Starting phenix.real_space_refine on Mon Aug 25 13:23:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m6b_30118/08_2025/6m6b_30118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m6b_30118/08_2025/6m6b_30118.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m6b_30118/08_2025/6m6b_30118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m6b_30118/08_2025/6m6b_30118.map" model { file = "/net/cci-nas-00/data/ceres_data/6m6b_30118/08_2025/6m6b_30118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m6b_30118/08_2025/6m6b_30118.cif" } resolution = 4.1 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= 0.001 sd= 0.008 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 59 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 17690 2.51 5 N 4998 2.21 5 O 5361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 159 residue(s): 0.03s 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: 28180 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1782 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1750 Classifications: {'peptide': 222} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 207} Chain: "C" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 8770 Classifications: {'peptide': 1111} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1038} Chain breaks: 1 Chain: "D" Number of atoms: 10300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10300 Classifications: {'peptide': 1305} Link IDs: {'PCIS': 2, 'PTRANS': 62, 'TRANS': 1240} Chain breaks: 2 Chain: "E" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 761 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 6, 'TRANS': 87} Chain: "M" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 3635 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 29, 'TRANS': 429} Chain breaks: 2 Chain: "T" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "N" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 574 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19686 SG CYS D1112 83.639 68.049 129.157 1.00143.09 S ATOM 20330 SG CYS D1194 82.345 68.479 125.745 1.00126.28 S ATOM 20386 SG CYS D1201 81.623 65.492 127.728 1.00136.20 S ATOM 20410 SG CYS D1204 79.425 68.601 129.001 1.00129.08 S Time building chain proxies: 5.70, per 1000 atoms: 0.20 Number of scatterers: 28180 At special positions: 0 Unit cell: (164.682, 141.156, 164.682, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 69 16.00 P 59 15.00 Mg 1 11.99 O 5361 8.00 N 4998 7.00 C 17690 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: 2.36 Conformation dependent library (CDL) restraints added in 912.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1194 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1204 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1112 " pdb="ZN ZN D2001 " - pdb=" SG CYS D1201 " Number of angles added : 6 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6306 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 50 sheets defined 40.6% alpha, 17.6% beta 30 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 3.44 Creating SS restraints... Processing helix chain 'A' and resid 31 through 47 Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.823A pdb=" N ILE A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 224 through 226 No H-bonds generated for 'chain 'A' and resid 224 through 226' Processing helix chain 'B' and resid 31 through 47 Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 74 through 84 removed outlier: 3.795A pdb=" N GLU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 152 through 157 removed outlier: 4.126A pdb=" N HIS B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'C' and resid 19 through 31 removed outlier: 3.630A pdb=" N VAL C 23 " --> pdb=" O THR C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.541A pdb=" N PHE C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 193 through 200 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 214 through 222 removed outlier: 4.024A pdb=" N GLY C 220 " --> pdb=" O GLU C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.556A pdb=" N MET C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 243 Processing helix chain 'C' and resid 249 through 262 Processing helix chain 'C' and resid 270 through 282 Processing helix chain 'C' and resid 302 through 315 removed outlier: 3.772A pdb=" N THR C 306 " --> pdb=" O VAL C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 360 removed outlier: 3.532A pdb=" N LEU C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 360 " --> pdb=" O ARG C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 373 removed outlier: 3.781A pdb=" N VAL C 373 " --> pdb=" O ALA C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 389 removed outlier: 3.766A pdb=" N SER C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 408 Processing helix chain 'C' and resid 445 through 449 removed outlier: 3.859A pdb=" N ASN C 448 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 525 through 529 removed outlier: 3.683A pdb=" N GLU C 528 " --> pdb=" O SER C 525 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 529 " --> pdb=" O PRO C 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 525 through 529' Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 554 through 565 Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 585 through 591 Processing helix chain 'C' and resid 692 through 697 Processing helix chain 'C' and resid 768 through 779 removed outlier: 3.512A pdb=" N GLY C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 854 through 858 Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.029A pdb=" N GLY C 875 " --> pdb=" O ASN C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 882 through 898 removed outlier: 3.682A pdb=" N LEU C 886 " --> pdb=" O LEU C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 932 removed outlier: 3.572A pdb=" N ILE C 914 " --> pdb=" O LYS C 910 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LYS C 928 " --> pdb=" O VAL C 924 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 937 through 949 Processing helix chain 'C' and resid 958 through 970 Processing helix chain 'C' and resid 1023 through 1027 removed outlier: 3.817A pdb=" N PHE C1027 " --> pdb=" O LYS C1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1044 Processing helix chain 'C' and resid 1045 through 1054 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1082 through 1095 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.515A pdb=" N PHE D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 removed outlier: 3.739A pdb=" N VAL D 85 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.981A pdb=" N VAL D 105 " --> pdb=" O HIS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 117 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 423 through 426 Processing helix chain 'D' and resid 457 through 466 Processing helix chain 'D' and resid 469 through 483 removed outlier: 3.651A pdb=" N LEU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 506 removed outlier: 3.746A pdb=" N GLY D 506 " --> pdb=" O PHE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 511 Processing helix chain 'D' and resid 538 through 561 removed outlier: 4.176A pdb=" N ASP D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 561 " --> pdb=" O LEU D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 584 removed outlier: 3.729A pdb=" N ILE D 567 " --> pdb=" O PRO D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 608 Processing helix chain 'D' and resid 615 through 619 removed outlier: 4.108A pdb=" N LEU D 618 " --> pdb=" O ARG D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 653 through 664 Processing helix chain 'D' and resid 669 through 678 Processing helix chain 'D' and resid 679 through 683 removed outlier: 3.770A pdb=" N ILE D 683 " --> pdb=" O GLN D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 709 through 711 No H-bonds generated for 'chain 'D' and resid 709 through 711' Processing helix chain 'D' and resid 729 through 733 removed outlier: 3.821A pdb=" N VAL D 732 " --> pdb=" O HIS D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 762 removed outlier: 3.719A pdb=" N GLN D 762 " --> pdb=" O GLU D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 764 through 768 Processing helix chain 'D' and resid 782 through 794 Processing helix chain 'D' and resid 808 through 818 removed outlier: 3.725A pdb=" N ALA D 812 " --> pdb=" O THR D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 836 through 841 removed outlier: 4.015A pdb=" N TYR D 841 " --> pdb=" O GLY D 837 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 855 removed outlier: 3.807A pdb=" N ALA D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 876 through 891 Processing helix chain 'D' and resid 892 through 900 removed outlier: 3.561A pdb=" N ILE D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) Processing helix chain 'D' and resid 907 through 923 removed outlier: 3.551A pdb=" N GLY D 923 " --> pdb=" O PHE D 919 " (cutoff:3.500A) Processing helix chain 'D' and resid 924 through 946 removed outlier: 3.569A pdb=" N SER D 945 " --> pdb=" O PHE D 941 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY D 946 " --> pdb=" O SER D 942 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 954 Processing helix chain 'D' and resid 958 through 980 removed outlier: 4.044A pdb=" N GLN D 962 " --> pdb=" O GLU D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 984 through 1015 Processing helix chain 'D' and resid 1018 through 1027 Processing helix chain 'D' and resid 1031 through 1040 Processing helix chain 'D' and resid 1066 through 1102 removed outlier: 4.408A pdb=" N HIS D1075 " --> pdb=" O PHE D1071 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY D1076 " --> pdb=" O ILE D1072 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA D1089 " --> pdb=" O ALA D1085 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D1090 " --> pdb=" O LEU D1086 " (cutoff:3.500A) Processing helix chain 'D' and resid 1136 through 1145 Processing helix chain 'D' and resid 1167 through 1181 Processing helix chain 'D' and resid 1220 through 1231 removed outlier: 4.141A pdb=" N VAL D1224 " --> pdb=" O ALA D1220 " (cutoff:3.500A) Processing helix chain 'D' and resid 1232 through 1236 removed outlier: 3.582A pdb=" N LEU D1236 " --> pdb=" O GLY D1233 " (cutoff:3.500A) Processing helix chain 'D' and resid 1255 through 1265 Processing helix chain 'D' and resid 1331 through 1359 removed outlier: 3.679A pdb=" N LEU D1335 " --> pdb=" O ASP D1331 " (cutoff:3.500A) Proline residue: D1341 - end of helix removed outlier: 3.915A pdb=" N VAL D1344 " --> pdb=" O GLY D1340 " (cutoff:3.500A) Processing helix chain 'D' and resid 1365 through 1376 Processing helix chain 'D' and resid 1397 through 1408 Processing helix chain 'D' and resid 1423 through 1430 Processing helix chain 'D' and resid 1433 through 1441 removed outlier: 3.980A pdb=" N GLN D1441 " --> pdb=" O ALA D1437 " (cutoff:3.500A) Processing helix chain 'D' and resid 1442 through 1454 removed outlier: 4.746A pdb=" N GLY D1454 " --> pdb=" O ALA D1450 " (cutoff:3.500A) Processing helix chain 'D' and resid 1462 through 1468 Processing helix chain 'D' and resid 1474 through 1478 Processing helix chain 'D' and resid 1489 through 1501 Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.627A pdb=" N VAL E 13 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 33 Processing helix chain 'E' and resid 59 through 71 removed outlier: 3.946A pdb=" N TRP E 63 " --> pdb=" O ASN E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 93 removed outlier: 3.579A pdb=" N LEU E 85 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 368 No H-bonds generated for 'chain 'M' and resid 366 through 368' Processing helix chain 'M' and resid 407 through 420 Processing helix chain 'M' and resid 430 through 438 removed outlier: 4.343A pdb=" N LEU M 434 " --> pdb=" O GLU M 430 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL M 435 " --> pdb=" O TRP M 431 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY M 438 " --> pdb=" O LEU M 434 " (cutoff:3.500A) Processing helix chain 'M' and resid 444 through 460 Processing helix chain 'M' and resid 475 through 490 removed outlier: 4.419A pdb=" N VAL M 479 " --> pdb=" O GLY M 475 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA M 480 " --> pdb=" O LYS M 476 " (cutoff:3.500A) Processing helix chain 'M' and resid 500 through 515 Processing helix chain 'M' and resid 530 through 543 Processing helix chain 'M' and resid 553 through 558 Processing helix chain 'M' and resid 572 through 576 removed outlier: 3.588A pdb=" N ARG M 575 " --> pdb=" O GLU M 572 " (cutoff:3.500A) Processing helix chain 'M' and resid 578 through 588 Processing helix chain 'M' and resid 605 through 613 removed outlier: 3.620A pdb=" N VAL M 610 " --> pdb=" O TYR M 606 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY M 611 " --> pdb=" O SER M 607 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU M 612 " --> pdb=" O ALA M 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 636 through 651 Processing helix chain 'M' and resid 664 through 675 Processing helix chain 'M' and resid 688 through 702 Processing helix chain 'M' and resid 734 through 745 removed outlier: 3.503A pdb=" N VAL M 745 " --> pdb=" O LEU M 741 " (cutoff:3.500A) Processing helix chain 'M' and resid 763 through 775 Processing helix chain 'M' and resid 781 through 796 Processing helix chain 'M' and resid 812 through 825 removed outlier: 3.830A pdb=" N ILE M 823 " --> pdb=" O LEU M 819 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG M 824 " --> pdb=" O GLU M 820 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 16 removed outlier: 6.115A pdb=" N ASP A 193 " --> pdb=" O PRO A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.570A pdb=" N ASN A 139 " --> pdb=" O ILE A 58 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE A 58 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU A 141 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL A 56 " --> pdb=" O GLU A 141 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 143 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.722A pdb=" N VAL A 109 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 16 removed outlier: 6.279A pdb=" N ASP B 193 " --> pdb=" O PRO B 27 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP B 191 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N THR B 184 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ASP B 193 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 182 " --> pdb=" O ASP B 193 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B 195 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN B 180 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU B 197 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA B 178 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE B 199 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG B 176 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N THR B 201 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL B 174 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 104 removed outlier: 7.145A pdb=" N ASN B 139 " --> pdb=" O ILE B 58 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 58 " --> pdb=" O ASN B 139 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU B 141 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL B 56 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ARG B 143 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.258A pdb=" N LYS B 107 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR B 131 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 109 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 150 through 151 Processing sheet with id=AB2, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 73 removed outlier: 6.793A pdb=" N ARG C 97 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR C 71 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR C 95 " --> pdb=" O TYR C 71 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU C 73 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA C 92 " --> pdb=" O HIS C 117 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N HIS C 117 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LEU C 94 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 108 " --> pdb=" O TYR M 362 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU C 110 " --> pdb=" O LYS M 360 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY M 359 " --> pdb=" O TYR M 355 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY M 337 " --> pdb=" O VAL M 352 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG M 354 " --> pdb=" O TYR M 335 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR M 335 " --> pdb=" O ARG M 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 334 removed outlier: 3.847A pdb=" N SER C 138 " --> pdb=" O ARG C 409 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 145 through 150 removed outlier: 7.716A pdb=" N TYR C 158 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL C 176 " --> pdb=" O TYR C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 294 Processing sheet with id=AB8, first strand: chain 'C' and resid 460 through 461 removed outlier: 6.152A pdb=" N ILE C 467 " --> pdb=" O MET C 486 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N MET C 486 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR C 469 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL C 484 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR C 471 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU C 482 " --> pdb=" O TYR C 471 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ARG C 473 " --> pdb=" O THR C 480 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 460 through 461 removed outlier: 4.180A pdb=" N PHE C 531 " --> pdb=" O THR C 495 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 503 through 504 Processing sheet with id=AC2, first strand: chain 'C' and resid 595 through 596 removed outlier: 6.793A pdb=" N LEU C 595 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 620 through 624 removed outlier: 7.051A pdb=" N ARG C 610 " --> pdb=" O VAL C 606 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL C 606 " --> pdb=" O ARG C 610 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL C 612 " --> pdb=" O ALA C 604 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY C 601 " --> pdb=" O VAL C 649 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 629 through 630 Processing sheet with id=AC5, first strand: chain 'C' and resid 661 through 662 Processing sheet with id=AC6, first strand: chain 'C' and resid 971 through 972 removed outlier: 3.647A pdb=" N ALA C 840 " --> pdb=" O MET C 995 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE C 688 " --> pdb=" O ALA C 850 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 852 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE C 690 " --> pdb=" O ILE C 852 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL C 689 " --> pdb=" O ILE C 870 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL C 988 " --> pdb=" O ILE C 676 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 702 through 713 removed outlier: 7.785A pdb=" N ARG C 820 " --> pdb=" O ARG C 807 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ARG C 807 " --> pdb=" O ARG C 820 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 822 " --> pdb=" O ARG C 805 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG C 805 " --> pdb=" O VAL C 822 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG C 824 " --> pdb=" O THR C 803 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N THR C 803 " --> pdb=" O ARG C 824 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TYR C 826 " --> pdb=" O VAL C 801 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 754 through 756 removed outlier: 6.582A pdb=" N LEU C 790 " --> pdb=" O LEU C 755 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 759 through 761 Processing sheet with id=AD1, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 6.059A pdb=" N CYS D 642 " --> pdb=" O VAL D 719 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL D 721 " --> pdb=" O CYS D 642 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU D 644 " --> pdb=" O VAL D 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1006 through 1008 removed outlier: 7.794A pdb=" N ILE D 726 " --> pdb=" O ARG D 628 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 630 " --> pdb=" O ILE D 726 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 728 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL D 632 " --> pdb=" O LEU D 728 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1031 through 1032 Processing sheet with id=AD4, first strand: chain 'C' and resid 1099 through 1102 Processing sheet with id=AD5, first strand: chain 'D' and resid 22 through 25 removed outlier: 7.488A pdb=" N HIS D 92 " --> pdb=" O TYR D 23 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N GLU D 25 " --> pdb=" O HIS D 92 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLU D 94 " --> pdb=" O GLU D 25 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N LEU D 95 " --> pdb=" O PRO D 518 " (cutoff:3.500A) removed outlier: 10.933A pdb=" N THR D 97 " --> pdb=" O ALA D 516 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA D 516 " --> pdb=" O THR D 97 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 152 through 153 removed outlier: 7.322A pdb=" N ASP D 453 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 141 through 142 Processing sheet with id=AD8, first strand: chain 'D' and resid 167 through 170 removed outlier: 3.692A pdb=" N GLY D 201 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU D 183 " --> pdb=" O ALA D 203 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 398 through 402 Processing sheet with id=AE1, first strand: chain 'D' and resid 419 through 422 removed outlier: 6.752A pdb=" N VAL D 427 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE3, first strand: chain 'D' and resid 827 through 828 Processing sheet with id=AE4, first strand: chain 'D' and resid 842 through 843 removed outlier: 6.652A pdb=" N PHE D 843 " --> pdb=" O ARG D 867 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1106 through 1109 removed outlier: 6.174A pdb=" N VAL D1106 " --> pdb=" O VAL D1200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 1118 through 1121 Processing sheet with id=AE7, first strand: chain 'D' and resid 1123 through 1126 Processing sheet with id=AE8, first strand: chain 'D' and resid 1153 through 1155 Processing sheet with id=AE9, first strand: chain 'D' and resid 1300 through 1305 removed outlier: 3.553A pdb=" N GLY D1279 " --> pdb=" O VAL D1319 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP D1317 " --> pdb=" O VAL D1281 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1394 through 1396 removed outlier: 7.174A pdb=" N ALA D1416 " --> pdb=" O THR D1382 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1485 through 1487 Processing sheet with id=AF3, first strand: chain 'E' and resid 47 through 49 Processing sheet with id=AF4, first strand: chain 'M' and resid 522 through 525 removed outlier: 6.593A pdb=" N VAL M 494 " --> pdb=" O VAL M 549 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLY M 551 " --> pdb=" O VAL M 494 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N PHE M 496 " --> pdb=" O GLY M 551 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA M 495 " --> pdb=" O ILE M 569 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LEU M 568 " --> pdb=" O LEU M 594 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG M 466 " --> pdb=" O THR M 593 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR M 595 " --> pdb=" O ARG M 466 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP M 614 " --> pdb=" O ASP M 465 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU M 467 " --> pdb=" O ASP M 614 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 629 through 633 removed outlier: 3.649A pdb=" N ALA M 754 " --> pdb=" O LYS M 629 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU M 756 " --> pdb=" O PHE M 631 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS M 653 " --> pdb=" O ASN M 723 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE M 725 " --> pdb=" O LYS M 653 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE M 655 " --> pdb=" O ILE M 725 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE M 727 " --> pdb=" O PHE M 655 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL M 654 " --> pdb=" O LEU M 707 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY M 681 " --> pdb=" O LEU M 708 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3252 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 6.89 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 9569 1.36 - 1.51: 8768 1.51 - 1.65: 10344 1.65 - 1.80: 106 1.80 - 1.94: 18 Bond restraints: 28805 Sorted by residual: bond pdb=" CA SER C 878 " pdb=" C SER C 878 " ideal model delta sigma weight residual 1.523 1.457 0.067 1.56e-02 4.11e+03 1.83e+01 bond pdb=" C PRO M 759 " pdb=" N PRO M 760 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.55e+01 bond pdb=" N VAL C 302 " pdb=" CA VAL C 302 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.25e-02 6.40e+03 1.33e+01 bond pdb=" N THR M 620 " pdb=" CA THR M 620 " ideal model delta sigma weight residual 1.457 1.485 -0.029 9.10e-03 1.21e+04 9.91e+00 bond pdb=" C THR M 620 " pdb=" O THR M 620 " ideal model delta sigma weight residual 1.233 1.248 -0.015 4.80e-03 4.34e+04 9.44e+00 ... (remaining 28800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 38303 2.61 - 5.23: 823 5.23 - 7.84: 68 7.84 - 10.45: 14 10.45 - 13.06: 3 Bond angle restraints: 39211 Sorted by residual: angle pdb=" O3' DT N 10 " pdb=" C3' DT N 10 " pdb=" C2' DT N 10 " ideal model delta sigma weight residual 111.50 98.44 13.06 1.50e+00 4.44e-01 7.59e+01 angle pdb=" O3' DG N 13 " pdb=" C3' DG N 13 " pdb=" C2' DG N 13 " ideal model delta sigma weight residual 111.50 99.17 12.33 1.50e+00 4.44e-01 6.76e+01 angle pdb=" C4' DG N 13 " pdb=" C3' DG N 13 " pdb=" O3' DG N 13 " ideal model delta sigma weight residual 110.00 121.86 -11.86 1.50e+00 4.44e-01 6.25e+01 angle pdb=" C2' DG N 13 " pdb=" C1' DG N 13 " pdb=" N9 DG N 13 " ideal model delta sigma weight residual 113.50 103.11 10.39 1.50e+00 4.44e-01 4.80e+01 angle pdb=" O3' DT N 9 " pdb=" C3' DT N 9 " pdb=" C2' DT N 9 " ideal model delta sigma weight residual 111.50 102.32 9.18 1.50e+00 4.44e-01 3.75e+01 ... (remaining 39206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.98: 15213 18.98 - 37.96: 1793 37.96 - 56.94: 425 56.94 - 75.93: 87 75.93 - 94.91: 15 Dihedral angle restraints: 17533 sinusoidal: 7722 harmonic: 9811 Sorted by residual: dihedral pdb=" CA ILE D1452 " pdb=" C ILE D1452 " pdb=" N ALA D1453 " pdb=" CA ALA D1453 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA M 633 " pdb=" C ALA M 633 " pdb=" N PRO M 634 " pdb=" CA PRO M 634 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TYR D1207 " pdb=" C TYR D1207 " pdb=" N ASP D1208 " pdb=" CA ASP D1208 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 17530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3197 0.055 - 0.110: 979 0.110 - 0.164: 220 0.164 - 0.219: 25 0.219 - 0.274: 8 Chirality restraints: 4429 Sorted by residual: chirality pdb=" CB VAL M 683 " pdb=" CA VAL M 683 " pdb=" CG1 VAL M 683 " pdb=" CG2 VAL M 683 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE C 726 " pdb=" CA ILE C 726 " pdb=" CG1 ILE C 726 " pdb=" CG2 ILE C 726 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE C 21 " pdb=" CA ILE C 21 " pdb=" CG1 ILE C 21 " pdb=" CG2 ILE C 21 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 4426 not shown) Planarity restraints: 4938 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG N 13 " 0.061 2.00e-02 2.50e+03 2.92e-02 2.57e+01 pdb=" N9 DG N 13 " -0.075 2.00e-02 2.50e+03 pdb=" C8 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" O6 DG N 13 " 0.028 2.00e-02 2.50e+03 pdb=" N1 DG N 13 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG N 13 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG N 13 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG N 13 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M 621 " -0.061 5.00e-02 4.00e+02 9.09e-02 1.32e+01 pdb=" N PRO M 622 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO M 622 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 622 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 172 " -0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO D 173 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO D 173 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 173 " -0.048 5.00e-02 4.00e+02 ... (remaining 4935 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1143 2.69 - 3.24: 26901 3.24 - 3.79: 49936 3.79 - 4.35: 59637 4.35 - 4.90: 94601 Nonbonded interactions: 232218 Sorted by model distance: nonbonded pdb=" OD1 ASP D 743 " pdb="MG MG D2003 " model vdw 2.133 2.170 nonbonded pdb=" OD2 ASP D 741 " pdb="MG MG D2003 " model vdw 2.143 2.170 nonbonded pdb=" O PRO D 39 " pdb="ZN ZN D2002 " model vdw 2.144 2.230 nonbonded pdb=" N GLU C1083 " pdb=" OE1 GLU C1083 " model vdw 2.187 3.120 nonbonded pdb=" CG2 THR C1054 " pdb=" OE2 GLU C1083 " model vdw 2.222 3.460 ... (remaining 232213 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 228) selection = chain 'B' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.080 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.007 0.138 28809 Z= 0.357 Angle : 0.966 19.544 39217 Z= 0.561 Chirality : 0.055 0.274 4429 Planarity : 0.008 0.091 4938 Dihedral : 16.972 94.906 11227 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.48 % Favored : 94.49 % Rotamer: Outliers : 0.38 % Allowed : 11.49 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -3.41 (0.12), residues: 3395 helix: -2.04 (0.11), residues: 1212 sheet: -2.25 (0.21), residues: 504 loop : -2.39 (0.13), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 808 TYR 0.025 0.002 TYR D1207 PHE 0.027 0.002 PHE D 403 TRP 0.012 0.002 TRP D 897 HIS 0.014 0.002 HIS M 574 Details of bonding type rmsd covalent geometry : bond 0.00733 (28805) covalent geometry : angle 0.95198 (39211) hydrogen bonds : bond 0.15629 ( 1248) hydrogen bonds : angle 7.07611 ( 3400) metal coordination : bond 0.11044 ( 4) metal coordination : angle 13.39790 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 503 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.8801 (pt0) cc_final: 0.8510 (tm-30) REVERT: A 64 GLU cc_start: 0.8818 (pm20) cc_final: 0.8607 (pm20) REVERT: A 72 LYS cc_start: 0.9210 (tttt) cc_final: 0.8804 (tptt) REVERT: A 94 LEU cc_start: 0.8588 (tp) cc_final: 0.8256 (tt) REVERT: A 110 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8470 (mtmm) REVERT: A 124 ASN cc_start: 0.8929 (p0) cc_final: 0.8123 (p0) REVERT: A 140 MET cc_start: 0.8704 (ppp) cc_final: 0.8349 (ppp) REVERT: A 168 ASP cc_start: 0.8662 (m-30) cc_final: 0.7887 (p0) REVERT: B 60 ASP cc_start: 0.9091 (m-30) cc_final: 0.8629 (p0) REVERT: B 206 THR cc_start: 0.7051 (m) cc_final: 0.6804 (p) REVERT: C 27 ARG cc_start: 0.8245 (tmm160) cc_final: 0.7914 (ttp80) REVERT: C 33 ASP cc_start: 0.8851 (p0) cc_final: 0.8551 (p0) REVERT: C 191 PHE cc_start: 0.7713 (p90) cc_final: 0.7314 (p90) REVERT: C 374 ASN cc_start: 0.7984 (t0) cc_final: 0.7393 (m-40) REVERT: C 422 ARG cc_start: 0.7388 (ttp-110) cc_final: 0.6307 (mmt180) REVERT: C 429 ASP cc_start: 0.8913 (t0) cc_final: 0.7995 (p0) REVERT: C 595 LEU cc_start: 0.8650 (tp) cc_final: 0.8012 (mp) REVERT: C 680 ASP cc_start: 0.9021 (t0) cc_final: 0.8470 (t0) REVERT: C 734 LEU cc_start: 0.9488 (mt) cc_final: 0.9172 (mt) REVERT: C 858 MET cc_start: 0.8964 (tpp) cc_final: 0.8575 (mmt) REVERT: C 1050 GLN cc_start: 0.8077 (tt0) cc_final: 0.7870 (tm-30) REVERT: C 1075 ASP cc_start: 0.7528 (t0) cc_final: 0.7322 (t0) REVERT: D 45 PHE cc_start: 0.7214 (m-80) cc_final: 0.6887 (m-80) REVERT: D 101 HIS cc_start: 0.8414 (t-90) cc_final: 0.8050 (t-90) REVERT: D 102 ILE cc_start: 0.8487 (tp) cc_final: 0.8274 (tp) REVERT: D 116 LEU cc_start: 0.9512 (mt) cc_final: 0.8791 (mm) REVERT: D 135 LEU cc_start: 0.9459 (mm) cc_final: 0.9208 (mp) REVERT: D 153 LEU cc_start: 0.9653 (tp) cc_final: 0.9432 (tp) REVERT: D 160 GLU cc_start: 0.9597 (tt0) cc_final: 0.9394 (pt0) REVERT: D 205 TYR cc_start: 0.7791 (m-10) cc_final: 0.7319 (m-80) REVERT: D 493 ARG cc_start: 0.8699 (tmm-80) cc_final: 0.8374 (tmt170) REVERT: D 615 ARG cc_start: 0.7136 (mtp180) cc_final: 0.5677 (tmt170) REVERT: D 685 ASP cc_start: 0.8441 (m-30) cc_final: 0.7908 (p0) REVERT: D 1198 TYR cc_start: 0.7523 (m-80) cc_final: 0.6966 (m-80) REVERT: D 1211 MET cc_start: 0.8594 (mtm) cc_final: 0.8070 (mmt) REVERT: D 1219 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7853 (tm-30) REVERT: D 1231 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7096 (tt0) REVERT: D 1339 LYS cc_start: 0.8687 (tttt) cc_final: 0.8446 (ttmt) REVERT: D 1376 MET cc_start: 0.8526 (mmm) cc_final: 0.8228 (mmm) REVERT: D 1426 LYS cc_start: 0.9043 (tttt) cc_final: 0.8578 (mttp) REVERT: E 57 ASP cc_start: 0.8648 (t70) cc_final: 0.8319 (t0) REVERT: E 90 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8942 (mp0) REVERT: M 363 LEU cc_start: 0.9475 (tp) cc_final: 0.9171 (tp) REVERT: M 464 MET cc_start: 0.7885 (tmm) cc_final: 0.7514 (tmm) REVERT: M 642 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8933 (tp30) REVERT: M 698 LEU cc_start: 0.9285 (mm) cc_final: 0.8275 (mm) REVERT: M 708 LEU cc_start: 0.9226 (tp) cc_final: 0.8934 (tp) REVERT: M 717 LEU cc_start: 0.9027 (mm) cc_final: 0.8795 (mm) REVERT: M 740 GLN cc_start: 0.9502 (tp40) cc_final: 0.8908 (tp40) REVERT: M 815 TYR cc_start: 0.9187 (t80) cc_final: 0.8930 (m-80) outliers start: 11 outliers final: 6 residues processed: 512 average time/residue: 0.2023 time to fit residues: 154.9509 Evaluate side-chains 269 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 263 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.0770 overall best weight: 1.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 139 ASN ** C 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 829 GLN C 860 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 GLN D 744 GLN D 748 HIS D1172 HIS D1323 GLN ** D1374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1442 ASN M 374 HIS ** M 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 783 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.134290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100451 restraints weight = 66769.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.098544 restraints weight = 70960.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099805 restraints weight = 64273.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100452 restraints weight = 41285.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100686 restraints weight = 38431.145| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28809 Z= 0.142 Angle : 0.628 8.890 39217 Z= 0.332 Chirality : 0.044 0.211 4429 Planarity : 0.006 0.060 4938 Dihedral : 14.125 112.379 4409 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -2.09 (0.13), residues: 3395 helix: -0.59 (0.14), residues: 1236 sheet: -1.78 (0.23), residues: 473 loop : -1.86 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 486 TYR 0.018 0.001 TYR D 989 PHE 0.017 0.001 PHE D 754 TRP 0.032 0.002 TRP D1398 HIS 0.012 0.001 HIS C1047 Details of bonding type rmsd covalent geometry : bond 0.00312 (28805) covalent geometry : angle 0.62591 (39211) hydrogen bonds : bond 0.05321 ( 1248) hydrogen bonds : angle 5.41645 ( 3400) metal coordination : bond 0.00942 ( 4) metal coordination : angle 3.74282 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 419 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8729 (tp) cc_final: 0.8525 (tt) REVERT: A 110 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8579 (mtmm) REVERT: A 124 ASN cc_start: 0.8521 (p0) cc_final: 0.8261 (p0) REVERT: B 91 ASN cc_start: 0.8488 (t0) cc_final: 0.8198 (p0) REVERT: C 33 ASP cc_start: 0.7392 (p0) cc_final: 0.7075 (p0) REVERT: C 229 MET cc_start: 0.6604 (ptm) cc_final: 0.5983 (ptm) REVERT: C 293 PHE cc_start: 0.4757 (t80) cc_final: 0.3904 (t80) REVERT: C 365 ASP cc_start: 0.8277 (p0) cc_final: 0.8057 (p0) REVERT: C 374 ASN cc_start: 0.7908 (t0) cc_final: 0.7065 (m-40) REVERT: C 422 ARG cc_start: 0.6929 (ttp-110) cc_final: 0.6419 (mmt180) REVERT: C 429 ASP cc_start: 0.8658 (t0) cc_final: 0.8454 (p0) REVERT: C 533 ASP cc_start: 0.8399 (m-30) cc_final: 0.7810 (m-30) REVERT: C 595 LEU cc_start: 0.9060 (tp) cc_final: 0.8588 (mp) REVERT: C 680 ASP cc_start: 0.8853 (t0) cc_final: 0.8578 (t0) REVERT: C 837 ASP cc_start: 0.7676 (m-30) cc_final: 0.7245 (m-30) REVERT: D 102 ILE cc_start: 0.9121 (tp) cc_final: 0.8790 (tp) REVERT: D 160 GLU cc_start: 0.8746 (tt0) cc_final: 0.8426 (tp30) REVERT: D 169 TYR cc_start: 0.7798 (m-80) cc_final: 0.7323 (m-80) REVERT: D 205 TYR cc_start: 0.6329 (m-10) cc_final: 0.5850 (m-80) REVERT: D 615 ARG cc_start: 0.7729 (mtp180) cc_final: 0.6518 (tmt170) REVERT: D 888 GLU cc_start: 0.6368 (tt0) cc_final: 0.5791 (tm-30) REVERT: D 1231 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7767 (tt0) REVERT: E 40 LEU cc_start: 0.7814 (mp) cc_final: 0.7565 (mt) REVERT: M 363 LEU cc_start: 0.8713 (tp) cc_final: 0.8364 (tt) REVERT: M 698 LEU cc_start: 0.7431 (mm) cc_final: 0.7005 (mm) REVERT: M 708 LEU cc_start: 0.8352 (tp) cc_final: 0.8096 (tp) REVERT: M 740 GLN cc_start: 0.8111 (tp40) cc_final: 0.7877 (tp40) outliers start: 2 outliers final: 0 residues processed: 421 average time/residue: 0.1812 time to fit residues: 119.0021 Evaluate side-chains 251 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 147 optimal weight: 0.9980 chunk 307 optimal weight: 40.0000 chunk 213 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 9 optimal weight: 9.9990 chunk 250 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 282 optimal weight: 0.9980 chunk 233 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN C 434 HIS C 498 GLN C 728 HIS C 829 GLN C 889 HIS C1006 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 575 GLN D 744 GLN ** M 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.131762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098385 restraints weight = 66767.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.096303 restraints weight = 78765.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097619 restraints weight = 68755.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.098391 restraints weight = 43095.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.098683 restraints weight = 39262.600| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28809 Z= 0.196 Angle : 0.639 8.191 39217 Z= 0.335 Chirality : 0.045 0.172 4429 Planarity : 0.006 0.059 4938 Dihedral : 13.888 113.392 4409 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.21 % Allowed : 4.90 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -1.60 (0.14), residues: 3395 helix: -0.00 (0.14), residues: 1243 sheet: -1.60 (0.23), residues: 486 loop : -1.70 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 354 TYR 0.027 0.002 TYR D 432 PHE 0.022 0.002 PHE M 699 TRP 0.029 0.002 TRP D1398 HIS 0.010 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00444 (28805) covalent geometry : angle 0.63696 (39211) hydrogen bonds : bond 0.05342 ( 1248) hydrogen bonds : angle 5.14686 ( 3400) metal coordination : bond 0.01009 ( 4) metal coordination : angle 3.95097 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 347 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8662 (p0) cc_final: 0.8354 (p0) REVERT: A 192 LEU cc_start: 0.8325 (mt) cc_final: 0.8061 (mt) REVERT: B 47 SER cc_start: 0.8782 (m) cc_final: 0.8470 (t) REVERT: B 91 ASN cc_start: 0.8490 (t0) cc_final: 0.8161 (p0) REVERT: B 139 ASN cc_start: 0.6801 (t0) cc_final: 0.6163 (t0) REVERT: C 293 PHE cc_start: 0.4914 (t80) cc_final: 0.4268 (t80) REVERT: C 374 ASN cc_start: 0.7790 (t0) cc_final: 0.6980 (m-40) REVERT: C 402 SER cc_start: 0.9041 (p) cc_final: 0.8718 (p) REVERT: C 429 ASP cc_start: 0.8728 (t0) cc_final: 0.8494 (p0) REVERT: C 443 THR cc_start: 0.9713 (t) cc_final: 0.9481 (m) REVERT: C 772 ARG cc_start: 0.7950 (tpt170) cc_final: 0.7522 (tmm-80) REVERT: C 1036 GLU cc_start: 0.8340 (mp0) cc_final: 0.7923 (mm-30) REVERT: D 169 TYR cc_start: 0.7712 (m-80) cc_final: 0.7079 (m-80) REVERT: D 205 TYR cc_start: 0.6081 (m-10) cc_final: 0.5663 (m-80) REVERT: D 463 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8359 (tp-100) REVERT: D 573 MET cc_start: 0.8033 (ttt) cc_final: 0.7812 (ttt) REVERT: D 615 ARG cc_start: 0.7793 (mtp180) cc_final: 0.6315 (tpt90) REVERT: D 745 MET cc_start: 0.8532 (tpp) cc_final: 0.8321 (ttm) REVERT: D 762 GLN cc_start: 0.7988 (mt0) cc_final: 0.7778 (mt0) REVERT: D 1211 MET cc_start: 0.7503 (mtp) cc_final: 0.6596 (mtt) REVERT: D 1231 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7524 (tm-30) REVERT: E 16 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7932 (ptmt) REVERT: E 90 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8092 (tp30) REVERT: M 363 LEU cc_start: 0.8655 (tp) cc_final: 0.8314 (tt) REVERT: M 708 LEU cc_start: 0.8429 (tp) cc_final: 0.8083 (tp) REVERT: M 740 GLN cc_start: 0.8051 (tp40) cc_final: 0.7847 (tp40) outliers start: 6 outliers final: 2 residues processed: 350 average time/residue: 0.1756 time to fit residues: 96.6829 Evaluate side-chains 243 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 77 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 chunk 321 optimal weight: 20.0000 chunk 45 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 305 optimal weight: 40.0000 chunk 76 optimal weight: 2.9990 chunk 214 optimal weight: 4.9990 chunk 309 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN B 139 ASN C 683 ASN C 829 GLN C1006 HIS C1100 GLN ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 GLN M 516 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.131765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.097508 restraints weight = 66269.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.094966 restraints weight = 71298.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.096182 restraints weight = 58103.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097040 restraints weight = 38714.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097257 restraints weight = 34179.708| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28809 Z= 0.186 Angle : 0.622 8.657 39217 Z= 0.327 Chirality : 0.045 0.310 4429 Planarity : 0.005 0.055 4938 Dihedral : 13.794 114.580 4409 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -1.28 (0.14), residues: 3395 helix: 0.24 (0.14), residues: 1242 sheet: -1.37 (0.23), residues: 494 loop : -1.50 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 793 TYR 0.019 0.001 TYR D 868 PHE 0.040 0.002 PHE M 646 TRP 0.028 0.002 TRP D1398 HIS 0.008 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00428 (28805) covalent geometry : angle 0.62103 (39211) hydrogen bonds : bond 0.05122 ( 1248) hydrogen bonds : angle 5.01731 ( 3400) metal coordination : bond 0.01213 ( 4) metal coordination : angle 2.58974 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8721 (p0) cc_final: 0.8429 (p0) REVERT: B 47 SER cc_start: 0.8824 (m) cc_final: 0.8512 (t) REVERT: B 91 ASN cc_start: 0.8541 (t0) cc_final: 0.8199 (p0) REVERT: B 102 LYS cc_start: 0.8862 (tppt) cc_final: 0.8565 (mmmt) REVERT: C 293 PHE cc_start: 0.5024 (t80) cc_final: 0.4350 (t80) REVERT: C 374 ASN cc_start: 0.7756 (t0) cc_final: 0.6953 (m-40) REVERT: C 402 SER cc_start: 0.9113 (p) cc_final: 0.8812 (p) REVERT: C 533 ASP cc_start: 0.8193 (m-30) cc_final: 0.7857 (m-30) REVERT: C 772 ARG cc_start: 0.8055 (tpt170) cc_final: 0.7658 (ttp80) REVERT: C 1088 LEU cc_start: 0.9070 (tp) cc_final: 0.8825 (tp) REVERT: D 169 TYR cc_start: 0.7516 (m-80) cc_final: 0.7207 (m-80) REVERT: D 463 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8491 (tp-100) REVERT: D 615 ARG cc_start: 0.7734 (mtp180) cc_final: 0.6306 (tpt90) REVERT: D 657 LEU cc_start: 0.8747 (tp) cc_final: 0.8546 (tt) REVERT: D 745 MET cc_start: 0.8450 (tpp) cc_final: 0.8177 (ttm) REVERT: D 1210 SER cc_start: 0.8869 (m) cc_final: 0.8611 (t) REVERT: M 363 LEU cc_start: 0.8766 (tp) cc_final: 0.8444 (tt) REVERT: M 708 LEU cc_start: 0.8556 (tp) cc_final: 0.8239 (tp) REVERT: M 740 GLN cc_start: 0.8174 (tp40) cc_final: 0.7967 (tp40) outliers start: 1 outliers final: 1 residues processed: 328 average time/residue: 0.1733 time to fit residues: 89.9077 Evaluate side-chains 224 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 223 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 255 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 158 optimal weight: 0.0670 chunk 79 optimal weight: 20.0000 chunk 235 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 199 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 188 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C 969 GLN C1006 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN D1010 ASN ** D1374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.128839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.097274 restraints weight = 66667.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093637 restraints weight = 75814.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094512 restraints weight = 66235.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.095351 restraints weight = 44850.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095603 restraints weight = 38573.079| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 28809 Z= 0.283 Angle : 0.708 8.793 39217 Z= 0.370 Chirality : 0.047 0.191 4429 Planarity : 0.006 0.056 4938 Dihedral : 13.841 116.552 4409 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.03 % Allowed : 4.14 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -1.35 (0.14), residues: 3395 helix: 0.23 (0.14), residues: 1240 sheet: -1.51 (0.22), residues: 480 loop : -1.56 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 668 TYR 0.034 0.002 TYR D 432 PHE 0.025 0.002 PHE D 716 TRP 0.033 0.002 TRP D1398 HIS 0.008 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00656 (28805) covalent geometry : angle 0.70645 (39211) hydrogen bonds : bond 0.05703 ( 1248) hydrogen bonds : angle 5.19882 ( 3400) metal coordination : bond 0.02035 ( 4) metal coordination : angle 3.22206 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8928 (tttt) cc_final: 0.8525 (tptt) REVERT: A 124 ASN cc_start: 0.8696 (p0) cc_final: 0.8346 (p0) REVERT: B 47 SER cc_start: 0.8748 (m) cc_final: 0.8364 (t) REVERT: B 91 ASN cc_start: 0.8655 (t0) cc_final: 0.8371 (p0) REVERT: B 102 LYS cc_start: 0.8946 (tppt) cc_final: 0.8439 (tptp) REVERT: C 229 MET cc_start: 0.7199 (pmm) cc_final: 0.6631 (pmm) REVERT: C 293 PHE cc_start: 0.5078 (t80) cc_final: 0.4321 (t80) REVERT: C 374 ASN cc_start: 0.7739 (t0) cc_final: 0.7069 (m-40) REVERT: C 402 SER cc_start: 0.9036 (p) cc_final: 0.8725 (p) REVERT: C 443 THR cc_start: 0.9704 (t) cc_final: 0.9431 (m) REVERT: C 708 TYR cc_start: 0.8265 (m-80) cc_final: 0.8027 (m-10) REVERT: D 159 ARG cc_start: 0.9144 (ttm-80) cc_final: 0.8840 (ttm-80) REVERT: D 615 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7038 (tmt170) REVERT: D 1100 ASP cc_start: 0.8253 (t70) cc_final: 0.7935 (t70) REVERT: D 1198 TYR cc_start: 0.7586 (m-80) cc_final: 0.7254 (m-80) REVERT: D 1440 PHE cc_start: 0.8462 (t80) cc_final: 0.8151 (t80) REVERT: E 88 GLU cc_start: 0.8763 (mp0) cc_final: 0.8403 (mp0) REVERT: M 363 LEU cc_start: 0.8936 (tp) cc_final: 0.8640 (tt) REVERT: M 708 LEU cc_start: 0.8738 (tp) cc_final: 0.8374 (tp) REVERT: M 740 GLN cc_start: 0.8452 (tp40) cc_final: 0.8170 (tp40) outliers start: 1 outliers final: 1 residues processed: 284 average time/residue: 0.1674 time to fit residues: 76.1450 Evaluate side-chains 209 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 265 optimal weight: 10.0000 chunk 154 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C1006 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 617 ASN M 574 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.131857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098620 restraints weight = 66240.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.096529 restraints weight = 72305.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098091 restraints weight = 63429.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097738 restraints weight = 46164.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.098458 restraints weight = 40022.150| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28809 Z= 0.145 Angle : 0.597 8.227 39217 Z= 0.311 Chirality : 0.044 0.195 4429 Planarity : 0.005 0.064 4938 Dihedral : 13.721 114.605 4409 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.99 (0.14), residues: 3395 helix: 0.54 (0.14), residues: 1240 sheet: -1.28 (0.22), residues: 502 loop : -1.37 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 681 TYR 0.034 0.001 TYR D 432 PHE 0.028 0.002 PHE C 48 TRP 0.034 0.002 TRP D1398 HIS 0.006 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00334 (28805) covalent geometry : angle 0.59420 (39211) hydrogen bonds : bond 0.04902 ( 1248) hydrogen bonds : angle 4.83831 ( 3400) metal coordination : bond 0.01600 ( 4) metal coordination : angle 4.48966 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 304 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.8678 (p0) cc_final: 0.8339 (p0) REVERT: B 47 SER cc_start: 0.8839 (m) cc_final: 0.8409 (t) REVERT: B 91 ASN cc_start: 0.8723 (t0) cc_final: 0.8404 (p0) REVERT: C 184 MET cc_start: 0.6728 (ttt) cc_final: 0.6503 (ttt) REVERT: C 229 MET cc_start: 0.6976 (pmm) cc_final: 0.6456 (pmm) REVERT: C 293 PHE cc_start: 0.4685 (t80) cc_final: 0.3945 (t80) REVERT: C 374 ASN cc_start: 0.7596 (t0) cc_final: 0.7091 (m-40) REVERT: C 402 SER cc_start: 0.9136 (p) cc_final: 0.8856 (p) REVERT: C 443 THR cc_start: 0.9660 (t) cc_final: 0.9438 (m) REVERT: C 564 MET cc_start: 0.7859 (mtm) cc_final: 0.7466 (ttm) REVERT: C 1036 GLU cc_start: 0.8083 (mp0) cc_final: 0.7488 (mm-30) REVERT: D 45 PHE cc_start: 0.7482 (m-80) cc_final: 0.7104 (m-80) REVERT: D 159 ARG cc_start: 0.8958 (ttm-80) cc_final: 0.8712 (ttm-80) REVERT: D 615 ARG cc_start: 0.7792 (mtp180) cc_final: 0.6532 (tpt90) REVERT: M 363 LEU cc_start: 0.8788 (tp) cc_final: 0.8453 (tt) REVERT: M 464 MET cc_start: 0.0742 (mmt) cc_final: -0.0396 (mmt) REVERT: M 708 LEU cc_start: 0.8619 (tp) cc_final: 0.8417 (tp) REVERT: M 740 GLN cc_start: 0.8191 (tp40) cc_final: 0.7975 (tp40) outliers start: 1 outliers final: 0 residues processed: 305 average time/residue: 0.1550 time to fit residues: 77.3645 Evaluate side-chains 228 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 282 optimal weight: 0.0030 chunk 50 optimal weight: 0.1980 chunk 329 optimal weight: 30.0000 chunk 108 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 242 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN C 829 GLN C1006 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.099561 restraints weight = 67677.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.097065 restraints weight = 70494.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098420 restraints weight = 69954.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.098653 restraints weight = 44827.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.099299 restraints weight = 38949.090| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28809 Z= 0.122 Angle : 0.590 12.136 39217 Z= 0.306 Chirality : 0.044 0.217 4429 Planarity : 0.005 0.057 4938 Dihedral : 13.630 113.941 4409 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.80 (0.14), residues: 3395 helix: 0.63 (0.15), residues: 1240 sheet: -1.04 (0.22), residues: 513 loop : -1.24 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 681 TYR 0.024 0.001 TYR A 224 PHE 0.036 0.001 PHE M 699 TRP 0.041 0.002 TRP D1398 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00276 (28805) covalent geometry : angle 0.58786 (39211) hydrogen bonds : bond 0.04612 ( 1248) hydrogen bonds : angle 4.70010 ( 3400) metal coordination : bond 0.00961 ( 4) metal coordination : angle 4.31306 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7208 (ptm-80) REVERT: A 124 ASN cc_start: 0.8683 (p0) cc_final: 0.8316 (p0) REVERT: A 192 LEU cc_start: 0.8205 (mt) cc_final: 0.7867 (mt) REVERT: B 47 SER cc_start: 0.8769 (m) cc_final: 0.8439 (t) REVERT: B 91 ASN cc_start: 0.8684 (t0) cc_final: 0.8441 (p0) REVERT: C 200 LEU cc_start: 0.8466 (tp) cc_final: 0.7152 (tp) REVERT: C 229 MET cc_start: 0.6825 (pmm) cc_final: 0.6574 (pmm) REVERT: C 293 PHE cc_start: 0.4776 (t80) cc_final: 0.4000 (t80) REVERT: C 374 ASN cc_start: 0.7676 (t0) cc_final: 0.7075 (m-40) REVERT: C 402 SER cc_start: 0.9128 (p) cc_final: 0.8758 (p) REVERT: C 443 THR cc_start: 0.9645 (t) cc_final: 0.9416 (m) REVERT: C 698 ASP cc_start: 0.8152 (p0) cc_final: 0.7887 (p0) REVERT: C 717 LEU cc_start: 0.8732 (mp) cc_final: 0.8265 (tt) REVERT: C 796 GLU cc_start: 0.7383 (pt0) cc_final: 0.6861 (pm20) REVERT: C 858 MET cc_start: 0.8470 (tpt) cc_final: 0.8040 (mmt) REVERT: C 1030 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8253 (mp10) REVERT: C 1036 GLU cc_start: 0.8068 (mp0) cc_final: 0.7412 (mm-30) REVERT: D 45 PHE cc_start: 0.7271 (m-80) cc_final: 0.6912 (m-80) REVERT: D 463 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8444 (tp-100) REVERT: D 551 ASN cc_start: 0.7865 (t0) cc_final: 0.7489 (t0) REVERT: D 615 ARG cc_start: 0.7816 (mtp180) cc_final: 0.6714 (tmt170) REVERT: D 1198 TYR cc_start: 0.7784 (m-80) cc_final: 0.7536 (m-80) REVERT: D 1219 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7987 (tt0) REVERT: E 87 LYS cc_start: 0.9471 (ptmm) cc_final: 0.9263 (pttm) REVERT: M 363 LEU cc_start: 0.8664 (tp) cc_final: 0.8310 (tt) REVERT: M 464 MET cc_start: 0.0685 (mmt) cc_final: 0.0107 (mmm) REVERT: M 708 LEU cc_start: 0.8597 (tp) cc_final: 0.8369 (tp) REVERT: M 740 GLN cc_start: 0.8214 (tp40) cc_final: 0.7973 (tp40) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1585 time to fit residues: 85.8315 Evaluate side-chains 244 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 114 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 87 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 310 optimal weight: 0.6980 chunk 189 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 GLN ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C1006 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 ASN ** M 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.132077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.100082 restraints weight = 68348.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.097574 restraints weight = 74761.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.099011 restraints weight = 66587.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.098911 restraints weight = 48353.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099794 restraints weight = 39852.581| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28809 Z= 0.157 Angle : 0.609 11.772 39217 Z= 0.314 Chirality : 0.044 0.178 4429 Planarity : 0.005 0.056 4938 Dihedral : 13.589 114.946 4409 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.79 (0.14), residues: 3395 helix: 0.66 (0.15), residues: 1241 sheet: -1.02 (0.23), residues: 500 loop : -1.25 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 761 TYR 0.018 0.001 TYR M 739 PHE 0.024 0.002 PHE A 65 TRP 0.033 0.002 TRP D1398 HIS 0.006 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00367 (28805) covalent geometry : angle 0.60754 (39211) hydrogen bonds : bond 0.04752 ( 1248) hydrogen bonds : angle 4.70291 ( 3400) metal coordination : bond 0.01263 ( 4) metal coordination : angle 3.82694 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7564 (ttp80) cc_final: 0.7198 (ptm-80) REVERT: A 124 ASN cc_start: 0.8691 (p0) cc_final: 0.8438 (p0) REVERT: A 192 LEU cc_start: 0.8249 (mt) cc_final: 0.7914 (mt) REVERT: B 47 SER cc_start: 0.8765 (m) cc_final: 0.8402 (t) REVERT: B 91 ASN cc_start: 0.8699 (t0) cc_final: 0.8446 (p0) REVERT: C 229 MET cc_start: 0.6983 (pmm) cc_final: 0.6758 (pmm) REVERT: C 293 PHE cc_start: 0.4747 (t80) cc_final: 0.3947 (t80) REVERT: C 374 ASN cc_start: 0.7781 (t0) cc_final: 0.7174 (m-40) REVERT: C 402 SER cc_start: 0.9082 (p) cc_final: 0.8725 (p) REVERT: C 443 THR cc_start: 0.9571 (t) cc_final: 0.9347 (m) REVERT: C 717 LEU cc_start: 0.8796 (mp) cc_final: 0.8282 (tt) REVERT: C 1030 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8269 (mp10) REVERT: C 1036 GLU cc_start: 0.8204 (mp0) cc_final: 0.7606 (mm-30) REVERT: D 45 PHE cc_start: 0.7571 (m-80) cc_final: 0.7320 (m-80) REVERT: D 551 ASN cc_start: 0.7703 (t0) cc_final: 0.7317 (t0) REVERT: D 615 ARG cc_start: 0.7717 (mtp180) cc_final: 0.6811 (tmt170) REVERT: D 1219 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8104 (tt0) REVERT: D 1458 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7965 (tt0) REVERT: E 16 LYS cc_start: 0.7984 (ptmt) cc_final: 0.7703 (ptpt) REVERT: E 51 LEU cc_start: 0.7557 (mt) cc_final: 0.7304 (pp) REVERT: E 79 LEU cc_start: 0.8647 (mt) cc_final: 0.8304 (mm) REVERT: M 363 LEU cc_start: 0.8756 (tp) cc_final: 0.8419 (tt) REVERT: M 464 MET cc_start: 0.0721 (mmt) cc_final: -0.0607 (mmm) REVERT: M 708 LEU cc_start: 0.8689 (tp) cc_final: 0.8462 (tp) REVERT: M 740 GLN cc_start: 0.8320 (tp40) cc_final: 0.8040 (tp40) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1727 time to fit residues: 86.3419 Evaluate side-chains 230 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 253 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 274 optimal weight: 6.9990 chunk 328 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 306 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 276 optimal weight: 30.0000 chunk 257 optimal weight: 1.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 ASN ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN ** C1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 516 GLN M 758 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.132485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099562 restraints weight = 66111.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097277 restraints weight = 70014.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.098896 restraints weight = 61780.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098715 restraints weight = 42858.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099514 restraints weight = 36748.100| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28809 Z= 0.143 Angle : 0.593 10.979 39217 Z= 0.306 Chirality : 0.044 0.246 4429 Planarity : 0.005 0.055 4938 Dihedral : 13.522 113.717 4409 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.71 (0.14), residues: 3395 helix: 0.67 (0.15), residues: 1243 sheet: -0.88 (0.23), residues: 504 loop : -1.20 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 793 TYR 0.023 0.001 TYR M 739 PHE 0.018 0.002 PHE M 699 TRP 0.041 0.002 TRP D1398 HIS 0.005 0.001 HIS C1006 Details of bonding type rmsd covalent geometry : bond 0.00335 (28805) covalent geometry : angle 0.59166 (39211) hydrogen bonds : bond 0.04594 ( 1248) hydrogen bonds : angle 4.64684 ( 3400) metal coordination : bond 0.00954 ( 4) metal coordination : angle 3.43807 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7582 (ttp80) cc_final: 0.7182 (ptm-80) REVERT: A 124 ASN cc_start: 0.8649 (p0) cc_final: 0.8355 (p0) REVERT: A 192 LEU cc_start: 0.8280 (mt) cc_final: 0.7985 (mt) REVERT: B 47 SER cc_start: 0.8818 (m) cc_final: 0.8489 (t) REVERT: B 91 ASN cc_start: 0.8771 (t0) cc_final: 0.8539 (p0) REVERT: C 307 LEU cc_start: 0.9085 (mt) cc_final: 0.8872 (mt) REVERT: C 374 ASN cc_start: 0.7751 (t0) cc_final: 0.7163 (m-40) REVERT: C 402 SER cc_start: 0.9046 (p) cc_final: 0.8718 (p) REVERT: C 443 THR cc_start: 0.9571 (t) cc_final: 0.9260 (m) REVERT: C 717 LEU cc_start: 0.8731 (mp) cc_final: 0.8255 (tt) REVERT: C 1030 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8307 (mp10) REVERT: C 1036 GLU cc_start: 0.8053 (mp0) cc_final: 0.7479 (mm-30) REVERT: D 159 ARG cc_start: 0.8796 (ttm-80) cc_final: 0.8339 (tpp80) REVERT: D 456 MET cc_start: 0.8321 (mtt) cc_final: 0.7944 (mtt) REVERT: D 551 ASN cc_start: 0.7799 (t0) cc_final: 0.7426 (t0) REVERT: D 615 ARG cc_start: 0.7728 (mtp180) cc_final: 0.6749 (tmt170) REVERT: D 1219 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8180 (tt0) REVERT: E 16 LYS cc_start: 0.8000 (ptmt) cc_final: 0.7732 (ptpt) REVERT: E 87 LYS cc_start: 0.9318 (pttm) cc_final: 0.9050 (pttm) REVERT: M 363 LEU cc_start: 0.8741 (tp) cc_final: 0.8449 (tp) REVERT: M 708 LEU cc_start: 0.8150 (tp) cc_final: 0.7853 (tp) REVERT: M 740 GLN cc_start: 0.8286 (tp40) cc_final: 0.8019 (tp40) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.1597 time to fit residues: 77.3573 Evaluate side-chains 224 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 226 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 295 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 122 optimal weight: 0.7980 chunk 298 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 241 optimal weight: 6.9990 chunk 251 optimal weight: 4.9990 chunk 88 optimal weight: 0.0470 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 HIS ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C1006 HIS ** D 101 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 = 0.3922 r_free = 0.3922 target = 0.133169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.100112 restraints weight = 66073.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.098546 restraints weight = 69206.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.099639 restraints weight = 63685.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099776 restraints weight = 43621.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.100424 restraints weight = 36898.003| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28809 Z= 0.126 Angle : 0.583 10.484 39217 Z= 0.302 Chirality : 0.044 0.248 4429 Planarity : 0.005 0.055 4938 Dihedral : 13.438 111.987 4409 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.57 (0.14), residues: 3395 helix: 0.78 (0.15), residues: 1247 sheet: -0.81 (0.23), residues: 509 loop : -1.11 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 198 TYR 0.015 0.001 TYR D 791 PHE 0.016 0.001 PHE C1085 TRP 0.036 0.002 TRP D1398 HIS 0.005 0.001 HIS C1006 Details of bonding type rmsd covalent geometry : bond 0.00291 (28805) covalent geometry : angle 0.58180 (39211) hydrogen bonds : bond 0.04428 ( 1248) hydrogen bonds : angle 4.54203 ( 3400) metal coordination : bond 0.00808 ( 4) metal coordination : angle 3.64386 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7601 (ttp80) cc_final: 0.7156 (ptm-80) REVERT: A 124 ASN cc_start: 0.8612 (p0) cc_final: 0.8334 (p0) REVERT: A 192 LEU cc_start: 0.8252 (mt) cc_final: 0.7973 (mt) REVERT: B 47 SER cc_start: 0.8930 (m) cc_final: 0.8604 (t) REVERT: B 91 ASN cc_start: 0.8750 (t0) cc_final: 0.8547 (p0) REVERT: C 374 ASN cc_start: 0.7618 (t0) cc_final: 0.7108 (m-40) REVERT: C 402 SER cc_start: 0.9142 (p) cc_final: 0.8807 (p) REVERT: C 717 LEU cc_start: 0.8706 (mp) cc_final: 0.8247 (tt) REVERT: C 796 GLU cc_start: 0.7458 (pt0) cc_final: 0.6964 (pm20) REVERT: C 1030 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8214 (mp10) REVERT: C 1036 GLU cc_start: 0.8150 (mp0) cc_final: 0.7493 (mm-30) REVERT: D 159 ARG cc_start: 0.8730 (ttm-80) cc_final: 0.8427 (tpp80) REVERT: D 551 ASN cc_start: 0.7818 (t0) cc_final: 0.7397 (t0) REVERT: D 615 ARG cc_start: 0.7641 (mtp180) cc_final: 0.6675 (tmt170) REVERT: E 79 LEU cc_start: 0.8581 (mt) cc_final: 0.8332 (mm) REVERT: M 363 LEU cc_start: 0.8639 (tp) cc_final: 0.8352 (tp) REVERT: M 708 LEU cc_start: 0.8096 (tp) cc_final: 0.7874 (tp) REVERT: M 740 GLN cc_start: 0.8147 (tp40) cc_final: 0.7901 (tp40) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.1628 time to fit residues: 78.2623 Evaluate side-chains 223 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 31 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 323 optimal weight: 6.9990 chunk 239 optimal weight: 0.6980 chunk 327 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN ** C1006 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 507 ASN D 824 ASN ** M 758 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 = 0.3903 r_free = 0.3903 target = 0.131919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.098811 restraints weight = 66339.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.095949 restraints weight = 68650.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.096936 restraints weight = 60155.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.097805 restraints weight = 40619.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.098127 restraints weight = 35061.517| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28809 Z= 0.165 Angle : 0.609 10.478 39217 Z= 0.315 Chirality : 0.045 0.240 4429 Planarity : 0.005 0.055 4938 Dihedral : 13.426 111.846 4409 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % 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: -0.56 (0.15), residues: 3395 helix: 0.79 (0.15), residues: 1248 sheet: -0.78 (0.23), residues: 501 loop : -1.13 (0.16), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 198 TYR 0.029 0.001 TYR D 432 PHE 0.019 0.002 PHE C1027 TRP 0.049 0.002 TRP C1038 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00384 (28805) covalent geometry : angle 0.60804 (39211) hydrogen bonds : bond 0.04669 ( 1248) hydrogen bonds : angle 4.62154 ( 3400) metal coordination : bond 0.01252 ( 4) metal coordination : angle 3.16623 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3845.40 seconds wall clock time: 67 minutes 30.37 seconds (4050.37 seconds total)