Starting phenix.real_space_refine on Sun Aug 24 15:09:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jhk_36271/08_2025/8jhk_36271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhk_36271/08_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_36271/08_2025/8jhk_36271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhk_36271/08_2025/8jhk_36271.map" model { file = "/net/cci-nas-00/data/ceres_data/8jhk_36271/08_2025/8jhk_36271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhk_36271/08_2025/8jhk_36271.cif" } resolution = 4.76 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.62, per 1000 atoms: 0.18 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: 1.65 Conformation dependent library (CDL) restraints added in 809.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.65 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: 3.61 Time building geometry restraints manager: 2.18 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.440 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG A 258 TYR 0.027 0.003 TYR A 588 PHE 0.020 0.002 PHE B 798 TRP 0.043 0.002 TRP A 41 HIS 0.011 0.002 HIS B 154 Details of bonding type rmsd covalent geometry : bond 0.00569 (20937) covalent geometry : angle 0.94031 (28247) hydrogen bonds : bond 0.17088 ( 1092) hydrogen bonds : angle 7.92875 ( 3222) *********************** 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 : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TRP cc_start: 0.3536 (m-90) cc_final: 0.3258 (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: 0.6885 (mmt) REVERT: A 309 MET cc_start: 0.6785 (ppp) cc_final: 0.5909 (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: 0.6352 (mmm) REVERT: B 283 ASP cc_start: 0.7035 (m-30) cc_final: 0.6554 (t0) REVERT: B 306 MET cc_start: -0.2201 (mtt) cc_final: -0.2603 (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: 0.6712 (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: 0.8292 (t) REVERT: B 1011 MET cc_start: 0.8991 (mpp) cc_final: 0.8480 (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: 0.9307 (mp0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1098 time to fit residues: 33.9268 Evaluate side-chains 151 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.0570 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 overall best weight: 2.3304 ------------------------------------------------------------------------------- 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 320 GLN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B1010 ASN ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1097 HIS 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** E1219 ASN ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.059079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.036685 restraints weight = 149350.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.038256 restraints weight = 89110.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.039320 restraints weight = 62170.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.040038 restraints weight = 48128.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.040538 restraints weight = 40048.924| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20937 Z= 0.179 Angle : 0.763 11.996 28247 Z= 0.401 Chirality : 0.046 0.176 3118 Planarity : 0.006 0.090 3616 Dihedral : 6.761 52.500 2731 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 22.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.31 % Allowed : 7.56 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.16), residues: 2503 helix: -0.74 (0.13), residues: 1370 sheet: -2.20 (0.33), residues: 207 loop : -2.61 (0.19), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1242 TYR 0.026 0.002 TYR B 969 PHE 0.018 0.002 PHE B 114 TRP 0.022 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00374 (20937) covalent geometry : angle 0.76282 (28247) hydrogen bonds : bond 0.05496 ( 1092) hydrogen bonds : angle 6.22633 ( 3222) *********************** 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 224 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 217 time to evaluate : 0.585 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: 0.7673 (ppp) cc_final: 0.7428 (ppp) REVERT: A 290 MET cc_start: 0.7343 (mmp) cc_final: 0.7049 (mmt) REVERT: A 309 MET cc_start: 0.6855 (ppp) cc_final: 0.6384 (ppp) REVERT: B 120 MET cc_start: 0.9088 (mmp) cc_final: 0.8851 (mmm) REVERT: B 283 ASP cc_start: 0.7106 (m-30) cc_final: 0.6632 (t0) REVERT: B 306 MET cc_start: -0.2905 (mtt) cc_final: -0.3290 (mtt) REVERT: B 680 MET cc_start: 0.8855 (ppp) cc_final: 0.8645 (ppp) REVERT: B 683 MET cc_start: 0.7025 (tmm) cc_final: 0.6676 (tmm) REVERT: B 694 PHE cc_start: 0.9345 (t80) cc_final: 0.8855 (t80) REVERT: B 787 PHE cc_start: 0.9399 (t80) cc_final: 0.8972 (t80) REVERT: B 798 PHE cc_start: 0.9522 (m-80) cc_final: 0.9212 (m-80) REVERT: B 964 MET cc_start: 0.6997 (ptm) cc_final: 0.6694 (ptm) REVERT: B 1007 MET cc_start: 0.8437 (ppp) cc_final: 0.7870 (ppp) REVERT: B 1008 VAL cc_start: 0.9040 (t) cc_final: 0.8493 (t) REVERT: B 1011 MET cc_start: 0.9134 (mpp) cc_final: 0.8444 (mpp) REVERT: B 1101 PHE cc_start: 0.8838 (m-80) cc_final: 0.8433 (m-80) REVERT: B 1265 LEU cc_start: 0.9280 (mp) cc_final: 0.9059 (mp) REVERT: B 1313 MET cc_start: 0.8496 (tmm) cc_final: 0.8275 (tmm) REVERT: B 1328 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.8035 (m-80) REVERT: B 1348 PHE cc_start: 0.8681 (m-10) cc_final: 0.8330 (m-10) REVERT: E 1228 LEU cc_start: 0.9426 (mt) cc_final: 0.9225 (mt) outliers start: 7 outliers final: 3 residues processed: 224 average time/residue: 0.1166 time to fit residues: 42.6402 Evaluate side-chains 169 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 165 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 248 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 56 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 154 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 A 278 HIS ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1535 GLN ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1577 GLN ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.057797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035653 restraints weight = 152104.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.037139 restraints weight = 91201.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.038152 restraints weight = 64037.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.038863 restraints weight = 49676.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.039326 restraints weight = 41492.141| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 20937 Z= 0.251 Angle : 0.823 13.829 28247 Z= 0.432 Chirality : 0.048 0.199 3118 Planarity : 0.006 0.085 3616 Dihedral : 6.884 45.954 2731 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 26.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.39 % Allowed : 7.74 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.16), residues: 2503 helix: -0.73 (0.13), residues: 1339 sheet: -2.20 (0.35), residues: 194 loop : -2.55 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 804 TYR 0.030 0.003 TYR A 588 PHE 0.018 0.002 PHE B1372 TRP 0.016 0.002 TRP B 102 HIS 0.008 0.002 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00527 (20937) covalent geometry : angle 0.82292 (28247) hydrogen bonds : bond 0.05682 ( 1092) hydrogen bonds : angle 6.26524 ( 3222) *********************** 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: 9 poor density : 200 time to evaluate : 0.515 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: 0.7857 (ppp) cc_final: 0.7656 (ppp) REVERT: A 208 MET cc_start: 0.8634 (tmm) cc_final: 0.8186 (tmm) REVERT: A 309 MET cc_start: 0.7017 (ppp) cc_final: 0.6720 (ppp) REVERT: B 283 ASP cc_start: 0.7155 (m-30) cc_final: 0.6677 (t0) REVERT: B 306 MET cc_start: -0.2572 (mtt) cc_final: -0.3010 (mtt) REVERT: B 680 MET cc_start: 0.8853 (ppp) cc_final: 0.8637 (ppp) REVERT: B 683 MET cc_start: 0.7092 (tmm) cc_final: 0.6829 (tmm) REVERT: B 694 PHE cc_start: 0.9368 (t80) cc_final: 0.8835 (t80) REVERT: B 798 PHE cc_start: 0.9549 (m-80) cc_final: 0.9239 (m-80) REVERT: B 1007 MET cc_start: 0.8621 (ppp) cc_final: 0.8040 (ppp) REVERT: B 1011 MET cc_start: 0.8896 (mpp) cc_final: 0.8255 (mpp) REVERT: B 1033 MET cc_start: 0.8872 (mmp) cc_final: 0.8533 (mmp) REVERT: B 1101 PHE cc_start: 0.8760 (m-80) cc_final: 0.8416 (m-80) REVERT: B 1265 LEU cc_start: 0.9304 (mp) cc_final: 0.9076 (mp) REVERT: B 1348 PHE cc_start: 0.8697 (m-10) cc_final: 0.8333 (m-10) REVERT: E 1228 LEU cc_start: 0.9470 (mt) cc_final: 0.9140 (mt) outliers start: 9 outliers final: 3 residues processed: 207 average time/residue: 0.1279 time to fit residues: 41.9912 Evaluate side-chains 157 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 49 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 242 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 88 optimal weight: 0.0870 chunk 191 optimal weight: 2.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** 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** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.058429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.036039 restraints weight = 155959.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.037609 restraints weight = 91161.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.038641 restraints weight = 63286.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.039374 restraints weight = 49117.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.039829 restraints weight = 41058.874| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20937 Z= 0.224 Angle : 0.786 11.309 28247 Z= 0.413 Chirality : 0.047 0.212 3118 Planarity : 0.006 0.083 3616 Dihedral : 6.734 42.331 2731 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer: Outliers : 0.13 % Allowed : 6.95 % Favored : 92.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.16), residues: 2503 helix: -0.63 (0.13), residues: 1351 sheet: -2.24 (0.34), residues: 208 loop : -2.49 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 534 TYR 0.030 0.002 TYR B 969 PHE 0.018 0.002 PHE A 574 TRP 0.017 0.002 TRP B 102 HIS 0.010 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00476 (20937) covalent geometry : angle 0.78587 (28247) hydrogen bonds : bond 0.05399 ( 1092) hydrogen bonds : angle 6.14093 ( 3222) *********************** 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 206 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7977 (mp0) cc_final: 0.7681 (mp0) REVERT: A 208 MET cc_start: 0.8718 (tmm) cc_final: 0.8312 (tmm) REVERT: A 309 MET cc_start: 0.6982 (ppp) cc_final: 0.6622 (ppp) REVERT: A 547 LEU cc_start: 0.9532 (mt) cc_final: 0.9290 (tp) REVERT: A 692 MET cc_start: 0.8925 (mmp) cc_final: 0.8634 (mmm) REVERT: B 283 ASP cc_start: 0.7504 (m-30) cc_final: 0.7159 (t70) REVERT: B 306 MET cc_start: -0.2166 (mtt) cc_final: -0.2443 (mtt) REVERT: B 465 ASN cc_start: 0.7149 (t0) cc_final: 0.6856 (t0) REVERT: B 680 MET cc_start: 0.8859 (ppp) cc_final: 0.8645 (ppp) REVERT: B 683 MET cc_start: 0.7116 (tmm) cc_final: 0.6865 (tmm) REVERT: B 694 PHE cc_start: 0.9247 (t80) cc_final: 0.8640 (t80) REVERT: B 787 PHE cc_start: 0.9391 (t80) cc_final: 0.8972 (t80) REVERT: B 798 PHE cc_start: 0.9541 (m-80) cc_final: 0.9176 (m-80) REVERT: B 860 MET cc_start: 0.8928 (mtp) cc_final: 0.8718 (mtp) REVERT: B 961 LEU cc_start: 0.8777 (pp) cc_final: 0.8513 (pp) REVERT: B 1007 MET cc_start: 0.8574 (ppp) cc_final: 0.7933 (ppp) REVERT: B 1008 VAL cc_start: 0.9185 (t) cc_final: 0.8435 (t) REVERT: B 1011 MET cc_start: 0.8982 (mpp) cc_final: 0.8291 (mpp) REVERT: B 1090 MET cc_start: 0.8723 (tpt) cc_final: 0.8425 (mtp) REVERT: B 1101 PHE cc_start: 0.8735 (m-80) cc_final: 0.8413 (m-80) REVERT: B 1348 PHE cc_start: 0.8711 (m-10) cc_final: 0.8424 (m-10) REVERT: E 1228 LEU cc_start: 0.9496 (mt) cc_final: 0.9252 (mt) REVERT: E 1313 MET cc_start: 0.6940 (tmm) cc_final: 0.6721 (tmm) outliers start: 3 outliers final: 0 residues processed: 206 average time/residue: 0.1241 time to fit residues: 41.8427 Evaluate side-chains 160 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 146 optimal weight: 9.9990 chunk 120 optimal weight: 20.0000 chunk 173 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 214 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 163 optimal weight: 0.0980 chunk 183 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 154 HIS B 199 GLN ** 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** B1545 HIS 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 = 0.3483 r_free = 0.3483 target = 0.059742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.037151 restraints weight = 144510.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.038687 restraints weight = 86951.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039755 restraints weight = 61353.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.040454 restraints weight = 47714.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.040975 restraints weight = 39947.023| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20937 Z= 0.157 Angle : 0.734 9.192 28247 Z= 0.383 Chirality : 0.046 0.188 3118 Planarity : 0.005 0.082 3616 Dihedral : 6.335 36.683 2731 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.04 % Allowed : 4.72 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.16), residues: 2503 helix: -0.37 (0.13), residues: 1372 sheet: -2.18 (0.33), residues: 225 loop : -2.36 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 258 TYR 0.029 0.002 TYR B 969 PHE 0.015 0.002 PHE A 574 TRP 0.021 0.001 TRP A 41 HIS 0.011 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00340 (20937) covalent geometry : angle 0.73425 (28247) hydrogen bonds : bond 0.04889 ( 1092) hydrogen bonds : angle 5.83520 ( 3222) *********************** 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 238 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.682 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: A 23 GLU cc_start: 0.7903 (mp0) cc_final: 0.7589 (mp0) REVERT: A 132 MET cc_start: 0.7738 (ppp) cc_final: 0.7459 (ppp) REVERT: A 147 MET cc_start: 0.2571 (ppp) cc_final: 0.2310 (ppp) REVERT: A 208 MET cc_start: 0.8639 (tmm) cc_final: 0.8230 (tmm) REVERT: A 309 MET cc_start: 0.6659 (ppp) cc_final: 0.5776 (ppp) REVERT: A 547 LEU cc_start: 0.9528 (mt) cc_final: 0.9211 (tp) REVERT: A 692 MET cc_start: 0.8812 (mmp) cc_final: 0.8578 (mmm) REVERT: B 283 ASP cc_start: 0.7595 (m-30) cc_final: 0.7229 (t70) REVERT: B 465 ASN cc_start: 0.7179 (t0) cc_final: 0.6900 (t0) REVERT: B 683 MET cc_start: 0.7063 (tmm) cc_final: 0.6828 (tmm) REVERT: B 694 PHE cc_start: 0.9330 (t80) cc_final: 0.8762 (t80) REVERT: B 722 LYS cc_start: 0.8892 (mmpt) cc_final: 0.8554 (pttm) REVERT: B 787 PHE cc_start: 0.9382 (t80) cc_final: 0.8971 (t80) REVERT: B 798 PHE cc_start: 0.9531 (m-80) cc_final: 0.9151 (m-80) REVERT: B 800 MET cc_start: 0.9418 (tpt) cc_final: 0.9105 (tpp) REVERT: B 860 MET cc_start: 0.8899 (mtp) cc_final: 0.8601 (mtp) REVERT: B 961 LEU cc_start: 0.8779 (pp) cc_final: 0.8513 (pp) REVERT: B 1007 MET cc_start: 0.8638 (ppp) cc_final: 0.7998 (ppp) REVERT: B 1008 VAL cc_start: 0.9187 (t) cc_final: 0.8429 (t) REVERT: B 1011 MET cc_start: 0.8944 (mpp) cc_final: 0.8185 (mpp) REVERT: B 1064 PHE cc_start: 0.7275 (m-10) cc_final: 0.7027 (m-10) REVERT: B 1101 PHE cc_start: 0.8656 (m-80) cc_final: 0.8334 (m-80) REVERT: B 1201 LEU cc_start: 0.9700 (mm) cc_final: 0.9280 (mm) REVERT: B 1348 PHE cc_start: 0.8677 (m-10) cc_final: 0.8466 (m-10) REVERT: E 1228 LEU cc_start: 0.9447 (mt) cc_final: 0.9207 (mt) REVERT: E 1238 ASP cc_start: 0.9353 (p0) cc_final: 0.8828 (p0) REVERT: E 1242 ARG cc_start: 0.9178 (mmt-90) cc_final: 0.8887 (mmt180) REVERT: E 1303 GLU cc_start: 0.9443 (mp0) cc_final: 0.9236 (mp0) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1272 time to fit residues: 48.8205 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 : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 23 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 212 optimal weight: 0.0770 chunk 10 optimal weight: 0.7980 chunk 201 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 228 optimal weight: 9.9990 chunk 59 optimal weight: 40.0000 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 464 ASN ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 971 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.037390 restraints weight = 150586.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.038969 restraints weight = 89126.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.040055 restraints weight = 62463.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.040807 restraints weight = 48587.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.041247 restraints weight = 40787.975| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20937 Z= 0.158 Angle : 0.729 8.720 28247 Z= 0.378 Chirality : 0.046 0.237 3118 Planarity : 0.005 0.079 3616 Dihedral : 6.154 30.554 2731 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.16), residues: 2503 helix: -0.18 (0.14), residues: 1353 sheet: -1.97 (0.35), residues: 204 loop : -2.28 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 534 TYR 0.029 0.002 TYR B 969 PHE 0.031 0.002 PHE E1348 TRP 0.020 0.001 TRP A 41 HIS 0.011 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00344 (20937) covalent geometry : angle 0.72922 (28247) hydrogen bonds : bond 0.04791 ( 1092) hydrogen bonds : angle 5.71886 ( 3222) *********************** 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 235 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7868 (mp0) cc_final: 0.7529 (mp0) REVERT: A 309 MET cc_start: 0.6544 (ppp) cc_final: 0.5912 (ppp) REVERT: A 692 MET cc_start: 0.8839 (mmp) cc_final: 0.8626 (mmm) REVERT: B 45 TYR cc_start: 0.7970 (m-10) cc_final: 0.7595 (m-80) REVERT: B 283 ASP cc_start: 0.7568 (m-30) cc_final: 0.7222 (t70) REVERT: B 683 MET cc_start: 0.7062 (tmm) cc_final: 0.6821 (tmm) REVERT: B 694 PHE cc_start: 0.9354 (t80) cc_final: 0.8879 (t80) REVERT: B 722 LYS cc_start: 0.8896 (mmpt) cc_final: 0.8549 (pttm) REVERT: B 785 ASP cc_start: 0.8758 (m-30) cc_final: 0.8547 (p0) REVERT: B 798 PHE cc_start: 0.9554 (m-80) cc_final: 0.9225 (m-80) REVERT: B 800 MET cc_start: 0.9419 (tpt) cc_final: 0.9080 (tpp) REVERT: B 860 MET cc_start: 0.8914 (mtp) cc_final: 0.8609 (mtp) REVERT: B 943 MET cc_start: 0.8122 (mtt) cc_final: 0.7687 (mtp) REVERT: B 961 LEU cc_start: 0.8663 (pp) cc_final: 0.8305 (pp) REVERT: B 1007 MET cc_start: 0.8729 (ppp) cc_final: 0.8186 (ppp) REVERT: B 1008 VAL cc_start: 0.9248 (t) cc_final: 0.8560 (t) REVERT: B 1009 MET cc_start: 0.9388 (mmt) cc_final: 0.9010 (mmt) REVERT: B 1011 MET cc_start: 0.9053 (mpp) cc_final: 0.8215 (mpp) REVERT: B 1033 MET cc_start: 0.8958 (mmp) cc_final: 0.8727 (mmm) REVERT: B 1043 TRP cc_start: 0.7945 (m-90) cc_final: 0.7578 (m-90) REVERT: B 1090 MET cc_start: 0.8744 (tpt) cc_final: 0.8216 (mtp) REVERT: B 1101 PHE cc_start: 0.8779 (m-80) cc_final: 0.8462 (m-80) REVERT: B 1169 LYS cc_start: 0.9522 (ttpp) cc_final: 0.9109 (ttmm) REVERT: B 1313 MET cc_start: 0.8623 (tmm) cc_final: 0.8401 (tmm) REVERT: E 1228 LEU cc_start: 0.9375 (mt) cc_final: 0.9124 (mt) REVERT: E 1245 TYR cc_start: 0.9240 (m-10) cc_final: 0.8915 (m-80) REVERT: E 1258 THR cc_start: 0.8407 (p) cc_final: 0.7740 (p) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1341 time to fit residues: 50.9301 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 : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 134 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 213 optimal weight: 0.0870 chunk 211 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 125 optimal weight: 30.0000 chunk 240 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 971 HIS ** B1294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1293 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.037005 restraints weight = 145607.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.038499 restraints weight = 88476.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.039543 restraints weight = 62883.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040243 restraints weight = 49239.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040751 restraints weight = 41355.974| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20937 Z= 0.179 Angle : 0.755 9.012 28247 Z= 0.395 Chirality : 0.046 0.183 3118 Planarity : 0.005 0.076 3616 Dihedral : 6.170 29.209 2731 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.16), residues: 2503 helix: -0.34 (0.13), residues: 1369 sheet: -2.15 (0.34), residues: 214 loop : -2.30 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 935 TYR 0.029 0.002 TYR E1262 PHE 0.032 0.002 PHE B 993 TRP 0.021 0.002 TRP B 102 HIS 0.009 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00386 (20937) covalent geometry : angle 0.75536 (28247) hydrogen bonds : bond 0.04866 ( 1092) hydrogen bonds : angle 5.84746 ( 3222) *********************** 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 223 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7899 (mp0) cc_final: 0.7550 (mp0) REVERT: A 132 MET cc_start: 0.7669 (ppp) cc_final: 0.7291 (ppp) REVERT: A 309 MET cc_start: 0.6842 (ppp) cc_final: 0.6169 (ppp) REVERT: A 310 MET cc_start: 0.8318 (mpp) cc_final: 0.7776 (mpp) REVERT: B 283 ASP cc_start: 0.7545 (m-30) cc_final: 0.7248 (t70) REVERT: B 694 PHE cc_start: 0.9320 (t80) cc_final: 0.8845 (t80) REVERT: B 722 LYS cc_start: 0.8887 (mmpt) cc_final: 0.8540 (pttp) REVERT: B 785 ASP cc_start: 0.8798 (m-30) cc_final: 0.8558 (p0) REVERT: B 798 PHE cc_start: 0.9540 (m-80) cc_final: 0.9233 (m-80) REVERT: B 800 MET cc_start: 0.9385 (tpt) cc_final: 0.9069 (tpp) REVERT: B 860 MET cc_start: 0.8928 (mtp) cc_final: 0.8551 (mtp) REVERT: B 943 MET cc_start: 0.8243 (mtt) cc_final: 0.7913 (mtp) REVERT: B 961 LEU cc_start: 0.8744 (pp) cc_final: 0.8406 (pp) REVERT: B 1007 MET cc_start: 0.8680 (ppp) cc_final: 0.8145 (ppp) REVERT: B 1008 VAL cc_start: 0.9211 (t) cc_final: 0.8455 (t) REVERT: B 1009 MET cc_start: 0.9390 (mmt) cc_final: 0.9153 (mmt) REVERT: B 1011 MET cc_start: 0.9079 (mpp) cc_final: 0.8161 (mpp) REVERT: B 1101 PHE cc_start: 0.8717 (m-80) cc_final: 0.8384 (m-80) REVERT: B 1169 LYS cc_start: 0.9488 (ttpp) cc_final: 0.9044 (tttm) REVERT: B 1173 GLU cc_start: 0.9568 (mm-30) cc_final: 0.9091 (mm-30) REVERT: B 1202 GLU cc_start: 0.8749 (pp20) cc_final: 0.8472 (pp20) REVERT: B 1348 PHE cc_start: 0.8736 (m-10) cc_final: 0.8465 (m-10) REVERT: E 1228 LEU cc_start: 0.9443 (mt) cc_final: 0.9227 (mt) REVERT: E 1238 ASP cc_start: 0.9323 (p0) cc_final: 0.8900 (p0) REVERT: E 1313 MET cc_start: 0.7426 (tmm) cc_final: 0.7097 (tmm) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1320 time to fit residues: 48.4800 Evaluate side-chains 172 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 225 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 ASN ** B 171 ASN ** 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** ** E1251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.059114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036587 restraints weight = 151763.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.038127 restraints weight = 89960.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.039173 restraints weight = 63007.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.039905 restraints weight = 49113.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.040328 restraints weight = 41227.038| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20937 Z= 0.202 Angle : 0.785 9.996 28247 Z= 0.409 Chirality : 0.047 0.192 3118 Planarity : 0.006 0.075 3616 Dihedral : 6.266 28.355 2731 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.16), residues: 2503 helix: -0.41 (0.13), residues: 1367 sheet: -2.22 (0.34), residues: 214 loop : -2.30 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E1242 TYR 0.023 0.002 TYR E1262 PHE 0.036 0.002 PHE E1348 TRP 0.020 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00433 (20937) covalent geometry : angle 0.78540 (28247) hydrogen bonds : bond 0.05010 ( 1092) hydrogen bonds : angle 5.89492 ( 3222) *********************** 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 221 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7866 (mp0) cc_final: 0.7565 (mp0) REVERT: A 132 MET cc_start: 0.7572 (ppp) cc_final: 0.7182 (ppp) REVERT: A 309 MET cc_start: 0.6769 (ppp) cc_final: 0.6162 (ppp) REVERT: A 310 MET cc_start: 0.8408 (mpp) cc_final: 0.8036 (mpp) REVERT: B 283 ASP cc_start: 0.7298 (m-30) cc_final: 0.6955 (t70) REVERT: B 689 TYR cc_start: 0.8459 (m-80) cc_final: 0.8237 (m-80) REVERT: B 694 PHE cc_start: 0.9304 (t80) cc_final: 0.8836 (t80) REVERT: B 722 LYS cc_start: 0.8905 (mmpt) cc_final: 0.8509 (pttp) REVERT: B 785 ASP cc_start: 0.8721 (m-30) cc_final: 0.8516 (p0) REVERT: B 798 PHE cc_start: 0.9537 (m-80) cc_final: 0.9254 (m-80) REVERT: B 800 MET cc_start: 0.9341 (tpt) cc_final: 0.8970 (tpp) REVERT: B 860 MET cc_start: 0.8943 (mtp) cc_final: 0.8560 (mtp) REVERT: B 943 MET cc_start: 0.8234 (mtt) cc_final: 0.7869 (mtp) REVERT: B 961 LEU cc_start: 0.8815 (pp) cc_final: 0.8426 (pp) REVERT: B 964 MET cc_start: 0.6790 (ppp) cc_final: 0.6562 (ppp) REVERT: B 1008 VAL cc_start: 0.9218 (t) cc_final: 0.8659 (t) REVERT: B 1101 PHE cc_start: 0.8672 (m-80) cc_final: 0.8345 (m-80) REVERT: B 1169 LYS cc_start: 0.9484 (ttpp) cc_final: 0.9050 (tttm) REVERT: B 1173 GLU cc_start: 0.9558 (mm-30) cc_final: 0.9071 (mm-30) REVERT: B 1202 GLU cc_start: 0.8749 (pp20) cc_final: 0.8483 (pp20) REVERT: B 1348 PHE cc_start: 0.8720 (m-10) cc_final: 0.8425 (m-10) REVERT: E 1228 LEU cc_start: 0.9429 (mt) cc_final: 0.9211 (mt) REVERT: E 1238 ASP cc_start: 0.9074 (p0) cc_final: 0.8323 (p0) REVERT: E 1281 HIS cc_start: 0.6716 (m170) cc_final: 0.6494 (m170) REVERT: E 1303 GLU cc_start: 0.9417 (mp0) cc_final: 0.9209 (mp0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1189 time to fit residues: 42.9702 Evaluate side-chains 165 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 68 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 128 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1066 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.058937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036520 restraints weight = 153431.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.038053 restraints weight = 90700.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.039085 restraints weight = 63545.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.039807 restraints weight = 49651.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.040260 restraints weight = 41776.353| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20937 Z= 0.211 Angle : 0.803 10.325 28247 Z= 0.420 Chirality : 0.048 0.293 3118 Planarity : 0.006 0.074 3616 Dihedral : 6.345 28.589 2731 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.16), residues: 2503 helix: -0.45 (0.13), residues: 1349 sheet: -2.18 (0.34), residues: 205 loop : -2.25 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.024 0.002 TYR E1328 PHE 0.020 0.002 PHE A 187 TRP 0.021 0.002 TRP A 41 HIS 0.008 0.001 HIS A 89 Details of bonding type rmsd covalent geometry : bond 0.00452 (20937) covalent geometry : angle 0.80275 (28247) hydrogen bonds : bond 0.05187 ( 1092) hydrogen bonds : angle 5.97988 ( 3222) *********************** 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 226 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.511 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 23 GLU cc_start: 0.7892 (mp0) cc_final: 0.7601 (mp0) REVERT: A 132 MET cc_start: 0.7642 (ppp) cc_final: 0.7359 (ppp) REVERT: A 309 MET cc_start: 0.6902 (ppp) cc_final: 0.6521 (ppp) REVERT: B 283 ASP cc_start: 0.7149 (m-30) cc_final: 0.6736 (t70) REVERT: B 689 TYR cc_start: 0.8532 (m-80) cc_final: 0.8330 (m-80) REVERT: B 694 PHE cc_start: 0.9298 (t80) cc_final: 0.8839 (t80) REVERT: B 722 LYS cc_start: 0.8903 (mmpt) cc_final: 0.8507 (pttp) REVERT: B 785 ASP cc_start: 0.8812 (m-30) cc_final: 0.8568 (p0) REVERT: B 798 PHE cc_start: 0.9551 (m-80) cc_final: 0.9270 (m-80) REVERT: B 800 MET cc_start: 0.9321 (tpt) cc_final: 0.8978 (tpp) REVERT: B 860 MET cc_start: 0.8969 (mtp) cc_final: 0.8596 (mtp) REVERT: B 943 MET cc_start: 0.8385 (mtt) cc_final: 0.8019 (mtp) REVERT: B 961 LEU cc_start: 0.8784 (pp) cc_final: 0.8448 (pp) REVERT: B 1007 MET cc_start: 0.8522 (ppp) cc_final: 0.8023 (ppp) REVERT: B 1011 MET cc_start: 0.8954 (mpp) cc_final: 0.8501 (mpp) REVERT: B 1064 PHE cc_start: 0.7367 (m-10) cc_final: 0.7165 (m-10) REVERT: B 1101 PHE cc_start: 0.8699 (m-80) cc_final: 0.8337 (m-80) REVERT: B 1169 LYS cc_start: 0.9482 (ttpp) cc_final: 0.9027 (tttm) REVERT: B 1173 GLU cc_start: 0.9559 (mm-30) cc_final: 0.9064 (mm-30) REVERT: B 1202 GLU cc_start: 0.8791 (pp20) cc_final: 0.8532 (pp20) REVERT: B 1348 PHE cc_start: 0.8733 (m-10) cc_final: 0.8444 (m-10) REVERT: E 1228 LEU cc_start: 0.9424 (mt) cc_final: 0.9113 (mt) REVERT: E 1303 GLU cc_start: 0.9427 (mp0) cc_final: 0.9224 (mp0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1354 time to fit residues: 50.4129 Evaluate side-chains 170 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 103 optimal weight: 5.9990 chunk 216 optimal weight: 0.0770 chunk 2 optimal weight: 6.9990 chunk 222 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 230 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 ASN ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 HIS ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 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** ** B1607 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.060134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.037324 restraints weight = 147081.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.038856 restraints weight = 89324.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.039918 restraints weight = 63426.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.040627 restraints weight = 49638.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.041117 restraints weight = 41761.064| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20937 Z= 0.172 Angle : 0.781 10.381 28247 Z= 0.406 Chirality : 0.047 0.271 3118 Planarity : 0.005 0.092 3616 Dihedral : 6.159 26.845 2731 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 21.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.16), residues: 2503 helix: -0.34 (0.14), residues: 1358 sheet: -2.16 (0.34), residues: 205 loop : -2.26 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 320 TYR 0.065 0.002 TYR E1328 PHE 0.044 0.002 PHE E1348 TRP 0.023 0.002 TRP A 41 HIS 0.008 0.001 HIS E1251 Details of bonding type rmsd covalent geometry : bond 0.00373 (20937) covalent geometry : angle 0.78090 (28247) hydrogen bonds : bond 0.04956 ( 1092) hydrogen bonds : angle 5.86451 ( 3222) ********************** 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 230 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.844 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: 0.8598 (pmm) cc_final: 0.8302 (pmm) REVERT: A 23 GLU cc_start: 0.7938 (mp0) cc_final: 0.7575 (mp0) REVERT: A 132 MET cc_start: 0.7751 (ppp) cc_final: 0.7458 (ppp) REVERT: A 309 MET cc_start: 0.6995 (ppp) cc_final: 0.6550 (ppp) REVERT: B 283 ASP cc_start: 0.7242 (m-30) cc_final: 0.6749 (t70) REVERT: B 694 PHE cc_start: 0.9272 (t80) cc_final: 0.8814 (t80) REVERT: B 722 LYS cc_start: 0.8909 (mmpt) cc_final: 0.8489 (pttp) REVERT: B 785 ASP cc_start: 0.8693 (m-30) cc_final: 0.8492 (p0) REVERT: B 798 PHE cc_start: 0.9519 (m-80) cc_final: 0.9234 (m-80) REVERT: B 800 MET cc_start: 0.9286 (tpt) cc_final: 0.8957 (tpp) REVERT: B 860 MET cc_start: 0.8910 (mtp) cc_final: 0.8560 (mtp) REVERT: B 943 MET cc_start: 0.8218 (mtt) cc_final: 0.7812 (mtp) REVERT: B 961 LEU cc_start: 0.8739 (pp) cc_final: 0.8401 (pp) REVERT: B 1007 MET cc_start: 0.8428 (ppp) cc_final: 0.7959 (ppp) REVERT: B 1008 VAL cc_start: 0.9126 (t) cc_final: 0.8589 (t) REVERT: B 1011 MET cc_start: 0.8780 (mpp) cc_final: 0.8324 (mpp) REVERT: B 1101 PHE cc_start: 0.8650 (m-80) cc_final: 0.8309 (m-80) REVERT: B 1169 LYS cc_start: 0.9483 (ttpp) cc_final: 0.8965 (tttm) REVERT: B 1173 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9093 (mm-30) REVERT: B 1202 GLU cc_start: 0.8722 (pp20) cc_final: 0.8453 (pp20) REVERT: B 1348 PHE cc_start: 0.8723 (m-10) cc_final: 0.8427 (m-10) REVERT: E 1238 ASP cc_start: 0.9287 (p0) cc_final: 0.8774 (p0) REVERT: E 1303 GLU cc_start: 0.9460 (mp0) cc_final: 0.9245 (mp0) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1371 time to fit residues: 51.8020 Evaluate side-chains 175 residues out of total 2287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 245 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 117 optimal weight: 40.0000 chunk 17 optimal weight: 7.9990 chunk 188 optimal weight: 0.8980 chunk 112 optimal weight: 20.0000 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3479 r_free = 0.3479 target = 0.059806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.037002 restraints weight = 151431.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.038563 restraints weight = 90116.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.039619 restraints weight = 63306.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.040317 restraints weight = 49386.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.040839 restraints weight = 41604.283| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20937 Z= 0.192 Angle : 0.795 11.372 28247 Z= 0.412 Chirality : 0.047 0.257 3118 Planarity : 0.005 0.082 3616 Dihedral : 6.200 27.978 2731 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.16), residues: 2503 helix: -0.38 (0.13), residues: 1360 sheet: -2.15 (0.34), residues: 199 loop : -2.27 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1069 TYR 0.033 0.002 TYR B1328 PHE 0.020 0.002 PHE A 187 TRP 0.036 0.002 TRP A 41 HIS 0.007 0.001 HIS B 949 Details of bonding type rmsd covalent geometry : bond 0.00415 (20937) covalent geometry : angle 0.79463 (28247) hydrogen bonds : bond 0.04978 ( 1092) hydrogen bonds : angle 5.88628 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4003.42 seconds wall clock time: 70 minutes 8.51 seconds (4208.51 seconds total)