 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 87 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 243 optimal weight: 0.0670 chunk 13 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 245 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 2 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 234 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 52 GLN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1293 GLN ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.061216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.037917 restraints weight = 147596.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.039570 restraints weight = 87211.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040706 restraints weight = 61064.054| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20937 Z= 0.152 Angle : 0.772 12.546 28247 Z= 0.396 Chirality : 0.047 0.220 3118 Planarity : 0.005 0.065 3616 Dihedral : 6.004 32.620 2731 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 19.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.58 (0.16), residues: 2503 helix: -0.16 (0.14), residues: 1378 sheet: -1.65 (0.36), residues: 197 loop : -2.19 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 41 HIS 0.011 0.001 HIS A 89 PHE 0.018 0.002 PHE B 976 TYR 0.029 0.002 TYR B1328 ARG 0.005 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.04749 ( 1092) hydrogen bonds : angle 5.73225 ( 3222) covalent geometry : bond 0.00329 (20937) covalent geometry : angle 0.77157 (28247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7108.54 seconds wall clock time: 125 minutes 28.15 seconds (7528.15 seconds total)