Starting phenix.real_space_refine on Wed Jun 18 06:04:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhk_36271/06_2025/8jhk_36271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhk_36271/06_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_36271/06_2025/8jhk_36271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhk_36271/06_2025/8jhk_36271.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhk_36271/06_2025/8jhk_36271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhk_36271/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 11.05, per 1000 atoms: 0.54 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: 5.15 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: 2.57 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: 8.36 Time building geometry restraints manager: 6.09 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: 0.780 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: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 47.110 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.330 ------------------------------------------------------------------------------- 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 : 2.294 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: 0.3003 time to fit residues: 92.0031 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 : 2.617 ------------------------------------------------------------------------------- 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 = 68)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.037049 restraints weight = 147733.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.038643 restraints weight = 87476.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.039737 restraints weight = 60734.685| |-----------------------------------------------------------------------------| 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 : 2.351 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: 0.7697 (ppp) cc_final: 0.7440 (ppp) REVERT: A 290 MET cc_start: 0.7325 (mmp) cc_final: 0.7044 (mmt) REVERT: A 309 MET cc_start: 0.6856 (ppp) cc_final: 0.6352 (ppp) REVERT: B 120 MET cc_start: 0.9089 (mmp) cc_final: 0.8862 (mmm) REVERT: B 283 ASP cc_start: 0.7151 (m-30) cc_final: 0.6672 (t0) REVERT: B 306 MET cc_start: -0.2468 (mtt) cc_final: -0.2891 (mtt) REVERT: B 470 MET cc_start: 0.6508 (ppp) cc_final: 0.6265 (ppp) REVERT: B 680 MET cc_start: 0.8880 (ppp) cc_final: 0.8659 (ppp) REVERT: B 683 MET cc_start: 0.7107 (tmm) cc_final: 0.6768 (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: 0.9521 (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: 0.6879 (ptm) cc_final: 0.6504 (ptm) REVERT: B 1007 MET cc_start: 0.8409 (ppp) cc_final: 0.7849 (ppp) REVERT: B 1008 VAL cc_start: 0.9028 (t) cc_final: 0.8477 (t) REVERT: B 1011 MET cc_start: 0.9152 (mpp) cc_final: 0.8451 (mpp) REVERT: B 1038 PHE cc_start: 0.7205 (p90) cc_final: 0.6905 (t80) REVERT: B 1101 PHE cc_start: 0.8847 (m-80) cc_final: 0.8397 (m-80) REVERT: B 1313 MET cc_start: 0.8434 (tmm) cc_final: 0.8193 (tmm) REVERT: B 1328 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: B 1348 PHE cc_start: 0.8679 (m-10) cc_final: 0.8332 (m-10) outliers start: 6 outliers final: 2 residues processed: 230 average time/residue: 0.3174 time to fit residues: 117.1813 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 : 2.344 ------------------------------------------------------------------------------- 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: 10.0000 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: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ** 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** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.058577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036296 restraints weight = 149825.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037799 restraints weight = 89262.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.038837 restraints weight = 62591.009| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20937 Z= 0.211 Angle : 0.774 12.495 28247 Z= 0.406 Chirality : 0.047 0.198 3118 Planarity : 0.006 0.085 3616 Dihedral : 6.631 45.159 2731 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.22 % Allowed : 6.38 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.21 (0.16), residues: 2503 helix: -0.59 (0.13), residues: 1356 sheet: -2.17 (0.34), residues: 211 loop : -2.51 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 41 HIS 0.006 0.001 HIS A 89 PHE 0.016 0.002 PHE B 869 TYR 0.026 0.002 TYR A 588 ARG 0.006 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.05369 ( 1092) hydrogen bonds : angle 6.11215 ( 3222) covalent geometry : bond 0.00448 (20937) covalent geometry : angle 0.77357 (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 209 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 204 time to evaluate : 2.404 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: 0.7884 (ppp) cc_final: 0.7677 (ppp) REVERT: A 208 MET cc_start: 0.8624 (tmm) cc_final: 0.8183 (tmm) REVERT: A 309 MET cc_start: 0.7263 (ppp) cc_final: 0.6628 (ppp) REVERT: B 283 ASP cc_start: 0.7208 (m-30) cc_final: 0.6730 (t0) REVERT: B 306 MET cc_start: -0.2522 (mtt) cc_final: -0.2763 (mtt) REVERT: B 680 MET cc_start: 0.8711 (ppp) cc_final: 0.8451 (ppp) REVERT: B 683 MET cc_start: 0.7021 (tmm) cc_final: 0.6661 (tmm) REVERT: B 694 PHE cc_start: 0.9452 (t80) cc_final: 0.9006 (t80) REVERT: B 785 ASP cc_start: 0.8617 (m-30) cc_final: 0.8346 (p0) REVERT: B 798 PHE cc_start: 0.9552 (m-80) cc_final: 0.9232 (m-80) REVERT: B 800 MET cc_start: 0.9278 (tmm) cc_final: 0.8871 (tmm) REVERT: B 1007 MET cc_start: 0.8549 (ppp) cc_final: 0.7992 (ppp) REVERT: B 1008 VAL cc_start: 0.9154 (t) cc_final: 0.8488 (t) REVERT: B 1011 MET cc_start: 0.8935 (mpp) cc_final: 0.8322 (mpp) REVERT: B 1033 MET cc_start: 0.8877 (mmp) cc_final: 0.8410 (mmp) REVERT: B 1090 MET cc_start: 0.8714 (tpt) cc_final: 0.8403 (mtp) REVERT: B 1101 PHE cc_start: 0.8770 (m-80) cc_final: 0.8434 (m-80) REVERT: B 1265 LEU cc_start: 0.9311 (mp) cc_final: 0.9097 (mp) REVERT: B 1348 PHE cc_start: 0.8723 (m-10) cc_final: 0.8446 (m-10) REVERT: E 1228 LEU cc_start: 0.9443 (mt) cc_final: 0.9155 (mt) outliers start: 5 outliers final: 1 residues processed: 208 average time/residue: 0.3083 time to fit residues: 103.5319 Evaluate side-chains 158 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 2.343 ------------------------------------------------------------------------------- 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: 4.9990 chunk 115 optimal weight: 0.0270 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 213 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 186 optimal weight: 0.8980 overall best weight: 1.3642 ------------------------------------------------------------------------------- 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 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 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 HIS ** 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** ** E1251 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 = 0.3495 r_free = 0.3495 target = 0.060319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037615 restraints weight = 146465.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.039207 restraints weight = 86878.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.040313 restraints weight = 60658.536| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20937 Z= 0.146 Angle : 0.707 8.735 28247 Z= 0.369 Chirality : 0.044 0.168 3118 Planarity : 0.005 0.079 3616 Dihedral : 6.199 38.727 2731 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.22 % Allowed : 5.42 % Favored : 94.36 % 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: -1.74 (0.17), residues: 2503 helix: -0.23 (0.14), residues: 1351 sheet: -2.02 (0.33), residues: 225 loop : -2.23 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 102 HIS 0.011 0.001 HIS A 89 PHE 0.020 0.002 PHE A 387 TYR 0.047 0.002 TYR E1328 ARG 0.009 0.001 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04824 ( 1092) hydrogen bonds : angle 5.72788 ( 3222) covalent geometry : bond 0.00314 (20937) covalent geometry : angle 0.70656 (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 248 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 243 time to evaluate : 2.469 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 132 MET cc_start: 0.7933 (ppp) cc_final: 0.7698 (ppp) REVERT: A 208 MET cc_start: 0.8586 (tmm) cc_final: 0.8170 (tmm) REVERT: A 290 MET cc_start: 0.8005 (mmm) cc_final: 0.7726 (mmt) REVERT: A 309 MET cc_start: 0.7001 (ppp) cc_final: 0.6534 (ppp) REVERT: B 283 ASP cc_start: 0.7720 (m-30) cc_final: 0.7254 (t70) REVERT: B 306 MET cc_start: -0.2433 (mtt) cc_final: -0.2732 (mtt) REVERT: B 551 PHE cc_start: 0.7289 (p90) cc_final: 0.7035 (p90) REVERT: B 683 MET cc_start: 0.6971 (tmm) cc_final: 0.6669 (tmm) REVERT: B 694 PHE cc_start: 0.9362 (t80) cc_final: 0.8904 (t80) REVERT: B 785 ASP cc_start: 0.8498 (m-30) cc_final: 0.8281 (p0) REVERT: B 787 PHE cc_start: 0.9386 (t80) cc_final: 0.8942 (t80) REVERT: B 798 PHE cc_start: 0.9521 (m-80) cc_final: 0.9171 (m-80) REVERT: B 961 LEU cc_start: 0.8773 (pp) cc_final: 0.8513 (pp) REVERT: B 1007 MET cc_start: 0.8475 (ppp) cc_final: 0.7868 (ppp) REVERT: B 1011 MET cc_start: 0.8934 (mpp) cc_final: 0.8291 (mpp) REVERT: B 1033 MET cc_start: 0.8976 (mmp) cc_final: 0.8736 (mmm) REVERT: B 1101 PHE cc_start: 0.8708 (m-80) cc_final: 0.8400 (m-80) REVERT: B 1265 LEU cc_start: 0.9226 (mp) cc_final: 0.9018 (mp) REVERT: B 1489 TYR cc_start: 0.8411 (m-80) cc_final: 0.8096 (m-80) REVERT: E 1228 LEU cc_start: 0.9447 (mt) cc_final: 0.9243 (mt) REVERT: E 1238 ASP cc_start: 0.9416 (p0) cc_final: 0.9131 (p0) outliers start: 5 outliers final: 2 residues processed: 247 average time/residue: 0.3046 time to fit residues: 121.4156 Evaluate side-chains 179 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 177 time to evaluate : 2.520 ------------------------------------------------------------------------------- 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: 2.9990 chunk 64 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 18 optimal weight: 0.3980 chunk 207 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 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** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.060073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.037167 restraints weight = 152515.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.038825 restraints weight = 87895.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.039931 restraints weight = 60504.953| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20937 Z= 0.163 Angle : 0.728 13.169 28247 Z= 0.379 Chirality : 0.045 0.212 3118 Planarity : 0.005 0.079 3616 Dihedral : 6.124 32.832 2731 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.09 % Allowed : 4.11 % Favored : 95.80 % 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: -1.66 (0.17), residues: 2503 helix: -0.18 (0.14), residues: 1345 sheet: -1.98 (0.33), residues: 225 loop : -2.16 (0.20), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 PHE 0.025 0.002 PHE A 187 TYR 0.044 0.002 TYR B 969 ARG 0.004 0.000 ARG B 534 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 1092) hydrogen bonds : angle 5.74690 ( 3222) covalent geometry : bond 0.00354 (20937) covalent geometry : angle 0.72778 (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 228 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7876 (mp0) cc_final: 0.7550 (mp0) REVERT: A 132 MET cc_start: 0.7967 (ppp) cc_final: 0.7747 (ppp) REVERT: A 208 MET cc_start: 0.8620 (tmm) cc_final: 0.8210 (tmm) REVERT: A 309 MET cc_start: 0.6632 (ppp) cc_final: 0.5821 (ppp) REVERT: A 310 MET cc_start: 0.8343 (mpp) cc_final: 0.7835 (mpp) REVERT: A 313 MET cc_start: -0.2044 (ttp) cc_final: -0.2710 (ttp) REVERT: A 692 MET cc_start: 0.8816 (mmp) cc_final: 0.8565 (mmm) REVERT: A 727 ASN cc_start: 0.6600 (t0) cc_final: 0.6398 (t0) REVERT: B 283 ASP cc_start: 0.7696 (m-30) cc_final: 0.7302 (t70) REVERT: B 306 MET cc_start: -0.1763 (mtt) cc_final: -0.2033 (mtt) REVERT: B 470 MET cc_start: 0.6057 (ppp) cc_final: 0.5773 (ppp) REVERT: B 680 MET cc_start: 0.8710 (ppp) cc_final: 0.8447 (ppp) REVERT: B 683 MET cc_start: 0.6998 (tmm) cc_final: 0.6771 (tmm) REVERT: B 694 PHE cc_start: 0.9369 (t80) cc_final: 0.8924 (t80) REVERT: B 785 ASP cc_start: 0.8494 (m-30) cc_final: 0.8280 (p0) REVERT: B 798 PHE cc_start: 0.9517 (m-80) cc_final: 0.9183 (m-80) REVERT: B 800 MET cc_start: 0.9441 (tpt) cc_final: 0.9137 (tpp) REVERT: B 943 MET cc_start: 0.8204 (mtt) cc_final: 0.8003 (mtp) REVERT: B 961 LEU cc_start: 0.8788 (pp) cc_final: 0.8547 (pp) REVERT: B 1007 MET cc_start: 0.8584 (ppp) cc_final: 0.7970 (ppp) REVERT: B 1008 VAL cc_start: 0.9161 (t) cc_final: 0.8450 (t) REVERT: B 1011 MET cc_start: 0.8916 (mpp) cc_final: 0.8183 (mpp) REVERT: B 1090 MET cc_start: 0.8681 (tpt) cc_final: 0.8381 (mtp) REVERT: B 1101 PHE cc_start: 0.8683 (m-80) cc_final: 0.8397 (m-80) REVERT: B 1247 LEU cc_start: 0.9230 (mm) cc_final: 0.9004 (mt) REVERT: B 1348 PHE cc_start: 0.8682 (m-10) cc_final: 0.8416 (m-10) REVERT: E 1238 ASP cc_start: 0.9166 (p0) cc_final: 0.8943 (p0) REVERT: E 1313 MET cc_start: 0.7432 (tmm) cc_final: 0.7149 (tmm) outliers start: 2 outliers final: 0 residues processed: 228 average time/residue: 0.3116 time to fit residues: 113.7714 Evaluate side-chains 163 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 2.352 ------------------------------------------------------------------------------- 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: 5.9990 chunk 60 optimal weight: 0.8980 chunk 132 optimal weight: 0.0040 chunk 110 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 215 optimal weight: 0.0060 chunk 4 optimal weight: 9.9990 chunk 199 optimal weight: 0.0470 chunk 144 optimal weight: 9.9990 overall best weight: 1.3908 ------------------------------------------------------------------------------- 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 154 HIS B 213 GLN ** B 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS B1022 ASN B1203 ASN ** 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** B1545 HIS ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.061604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.038227 restraints weight = 148000.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039875 restraints weight = 87515.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.041006 restraints weight = 61283.183| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3100 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= 0.145 Angle : 0.712 10.772 28247 Z= 0.369 Chirality : 0.045 0.202 3118 Planarity : 0.005 0.077 3616 Dihedral : 5.886 30.489 2731 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: -1.52 (0.17), residues: 2503 helix: -0.06 (0.14), residues: 1364 sheet: -1.91 (0.34), residues: 226 loop : -2.16 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 102 HIS 0.009 0.001 HIS A 89 PHE 0.033 0.001 PHE B 993 TYR 0.044 0.002 TYR B 969 ARG 0.005 0.000 ARG A 683 Details of bonding type rmsd hydrogen bonds : bond 0.04581 ( 1092) hydrogen bonds : angle 5.56351 ( 3222) covalent geometry : bond 0.00311 (20937) covalent geometry : angle 0.71188 (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 244 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 2.510 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 22 MET cc_start: 0.8551 (pmm) cc_final: 0.8063 (pmm) REVERT: A 23 GLU cc_start: 0.8123 (mp0) cc_final: 0.7851 (mp0) REVERT: A 290 MET cc_start: 0.8011 (mmm) cc_final: 0.7748 (mmt) REVERT: A 309 MET cc_start: 0.6530 (ppp) cc_final: 0.5915 (ppp) REVERT: A 692 MET cc_start: 0.8811 (mmp) cc_final: 0.8573 (mmm) REVERT: B 185 LYS cc_start: 0.9563 (mmmt) cc_final: 0.9297 (mtpp) REVERT: B 283 ASP cc_start: 0.7684 (m-30) cc_final: 0.7220 (t70) REVERT: B 551 PHE cc_start: 0.7366 (p90) cc_final: 0.7144 (p90) REVERT: B 593 MET cc_start: 0.3134 (mpp) cc_final: 0.2782 (mpp) REVERT: B 694 PHE cc_start: 0.9419 (t80) cc_final: 0.9064 (t80) REVERT: B 722 LYS cc_start: 0.8915 (mmpt) cc_final: 0.8527 (pttp) REVERT: B 787 PHE cc_start: 0.9373 (t80) cc_final: 0.8939 (t80) REVERT: B 798 PHE cc_start: 0.9513 (m-80) cc_final: 0.9192 (m-80) REVERT: B 800 MET cc_start: 0.9419 (tpt) cc_final: 0.9116 (tpp) REVERT: B 878 LEU cc_start: 0.9281 (mp) cc_final: 0.9074 (mp) REVERT: B 943 MET cc_start: 0.8243 (mtt) cc_final: 0.7997 (mtp) REVERT: B 961 LEU cc_start: 0.8670 (pp) cc_final: 0.8417 (pp) REVERT: B 1007 MET cc_start: 0.8601 (ppp) cc_final: 0.7980 (ppp) REVERT: B 1008 VAL cc_start: 0.9209 (t) cc_final: 0.8465 (t) REVERT: B 1011 MET cc_start: 0.9007 (mpp) cc_final: 0.8188 (mpp) REVERT: B 1033 MET cc_start: 0.8768 (mmm) cc_final: 0.8494 (mmm) REVERT: B 1090 MET cc_start: 0.8566 (tpt) cc_final: 0.8187 (tpt) REVERT: B 1101 PHE cc_start: 0.8645 (m-80) cc_final: 0.8349 (m-80) REVERT: B 1201 LEU cc_start: 0.9668 (mm) cc_final: 0.9257 (mm) REVERT: B 1202 GLU cc_start: 0.8733 (pp20) cc_final: 0.8492 (pp20) REVERT: B 1212 MET cc_start: 0.8902 (pmm) cc_final: 0.8666 (pmm) REVERT: B 1247 LEU cc_start: 0.9116 (mm) cc_final: 0.8840 (mt) REVERT: B 1303 GLU cc_start: 0.8921 (mp0) cc_final: 0.8648 (mp0) REVERT: B 1348 PHE cc_start: 0.8683 (m-10) cc_final: 0.8431 (m-10) REVERT: E 1231 TYR cc_start: 0.9040 (m-80) cc_final: 0.8679 (m-80) REVERT: E 1240 TYR cc_start: 0.8753 (t80) cc_final: 0.8314 (t80) REVERT: E 1242 ARG cc_start: 0.8371 (ptt180) cc_final: 0.7887 (ptt180) REVERT: E 1243 TYR cc_start: 0.8054 (m-80) cc_final: 0.7260 (m-80) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3109 time to fit residues: 121.7303 Evaluate side-chains 176 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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: 0.0370 chunk 214 optimal weight: 8.9990 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 161 optimal weight: 0.7980 chunk 173 optimal weight: 0.4980 chunk 69 optimal weight: 10.0000 chunk 130 optimal weight: 0.0670 chunk 220 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 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 ** 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 = 0.3524 r_free = 0.3524 target = 0.061652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.038451 restraints weight = 146609.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.040074 restraints weight = 87078.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.041173 restraints weight = 60889.690| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20937 Z= 0.143 Angle : 0.720 10.512 28247 Z= 0.373 Chirality : 0.045 0.249 3118 Planarity : 0.005 0.075 3616 Dihedral : 5.810 31.353 2731 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -1.40 (0.17), residues: 2503 helix: 0.01 (0.14), residues: 1356 sheet: -1.66 (0.35), residues: 211 loop : -2.09 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1043 HIS 0.015 0.001 HIS A 89 PHE 0.037 0.001 PHE E1348 TYR 0.040 0.002 TYR B 969 ARG 0.009 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 1092) hydrogen bonds : angle 5.56505 ( 3222) covalent geometry : bond 0.00307 (20937) covalent geometry : angle 0.71990 (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 239 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.461 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: 0.8501 (pmm) cc_final: 0.8114 (pmm) REVERT: A 23 GLU cc_start: 0.8078 (mp0) cc_final: 0.7869 (mp0) REVERT: A 132 MET cc_start: 0.7755 (ppp) cc_final: 0.7393 (ppp) REVERT: A 290 MET cc_start: 0.7783 (mmm) cc_final: 0.7545 (mmt) REVERT: A 309 MET cc_start: 0.6806 (ppp) cc_final: 0.6007 (ppp) REVERT: A 310 MET cc_start: 0.8326 (mpp) cc_final: 0.7862 (mpp) REVERT: A 692 MET cc_start: 0.8808 (mmp) cc_final: 0.8583 (mmm) REVERT: A 726 CYS cc_start: 0.7818 (m) cc_final: 0.7517 (p) REVERT: B 45 TYR cc_start: 0.7980 (m-10) cc_final: 0.7603 (m-80) REVERT: B 185 LYS cc_start: 0.9569 (mmmt) cc_final: 0.9315 (mtpp) REVERT: B 283 ASP cc_start: 0.7687 (m-30) cc_final: 0.7255 (t70) REVERT: B 551 PHE cc_start: 0.7372 (p90) cc_final: 0.7130 (p90) REVERT: B 593 MET cc_start: 0.3301 (mpp) cc_final: 0.2835 (mpp) REVERT: B 694 PHE cc_start: 0.9386 (t80) cc_final: 0.8938 (t80) REVERT: B 722 LYS cc_start: 0.8893 (mmpt) cc_final: 0.8483 (pttp) REVERT: B 787 PHE cc_start: 0.9372 (t80) cc_final: 0.8937 (t80) REVERT: B 798 PHE cc_start: 0.9519 (m-80) cc_final: 0.9204 (m-80) REVERT: B 800 MET cc_start: 0.9415 (tpt) cc_final: 0.9077 (tpp) REVERT: B 878 LEU cc_start: 0.9316 (mp) cc_final: 0.9072 (mp) REVERT: B 943 MET cc_start: 0.8328 (mtt) cc_final: 0.8059 (mtp) REVERT: B 961 LEU cc_start: 0.8672 (pp) cc_final: 0.8420 (pp) REVERT: B 1007 MET cc_start: 0.8598 (ppp) cc_final: 0.7987 (ppp) REVERT: B 1008 VAL cc_start: 0.9253 (t) cc_final: 0.8576 (t) REVERT: B 1011 MET cc_start: 0.9023 (mpp) cc_final: 0.8255 (mpp) REVERT: B 1033 MET cc_start: 0.8663 (mmm) cc_final: 0.8427 (mmm) REVERT: B 1169 LYS cc_start: 0.9581 (ttpp) cc_final: 0.9209 (ttmm) REVERT: B 1202 GLU cc_start: 0.8556 (pp20) cc_final: 0.8301 (pp20) REVERT: B 1247 LEU cc_start: 0.9121 (mm) cc_final: 0.8829 (mt) REVERT: B 1348 PHE cc_start: 0.8705 (m-10) cc_final: 0.8454 (m-10) REVERT: E 1228 LEU cc_start: 0.9410 (mt) cc_final: 0.9162 (mt) REVERT: E 1231 TYR cc_start: 0.8997 (m-80) cc_final: 0.8637 (m-80) REVERT: E 1238 ASP cc_start: 0.9162 (p0) cc_final: 0.8933 (p0) REVERT: E 1242 ARG cc_start: 0.8409 (ptt180) cc_final: 0.7933 (ptt180) REVERT: E 1243 TYR cc_start: 0.8056 (m-80) cc_final: 0.7240 (m-80) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3010 time to fit residues: 115.9533 Evaluate side-chains 188 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 2.406 ------------------------------------------------------------------------------- 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: 5.9990 chunk 127 optimal weight: 7.9990 chunk 224 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 89 optimal weight: 0.0060 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 171 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.035885 restraints weight = 156126.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.037399 restraints weight = 92367.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.038429 restraints weight = 64619.728| |-----------------------------------------------------------------------------| r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 20937 Z= 0.278 Angle : 0.865 14.821 28247 Z= 0.452 Chirality : 0.050 0.233 3118 Planarity : 0.006 0.074 3616 Dihedral : 6.464 31.080 2731 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 25.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.88 (0.16), residues: 2503 helix: -0.39 (0.13), residues: 1337 sheet: -2.15 (0.34), residues: 209 loop : -2.18 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1043 HIS 0.009 0.002 HIS B 949 PHE 0.020 0.002 PHE A 441 TYR 0.037 0.003 TYR B 969 ARG 0.009 0.001 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.05436 ( 1092) hydrogen bonds : angle 6.08113 ( 3222) covalent geometry : bond 0.00585 (20937) covalent geometry : angle 0.86501 (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 206 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7881 (mp0) cc_final: 0.7588 (mp0) REVERT: A 132 MET cc_start: 0.7689 (ppp) cc_final: 0.7413 (ppp) REVERT: A 208 MET cc_start: 0.8491 (tmm) cc_final: 0.8094 (tmm) REVERT: A 290 MET cc_start: 0.8145 (mmm) cc_final: 0.7796 (mmt) REVERT: A 309 MET cc_start: 0.7021 (ppp) cc_final: 0.6425 (ppp) REVERT: A 310 MET cc_start: 0.8378 (mpp) cc_final: 0.7999 (mpp) REVERT: A 692 MET cc_start: 0.8948 (mmp) cc_final: 0.8645 (mmm) REVERT: B 158 MET cc_start: 0.8829 (mtp) cc_final: 0.8543 (mmp) REVERT: B 680 MET cc_start: 0.8728 (ppp) cc_final: 0.8527 (ppp) REVERT: B 694 PHE cc_start: 0.9303 (t80) cc_final: 0.8914 (t80) REVERT: B 798 PHE cc_start: 0.9547 (m-80) cc_final: 0.9278 (m-80) REVERT: B 800 MET cc_start: 0.9363 (tpt) cc_final: 0.8978 (tpp) REVERT: B 878 LEU cc_start: 0.9325 (mp) cc_final: 0.9115 (mp) REVERT: B 961 LEU cc_start: 0.8786 (pp) cc_final: 0.8399 (pp) REVERT: B 1008 VAL cc_start: 0.9316 (t) cc_final: 0.8783 (t) REVERT: B 1101 PHE cc_start: 0.8906 (m-80) cc_final: 0.8578 (m-80) REVERT: B 1169 LYS cc_start: 0.9442 (ttpp) cc_final: 0.8947 (tttt) REVERT: B 1173 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9103 (mm-30) REVERT: B 1348 PHE cc_start: 0.8775 (m-10) cc_final: 0.8488 (m-10) REVERT: B 1356 MET cc_start: 0.6036 (ppp) cc_final: 0.5797 (ppp) REVERT: E 1238 ASP cc_start: 0.9164 (p0) cc_final: 0.8913 (p0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2976 time to fit residues: 100.0518 Evaluate side-chains 157 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 2.278 ------------------------------------------------------------------------------- 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: 0.9980 chunk 88 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 164 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 97 optimal weight: 0.0470 chunk 90 optimal weight: 1.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 503 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.060780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.037592 restraints weight = 149012.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.039215 restraints weight = 88582.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.040288 restraints weight = 62059.939| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20937 Z= 0.157 Angle : 0.755 10.911 28247 Z= 0.390 Chirality : 0.046 0.196 3118 Planarity : 0.005 0.071 3616 Dihedral : 6.048 27.595 2731 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 19.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % 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: -1.59 (0.16), residues: 2503 helix: -0.14 (0.14), residues: 1347 sheet: -1.98 (0.34), residues: 221 loop : -2.09 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 41 HIS 0.011 0.001 HIS A 89 PHE 0.045 0.002 PHE E1348 TYR 0.038 0.002 TYR B 969 ARG 0.007 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 1092) hydrogen bonds : angle 5.75451 ( 3222) covalent geometry : bond 0.00339 (20937) covalent geometry : angle 0.75456 (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 227 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 2.542 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: A 22 MET cc_start: 0.8650 (pmm) cc_final: 0.8262 (pmm) REVERT: A 23 GLU cc_start: 0.7897 (mp0) cc_final: 0.7544 (mp0) REVERT: A 132 MET cc_start: 0.7819 (ppp) cc_final: 0.7495 (ppp) REVERT: A 290 MET cc_start: 0.8096 (mmm) cc_final: 0.7748 (mmt) REVERT: A 309 MET cc_start: 0.7071 (ppp) cc_final: 0.6596 (ppp) REVERT: A 692 MET cc_start: 0.8855 (mmp) cc_final: 0.8635 (mmm) REVERT: B 283 ASP cc_start: 0.7385 (m-30) cc_final: 0.6864 (t70) REVERT: B 551 PHE cc_start: 0.7407 (p90) cc_final: 0.7177 (p90) REVERT: B 689 TYR cc_start: 0.8432 (m-80) cc_final: 0.8168 (m-80) REVERT: B 694 PHE cc_start: 0.9353 (t80) cc_final: 0.8931 (t80) REVERT: B 722 LYS cc_start: 0.8903 (mmpt) cc_final: 0.8515 (pttp) REVERT: B 787 PHE cc_start: 0.9383 (t80) cc_final: 0.8978 (t80) REVERT: B 798 PHE cc_start: 0.9557 (m-80) cc_final: 0.9190 (m-80) REVERT: B 800 MET cc_start: 0.9399 (tpt) cc_final: 0.9096 (tpp) REVERT: B 878 LEU cc_start: 0.9276 (mp) cc_final: 0.9008 (mp) REVERT: B 961 LEU cc_start: 0.8749 (pp) cc_final: 0.8412 (pp) REVERT: B 1007 MET cc_start: 0.8497 (ppp) cc_final: 0.7984 (ppp) REVERT: B 1008 VAL cc_start: 0.9163 (t) cc_final: 0.8559 (t) REVERT: B 1011 MET cc_start: 0.8824 (mpp) cc_final: 0.8264 (mpp) REVERT: B 1060 GLN cc_start: 0.8302 (pp30) cc_final: 0.8034 (pp30) REVERT: B 1090 MET cc_start: 0.8690 (tpt) cc_final: 0.8460 (mtp) REVERT: B 1101 PHE cc_start: 0.8851 (m-80) cc_final: 0.8463 (m-80) REVERT: B 1169 LYS cc_start: 0.9425 (ttpp) cc_final: 0.8949 (tttm) REVERT: B 1173 GLU cc_start: 0.9565 (mm-30) cc_final: 0.9141 (mm-30) REVERT: B 1212 MET cc_start: 0.8877 (pmm) cc_final: 0.8645 (pmm) REVERT: B 1247 LEU cc_start: 0.9107 (mm) cc_final: 0.8865 (mt) REVERT: B 1348 PHE cc_start: 0.8700 (m-10) cc_final: 0.8420 (m-10) REVERT: E 1231 TYR cc_start: 0.9012 (m-80) cc_final: 0.8694 (m-80) REVERT: E 1238 ASP cc_start: 0.9106 (p0) cc_final: 0.8845 (p0) REVERT: E 1242 ARG cc_start: 0.8474 (ptt180) cc_final: 0.7977 (ptt180) REVERT: E 1243 TYR cc_start: 0.8245 (m-80) cc_final: 0.7421 (m-80) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.3048 time to fit residues: 111.0229 Evaluate side-chains 179 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 2.264 ------------------------------------------------------------------------------- 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: 0.0670 chunk 80 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 67 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 GLN 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** ** E1293 GLN ** 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 = 0.3511 r_free = 0.3511 target = 0.061079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.037857 restraints weight = 148679.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039504 restraints weight = 87996.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.040626 restraints weight = 61561.156| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20937 Z= 0.152 Angle : 0.741 10.696 28247 Z= 0.382 Chirality : 0.046 0.211 3118 Planarity : 0.005 0.071 3616 Dihedral : 5.873 29.732 2731 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -1.51 (0.16), residues: 2503 helix: -0.07 (0.14), residues: 1366 sheet: -1.78 (0.35), residues: 207 loop : -2.15 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 41 HIS 0.010 0.001 HIS A 89 PHE 0.014 0.001 PHE B 114 TYR 0.039 0.002 TYR B 969 ARG 0.007 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 1092) hydrogen bonds : angle 5.65425 ( 3222) covalent geometry : bond 0.00328 (20937) covalent geometry : angle 0.74125 (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 236 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 2.395 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 22 MET cc_start: 0.8675 (pmm) cc_final: 0.8323 (pmm) REVERT: A 23 GLU cc_start: 0.7852 (mp0) cc_final: 0.7484 (mp0) REVERT: A 132 MET cc_start: 0.7566 (ppp) cc_final: 0.7360 (ppp) REVERT: A 147 MET cc_start: 0.2775 (ppp) cc_final: 0.1580 (mmm) REVERT: A 290 MET cc_start: 0.7929 (mmm) cc_final: 0.7567 (mmt) REVERT: A 309 MET cc_start: 0.6801 (ppp) cc_final: 0.6232 (ppp) REVERT: A 692 MET cc_start: 0.8863 (mmp) cc_final: 0.8652 (mmm) REVERT: A 726 CYS cc_start: 0.7872 (m) cc_final: 0.7580 (p) REVERT: B 283 ASP cc_start: 0.7417 (m-30) cc_final: 0.6791 (t70) REVERT: B 287 MET cc_start: 0.8619 (tpt) cc_final: 0.8292 (mpp) REVERT: B 306 MET cc_start: -0.2976 (mmm) cc_final: -0.3378 (tpp) REVERT: B 431 MET cc_start: 0.7249 (tpt) cc_final: 0.6956 (tpt) REVERT: B 551 PHE cc_start: 0.7493 (p90) cc_final: 0.7164 (p90) REVERT: B 689 TYR cc_start: 0.8463 (m-80) cc_final: 0.8244 (m-80) REVERT: B 694 PHE cc_start: 0.9354 (t80) cc_final: 0.8853 (t80) REVERT: B 722 LYS cc_start: 0.8894 (mmpt) cc_final: 0.8467 (pttp) REVERT: B 787 PHE cc_start: 0.9373 (t80) cc_final: 0.8964 (t80) REVERT: B 798 PHE cc_start: 0.9552 (m-80) cc_final: 0.9177 (m-80) REVERT: B 800 MET cc_start: 0.9360 (tpt) cc_final: 0.9022 (tpp) REVERT: B 878 LEU cc_start: 0.9324 (mp) cc_final: 0.9074 (mp) REVERT: B 961 LEU cc_start: 0.8706 (pp) cc_final: 0.8328 (pp) REVERT: B 1007 MET cc_start: 0.8531 (ppp) cc_final: 0.7998 (ppp) REVERT: B 1008 VAL cc_start: 0.9074 (t) cc_final: 0.8501 (t) REVERT: B 1011 MET cc_start: 0.8712 (mpp) cc_final: 0.8354 (mpp) REVERT: B 1101 PHE cc_start: 0.8845 (m-80) cc_final: 0.8488 (m-80) REVERT: B 1169 LYS cc_start: 0.9430 (ttpp) cc_final: 0.8973 (ttmm) REVERT: B 1212 MET cc_start: 0.8896 (pmm) cc_final: 0.8626 (pmm) REVERT: B 1247 LEU cc_start: 0.9152 (mm) cc_final: 0.8905 (mt) REVERT: B 1348 PHE cc_start: 0.8688 (m-10) cc_final: 0.8411 (m-10) REVERT: E 1231 TYR cc_start: 0.9020 (m-80) cc_final: 0.8677 (m-80) REVERT: E 1238 ASP cc_start: 0.9086 (p0) cc_final: 0.8785 (p0) REVERT: E 1242 ARG cc_start: 0.8436 (ptt180) cc_final: 0.8016 (ptt180) REVERT: E 1243 TYR cc_start: 0.8131 (m-80) cc_final: 0.7387 (m-80) REVERT: E 1269 GLU cc_start: 0.9237 (tt0) cc_final: 0.8911 (mm-30) REVERT: E 1303 GLU cc_start: 0.9106 (pm20) cc_final: 0.8854 (pm20) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.3103 time to fit residues: 116.7380 Evaluate side-chains 178 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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: 0.9990 chunk 148 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 190 optimal weight: 8.9990 chunk 245 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 146 optimal weight: 7.9990 chunk 234 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- 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 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 503 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** ** E1293 GLN ** 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 = 0.3506 r_free = 0.3506 target = 0.060889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.037787 restraints weight = 149031.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.039405 restraints weight = 88474.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.040487 restraints weight = 61936.861| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20937 Z= 0.161 Angle : 0.750 13.110 28247 Z= 0.389 Chirality : 0.046 0.201 3118 Planarity : 0.005 0.069 3616 Dihedral : 5.884 30.774 2731 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % 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 : 0.00 % 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: -1.50 (0.16), residues: 2503 helix: -0.08 (0.14), residues: 1373 sheet: -1.77 (0.35), residues: 212 loop : -2.14 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 41 HIS 0.010 0.001 HIS A 89 PHE 0.041 0.002 PHE E1348 TYR 0.037 0.002 TYR B 969 ARG 0.006 0.000 ARG A 552 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 1092) hydrogen bonds : angle 5.65885 ( 3222) covalent geometry : bond 0.00347 (20937) covalent geometry : angle 0.75029 (28247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7474.17 seconds wall clock time: 130 minutes 31.83 seconds (7831.83 seconds total)