Starting phenix.real_space_refine on Mon Sep 14 05:00:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_30118.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_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 { model { file = "/net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_30118.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_30118.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_30118.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_30118.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_30118.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6m6b_30118/09_2026/6m6b_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 4.77, per 1000 atoms: 0.17 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.43 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: 7.80 Time building geometry restraints manager: 3.06 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=" C1' DC T 33 " pdb=" N1 DC T 33 " ideal model delta sigma weight residual 1.468 1.415 0.053 1.40e-02 5.10e+03 1.42e+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=" C5' DC N 31 " pdb=" C4' DC N 31 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.22e+01 ... (remaining 28800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 38055 2.43 - 4.86: 1040 4.86 - 7.29: 99 7.29 - 9.73: 11 9.73 - 12.16: 6 Bond angle restraints: 39211 Sorted by residual: angle pdb=" C2' DG N 13 " pdb=" C1' DG N 13 " pdb=" N9 DG N 13 " ideal model delta sigma weight residual 114.30 103.11 11.19 1.40e+00 5.10e-01 6.39e+01 angle pdb=" C GLN M 619 " pdb=" N THR M 620 " pdb=" CA THR M 620 " ideal model delta sigma weight residual 123.10 117.23 5.87 9.60e-01 1.09e+00 3.74e+01 angle pdb=" N PHE C 303 " pdb=" CA PHE C 303 " pdb=" C PHE C 303 " ideal model delta sigma weight residual 111.28 117.78 -6.50 1.09e+00 8.42e-01 3.55e+01 angle pdb=" N GLY D 457 " pdb=" CA GLY D 457 " pdb=" C GLY D 457 " ideal model delta sigma weight residual 111.09 118.25 -7.16 1.33e+00 5.65e-01 2.90e+01 angle pdb=" O4' DT N 35 " pdb=" C1' DT N 35 " pdb=" N1 DT N 35 " ideal model delta sigma weight residual 108.00 111.46 -3.46 7.00e-01 2.04e+00 2.44e+01 ... (remaining 39206 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.98: 15213 18.98 - 37.96: 1782 37.96 - 56.94: 425 56.94 - 75.93: 87 75.93 - 94.91: 15 Dihedral angle restraints: 17522 sinusoidal: 7711 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 17519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3176 0.055 - 0.110: 990 0.110 - 0.164: 231 0.164 - 0.219: 24 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=" C4' DG N 12 " pdb=" C5' DG N 12 " pdb=" O4' DG N 12 " pdb=" C3' DG N 12 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.27 2.00e-01 2.50e+01 1.78e+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: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 30.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 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= 0.398 Angle : 0.975 19.544 39217 Z= 0.592 Chirality : 0.056 0.274 4429 Planarity : 0.008 0.091 4938 Dihedral : 16.956 94.906 11216 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 are 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/Z covalent geometry : bond 0.00739 / 0.40 (28805) covalent geometry : angle 0.96078 / 0.59 (39211) hydrogen bonds : bond 0.15629 / 10.47 ( 1248) hydrogen bonds : angle 7.07611 / 4.95 ( 3400) metal coordination : bond 0.11044 / 5.56 ( 4) metal coordination : angle 13.39790 / 7.20 ( 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 : 1.356 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: 0.8805 (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: 0.7915 (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: 0.8912 (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: 0.7137 (mtp180) cc_final: 0.5679 (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: 0.7854 (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: 0.9474 (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: 0.9286 (mm) cc_final: 0.8275 (mm) REVERT: M 708 LEU cc_start: 0.9226 (tp) cc_final: 0.8935 (tp) REVERT: M 717 LEU cc_start: 0.9027 (mm) cc_final: 0.8795 (mm) REVERT: M 740 GLN cc_start: 0.9503 (tp40) cc_final: 0.8907 (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: 0.2151 time to fit residues: 166.2683 Evaluate side-chains 268 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 262 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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... 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 ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 GLN D 744 GLN D 748 HIS D1172 HIS D1442 ASN D1465 ASN M 374 HIS ** M 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 574 HIS M 783 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.134015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.101601 restraints weight = 66643.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100071 restraints weight = 68310.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101287 restraints weight = 64876.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101404 restraints weight = 44601.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102589 restraints weight = 38480.846| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28809 Z= 0.156 Angle : 0.661 8.842 39217 Z= 0.351 Chirality : 0.046 0.214 4429 Planarity : 0.006 0.062 4938 Dihedral : 14.239 112.928 4398 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.17 % Allowed : 4.07 % Favored : 95.76 % 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 are not related in a simple way. whole: -2.23 (0.13), residues: 3395 helix: -0.76 (0.13), residues: 1233 sheet: -1.84 (0.22), residues: 481 loop : -1.89 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 486 TYR 0.019 0.001 TYR D 989 PHE 0.018 0.001 PHE D 754 TRP 0.038 0.002 TRP D1398 HIS 0.010 0.001 HIS C1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (28805) covalent geometry : angle 0.65960 / 0.35 (39211) hydrogen bonds : bond 0.05842 / 3.91 ( 1248) hydrogen bonds : angle 5.63068 / 3.98 ( 3400) metal coordination : bond 0.01371 / 0.68 ( 4) metal coordination : angle 3.90011 / 2.17 ( 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 417 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 412 time to evaluate : 1.093 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 110 LYS cc_start: 0.8781 (mmtt) cc_final: 0.8573 (mtmm) REVERT: A 124 ASN cc_start: 0.8497 (p0) cc_final: 0.8064 (p0) REVERT: B 91 ASN cc_start: 0.8450 (t0) cc_final: 0.8186 (p0) REVERT: C 33 ASP cc_start: 0.7394 (p0) cc_final: 0.6999 (p0) REVERT: C 229 MET cc_start: 0.6425 (ptm) cc_final: 0.4495 (ptm) REVERT: C 293 PHE cc_start: 0.4753 (t80) cc_final: 0.4075 (t80) REVERT: C 374 ASN cc_start: 0.7923 (t0) cc_final: 0.7062 (m-40) REVERT: C 422 ARG cc_start: 0.6903 (ttp-110) cc_final: 0.6431 (mmt180) REVERT: C 533 ASP cc_start: 0.8314 (m-30) cc_final: 0.7733 (m-30) REVERT: C 595 LEU cc_start: 0.9037 (tp) cc_final: 0.8613 (mp) REVERT: C 680 ASP cc_start: 0.8874 (t0) cc_final: 0.8603 (t0) REVERT: C 837 ASP cc_start: 0.7556 (m-30) cc_final: 0.7222 (m-30) REVERT: C 1059 ASP cc_start: 0.6285 (t0) cc_final: 0.5997 (t70) REVERT: D 102 ILE cc_start: 0.9100 (tp) cc_final: 0.8761 (tp) REVERT: D 160 GLU cc_start: 0.8724 (tt0) cc_final: 0.8429 (tp30) REVERT: D 205 TYR cc_start: 0.6313 (m-10) cc_final: 0.5842 (m-80) REVERT: D 615 ARG cc_start: 0.7727 (mtp180) cc_final: 0.6564 (tmt170) REVERT: D 1231 GLU cc_start: 0.8338 (tm-30) cc_final: 0.7820 (tt0) REVERT: E 40 LEU cc_start: 0.7813 (mp) cc_final: 0.7313 (mt) REVERT: M 363 LEU cc_start: 0.8663 (tp) cc_final: 0.8320 (tt) REVERT: M 698 LEU cc_start: 0.7400 (mm) cc_final: 0.6993 (mm) REVERT: M 708 LEU cc_start: 0.8320 (tp) cc_final: 0.8057 (tp) REVERT: M 740 GLN cc_start: 0.8055 (tp40) cc_final: 0.7823 (tp40) outliers start: 5 outliers final: 1 residues processed: 417 average time/residue: 0.1994 time to fit residues: 130.2988 Evaluate side-chains 245 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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: 3.9990 chunk 307 optimal weight: 50.0000 chunk 213 optimal weight: 0.8980 chunk 239 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 258 optimal weight: 7.9990 chunk 282 optimal weight: 0.1980 chunk 233 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN ** C 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 728 HIS C 829 GLN C1006 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 744 GLN D1323 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.133658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100965 restraints weight = 66571.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098850 restraints weight = 73042.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.100437 restraints weight = 66656.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.100402 restraints weight = 45498.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101121 restraints weight = 39247.158| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28809 Z= 0.148 Angle : 0.623 8.183 39217 Z= 0.328 Chirality : 0.045 0.191 4429 Planarity : 0.006 0.060 4938 Dihedral : 13.965 113.873 4398 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.17 % Allowed : 4.31 % Favored : 95.52 % 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 are not related in a simple way. whole: -1.65 (0.14), residues: 3395 helix: -0.13 (0.14), residues: 1234 sheet: -1.53 (0.23), residues: 486 loop : -1.68 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 550 TYR 0.035 0.001 TYR D 432 PHE 0.022 0.001 PHE C 191 TRP 0.030 0.002 TRP D1398 HIS 0.010 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (28805) covalent geometry : angle 0.62115 / 0.33 (39211) hydrogen bonds : bond 0.05281 / 3.51 ( 1248) hydrogen bonds : angle 5.22421 / 3.70 ( 3400) metal coordination : bond 0.01217 / 0.61 ( 4) metal coordination : angle 4.03846 / 2.24 ( 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 368 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 363 time to evaluate : 1.047 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: 0.8539 (p0) cc_final: 0.8194 (p0) REVERT: A 192 LEU cc_start: 0.8312 (mt) cc_final: 0.8092 (mt) REVERT: B 47 SER cc_start: 0.8751 (m) cc_final: 0.8502 (t) REVERT: B 91 ASN cc_start: 0.8452 (t0) cc_final: 0.8162 (p0) REVERT: C 33 ASP cc_start: 0.7146 (p0) cc_final: 0.6704 (p0) REVERT: C 200 LEU cc_start: 0.8172 (tp) cc_final: 0.7533 (tp) REVERT: C 293 PHE cc_start: 0.4899 (t80) cc_final: 0.4221 (t80) REVERT: C 374 ASN cc_start: 0.7775 (t0) cc_final: 0.6950 (m-40) REVERT: C 399 ASN cc_start: 0.8256 (p0) cc_final: 0.7699 (p0) REVERT: C 402 SER cc_start: 0.8980 (p) cc_final: 0.8226 (p) REVERT: C 443 THR cc_start: 0.9706 (t) cc_final: 0.9468 (m) REVERT: C 533 ASP cc_start: 0.8203 (m-30) cc_final: 0.7639 (m-30) REVERT: C 595 LEU cc_start: 0.9059 (tp) cc_final: 0.8567 (mp) REVERT: C 772 ARG cc_start: 0.7970 (tpt170) cc_final: 0.7671 (ttp80) REVERT: D 45 PHE cc_start: 0.7434 (m-80) cc_final: 0.7225 (m-80) REVERT: D 205 TYR cc_start: 0.6262 (m-10) cc_final: 0.5788 (m-80) REVERT: D 463 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8403 (tp-100) REVERT: D 527 MET cc_start: 0.7625 (ptm) cc_final: 0.7411 (ppp) REVERT: D 615 ARG cc_start: 0.7752 (mtp180) cc_final: 0.6069 (tpt90) REVERT: D 754 PHE cc_start: 0.7809 (t80) cc_final: 0.7264 (t80) REVERT: D 1231 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7782 (tt0) REVERT: E 90 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: M 363 LEU cc_start: 0.8667 (tp) cc_final: 0.8316 (tt) REVERT: M 708 LEU cc_start: 0.8226 (tp) cc_final: 0.7925 (tp) outliers start: 5 outliers final: 1 residues processed: 367 average time/residue: 0.1875 time to fit residues: 109.4614 Evaluate side-chains 254 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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: 10.0000 chunk 321 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 255 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 305 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN C 80 GLN C 434 HIS C 498 GLN C 683 ASN C 829 GLN C 889 HIS C1006 HIS C1093 GLN ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.132062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098732 restraints weight = 66525.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097087 restraints weight = 73314.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098384 restraints weight = 64281.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098392 restraints weight = 45229.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.099071 restraints weight = 38550.855| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28809 Z= 0.188 Angle : 0.635 8.223 39217 Z= 0.335 Chirality : 0.045 0.276 4429 Planarity : 0.005 0.060 4938 Dihedral : 13.868 117.634 4398 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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 are not related in a simple way. whole: -1.36 (0.14), residues: 3395 helix: 0.17 (0.14), residues: 1241 sheet: -1.42 (0.22), residues: 491 loop : -1.55 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D1189 TYR 0.041 0.002 TYR D 432 PHE 0.016 0.002 PHE D 716 TRP 0.028 0.002 TRP D1398 HIS 0.007 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (28805) covalent geometry : angle 0.63396 / 0.33 (39211) hydrogen bonds : bond 0.05266 / 3.53 ( 1248) hydrogen bonds : angle 5.12240 / 3.62 ( 3400) metal coordination : bond 0.01393 / 0.70 ( 4) metal coordination : angle 3.33343 / 1.81 ( 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 338 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 1.137 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: A 124 ASN cc_start: 0.8640 (p0) cc_final: 0.8289 (p0) REVERT: A 192 LEU cc_start: 0.8279 (mt) cc_final: 0.8020 (mt) REVERT: B 47 SER cc_start: 0.8767 (m) cc_final: 0.8525 (t) REVERT: B 91 ASN cc_start: 0.8501 (t0) cc_final: 0.8182 (p0) REVERT: B 102 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8535 (mmmt) REVERT: C 293 PHE cc_start: 0.4829 (t80) cc_final: 0.4138 (t80) REVERT: C 374 ASN cc_start: 0.7722 (t0) cc_final: 0.6916 (m-40) REVERT: C 402 SER cc_start: 0.9071 (p) cc_final: 0.8710 (p) REVERT: C 498 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7311 (mm-40) REVERT: C 772 ARG cc_start: 0.8005 (tpt170) cc_final: 0.7621 (ttp80) REVERT: D 527 MET cc_start: 0.7725 (ptm) cc_final: 0.7153 (ppp) REVERT: D 557 LEU cc_start: 0.9020 (tp) cc_final: 0.8811 (tp) REVERT: D 615 ARG cc_start: 0.7927 (mtp180) cc_final: 0.6167 (tpt90) REVERT: D 754 PHE cc_start: 0.8041 (t80) cc_final: 0.7709 (t80) REVERT: D 1231 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7533 (tm-30) REVERT: E 90 GLU cc_start: 0.8592 (pm20) cc_final: 0.8211 (tp30) REVERT: M 363 LEU cc_start: 0.8690 (tp) cc_final: 0.8340 (tt) REVERT: M 708 LEU cc_start: 0.8490 (tp) cc_final: 0.8136 (tp) REVERT: M 740 GLN cc_start: 0.8225 (tp40) cc_final: 0.8005 (tp40) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1959 time to fit residues: 105.7848 Evaluate side-chains 240 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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: 5.9990 chunk 306 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 79 optimal weight: 30.0000 chunk 235 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 199 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 188 optimal weight: 0.0770 chunk 316 optimal weight: 1.9990 chunk 310 optimal weight: 8.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN C 829 GLN C 889 HIS C1006 HIS ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 744 GLN ** D1374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 516 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.131703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097232 restraints weight = 66202.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.095158 restraints weight = 67561.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.096268 restraints weight = 55806.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.096927 restraints weight = 37234.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.097244 restraints weight = 33188.516| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3344 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28809 Z= 0.189 Angle : 0.624 9.444 39217 Z= 0.328 Chirality : 0.045 0.198 4429 Planarity : 0.005 0.070 4938 Dihedral : 13.810 118.338 4398 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.72 % 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 are not related in a simple way. whole: -1.22 (0.14), residues: 3395 helix: 0.31 (0.14), residues: 1233 sheet: -1.34 (0.23), residues: 484 loop : -1.48 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 550 TYR 0.022 0.002 TYR D1198 PHE 0.036 0.002 PHE M 646 TRP 0.040 0.002 TRP D1398 HIS 0.006 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (28805) covalent geometry : angle 0.62318 / 0.33 (39211) hydrogen bonds : bond 0.05188 / 3.47 ( 1248) hydrogen bonds : angle 5.04476 / 3.56 ( 3400) metal coordination : bond 0.01106 / 0.56 ( 4) metal coordination : angle 2.93979 / 1.43 ( 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 320 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 1.185 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 124 ASN cc_start: 0.8710 (p0) cc_final: 0.8344 (p0) REVERT: B 47 SER cc_start: 0.8831 (m) cc_final: 0.8519 (t) REVERT: B 91 ASN cc_start: 0.8531 (t0) cc_final: 0.8189 (p0) REVERT: C 293 PHE cc_start: 0.4801 (t80) cc_final: 0.4055 (t80) REVERT: C 374 ASN cc_start: 0.7715 (t0) cc_final: 0.6947 (m-40) REVERT: C 402 SER cc_start: 0.9142 (p) cc_final: 0.8790 (p) REVERT: C 486 MET cc_start: 0.8517 (mpp) cc_final: 0.8306 (mpp) REVERT: C 772 ARG cc_start: 0.8075 (tpt170) cc_final: 0.7659 (ttp80) REVERT: D 45 PHE cc_start: 0.7526 (m-80) cc_final: 0.7247 (m-80) REVERT: D 463 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8480 (tp-100) REVERT: D 527 MET cc_start: 0.7758 (ptm) cc_final: 0.7142 (ppp) REVERT: D 551 ASN cc_start: 0.7770 (t0) cc_final: 0.7479 (t0) REVERT: D 615 ARG cc_start: 0.7814 (mtp180) cc_final: 0.6328 (tpt90) REVERT: E 90 GLU cc_start: 0.8723 (pm20) cc_final: 0.8194 (tp30) REVERT: M 363 LEU cc_start: 0.8752 (tp) cc_final: 0.8423 (tt) REVERT: M 708 LEU cc_start: 0.8553 (tp) cc_final: 0.8183 (tp) REVERT: M 740 GLN cc_start: 0.8286 (tp40) cc_final: 0.8059 (tp40) outliers start: 1 outliers final: 1 residues processed: 320 average time/residue: 0.1832 time to fit residues: 94.1305 Evaluate side-chains 233 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 232 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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: 7.9990 chunk 154 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 88 optimal weight: 0.0050 chunk 135 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 chunk 282 optimal weight: 1.9990 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 ASN C 829 GLN C 889 HIS C1006 HIS ** C1100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1374 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 = 0.3907 r_free = 0.3907 target = 0.131994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098915 restraints weight = 66348.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096981 restraints weight = 76078.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.098647 restraints weight = 65417.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.098430 restraints weight = 44405.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.099113 restraints weight = 39105.589| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28809 Z= 0.171 Angle : 0.619 8.408 39217 Z= 0.324 Chirality : 0.045 0.281 4429 Planarity : 0.005 0.062 4938 Dihedral : 13.759 118.541 4398 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.76 % 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 are not related in a simple way. whole: -1.11 (0.14), residues: 3395 helix: 0.40 (0.14), residues: 1236 sheet: -1.30 (0.23), residues: 491 loop : -1.41 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 681 TYR 0.016 0.001 TYR D 791 PHE 0.027 0.001 PHE M 646 TRP 0.054 0.002 TRP D1398 HIS 0.006 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (28805) covalent geometry : angle 0.61612 / 0.32 (39211) hydrogen bonds : bond 0.05103 / 3.43 ( 1248) hydrogen bonds : angle 5.01196 / 3.54 ( 3400) metal coordination : bond 0.01154 / 0.58 ( 4) metal coordination : angle 4.57031 / 2.39 ( 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 308 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 1.065 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: A 124 ASN cc_start: 0.8693 (p0) cc_final: 0.8334 (p0) REVERT: B 47 SER cc_start: 0.8779 (m) cc_final: 0.8445 (t) REVERT: B 91 ASN cc_start: 0.8526 (t0) cc_final: 0.8311 (p0) REVERT: C 293 PHE cc_start: 0.4678 (t80) cc_final: 0.3963 (t80) REVERT: C 374 ASN cc_start: 0.7639 (t0) cc_final: 0.6972 (m-40) REVERT: C 402 SER cc_start: 0.9119 (p) cc_final: 0.8771 (p) REVERT: C 708 TYR cc_start: 0.7979 (m-80) cc_final: 0.7779 (m-10) REVERT: D 45 PHE cc_start: 0.7559 (m-80) cc_final: 0.7316 (m-80) REVERT: D 527 MET cc_start: 0.7668 (ptm) cc_final: 0.7160 (ppp) REVERT: D 615 ARG cc_start: 0.7673 (mtp180) cc_final: 0.6160 (tpt90) REVERT: E 90 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: M 363 LEU cc_start: 0.8674 (tp) cc_final: 0.8349 (tt) REVERT: M 708 LEU cc_start: 0.8243 (tp) cc_final: 0.7897 (tp) outliers start: 1 outliers final: 0 residues processed: 307 average time/residue: 0.1901 time to fit residues: 93.9223 Evaluate side-chains 230 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 229 time to evaluate : 1.086 ------------------------------------------------------------------------------- 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: 1.9990 chunk 50 optimal weight: 0.0030 chunk 329 optimal weight: 7.9990 chunk 108 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 chunk 242 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 237 optimal weight: 0.0270 chunk 130 optimal weight: 0.9990 overall best weight: 1.0054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C 889 HIS C 962 GLN C1006 HIS C1100 GLN D 101 HIS ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN D 762 GLN E 33 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.133980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099784 restraints weight = 65938.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097983 restraints weight = 68383.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.099646 restraints weight = 56667.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099511 restraints weight = 40707.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.100732 restraints weight = 34315.908| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3409 r_free = 0.3409 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 = 0.3409 r_free = 0.3409 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28809 Z= 0.121 Angle : 0.596 8.108 39217 Z= 0.310 Chirality : 0.045 0.334 4429 Planarity : 0.005 0.059 4938 Dihedral : 13.650 117.492 4398 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.03 % Allowed : 1.55 % Favored : 98.41 % 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 are not related in a simple way. whole: -0.88 (0.14), residues: 3395 helix: 0.57 (0.15), residues: 1238 sheet: -1.14 (0.23), residues: 486 loop : -1.28 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 27 TYR 0.026 0.001 TYR M 739 PHE 0.023 0.001 PHE M 646 TRP 0.032 0.002 TRP D1398 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (28805) covalent geometry : angle 0.59350 / 0.31 (39211) hydrogen bonds : bond 0.04741 / 3.21 ( 1248) hydrogen bonds : angle 4.79576 / 3.38 ( 3400) metal coordination : bond 0.00684 / 0.35 ( 4) metal coordination : angle 4.17149 / 2.20 ( 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 324 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.096 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 124 ASN cc_start: 0.8673 (p0) cc_final: 0.8279 (p0) REVERT: A 192 LEU cc_start: 0.8200 (mt) cc_final: 0.7865 (mt) REVERT: A 213 GLN cc_start: 0.7806 (tt0) cc_final: 0.7598 (tt0) REVERT: B 47 SER cc_start: 0.8790 (m) cc_final: 0.8395 (t) REVERT: C 200 LEU cc_start: 0.8470 (tp) cc_final: 0.7172 (tp) REVERT: C 293 PHE cc_start: 0.4706 (t80) cc_final: 0.3966 (t80) REVERT: C 374 ASN cc_start: 0.7731 (t0) cc_final: 0.6995 (m-40) REVERT: C 402 SER cc_start: 0.9163 (p) cc_final: 0.8771 (p) REVERT: C 1030 GLN cc_start: 0.9021 (mm-40) cc_final: 0.8255 (mm-40) REVERT: C 1036 GLU cc_start: 0.8136 (mp0) cc_final: 0.7868 (mp0) REVERT: D 45 PHE cc_start: 0.7487 (m-80) cc_final: 0.7185 (m-80) REVERT: D 463 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8507 (tp-100) REVERT: D 527 MET cc_start: 0.7410 (ptm) cc_final: 0.7033 (ppp) REVERT: D 615 ARG cc_start: 0.7861 (mtp180) cc_final: 0.5897 (tpt90) REVERT: D 754 PHE cc_start: 0.7964 (t80) cc_final: 0.7562 (t80) REVERT: D 1376 MET cc_start: 0.8598 (mmm) cc_final: 0.8258 (mmm) REVERT: E 90 GLU cc_start: 0.8858 (pm20) cc_final: 0.8457 (tp30) REVERT: M 363 LEU cc_start: 0.8775 (tp) cc_final: 0.8434 (tt) REVERT: M 740 GLN cc_start: 0.8313 (tp40) cc_final: 0.8099 (tp40) outliers start: 1 outliers final: 1 residues processed: 324 average time/residue: 0.1843 time to fit residues: 95.9625 Evaluate side-chains 229 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.084 ------------------------------------------------------------------------------- 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: 9.9990 chunk 192 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 191 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 95 optimal weight: 0.0470 chunk 293 optimal weight: 4.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C 889 HIS C1006 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 767 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 GLN ** 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 = 0.3907 r_free = 0.3907 target = 0.132080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.100117 restraints weight = 67324.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095326 restraints weight = 59714.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097295 restraints weight = 66942.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.096898 restraints weight = 48680.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.097552 restraints weight = 41050.085| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3633 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= 0.183 Angle : 0.626 11.631 39217 Z= 0.328 Chirality : 0.045 0.298 4429 Planarity : 0.005 0.099 4938 Dihedral : 13.611 118.509 4398 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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 are not related in a simple way. whole: -0.93 (0.14), residues: 3395 helix: 0.52 (0.14), residues: 1244 sheet: -1.17 (0.23), residues: 493 loop : -1.30 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG D1197 TYR 0.033 0.001 TYR A 224 PHE 0.026 0.002 PHE C 48 TRP 0.031 0.003 TRP D 21 HIS 0.007 0.001 HIS M 758 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 (28805) covalent geometry : angle 0.62394 / 0.33 (39211) hydrogen bonds : bond 0.04972 / 3.35 ( 1248) hydrogen bonds : angle 4.86005 / 3.41 ( 3400) metal coordination : bond 0.01204 / 0.61 ( 4) metal coordination : angle 3.86575 / 1.89 ( 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 297 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 1.105 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 124 ASN cc_start: 0.8689 (p0) cc_final: 0.8322 (p0) REVERT: A 192 LEU cc_start: 0.8209 (mt) cc_final: 0.7861 (mt) REVERT: B 47 SER cc_start: 0.8763 (m) cc_final: 0.8342 (t) REVERT: C 191 PHE cc_start: 0.7758 (p90) cc_final: 0.7302 (p90) REVERT: C 229 MET cc_start: 0.7009 (pmm) cc_final: 0.6757 (pmm) REVERT: C 293 PHE cc_start: 0.5333 (t80) cc_final: 0.4526 (t80) REVERT: C 307 LEU cc_start: 0.9326 (mt) cc_final: 0.9081 (mt) REVERT: C 374 ASN cc_start: 0.7696 (t0) cc_final: 0.7001 (m-40) REVERT: C 402 SER cc_start: 0.9129 (p) cc_final: 0.8716 (p) REVERT: C 1002 GLU cc_start: 0.8280 (mp0) cc_final: 0.7981 (mm-30) REVERT: D 45 PHE cc_start: 0.7606 (m-80) cc_final: 0.7267 (m-80) REVERT: D 456 MET cc_start: 0.8449 (mtt) cc_final: 0.8097 (mtt) REVERT: D 527 MET cc_start: 0.7624 (ptm) cc_final: 0.7091 (ppp) REVERT: D 615 ARG cc_start: 0.7635 (mtp180) cc_final: 0.6717 (tmt170) REVERT: D 1198 TYR cc_start: 0.7674 (m-10) cc_final: 0.7202 (m-80) REVERT: E 47 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8088 (mmtp) REVERT: E 90 GLU cc_start: 0.8886 (pm20) cc_final: 0.8340 (tp30) REVERT: M 363 LEU cc_start: 0.9041 (tp) cc_final: 0.8692 (tt) REVERT: M 464 MET cc_start: 0.2007 (mmt) cc_final: 0.1225 (mmt) REVERT: M 740 GLN cc_start: 0.8732 (tp40) cc_final: 0.8367 (tp40) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1796 time to fit residues: 87.7502 Evaluate side-chains 218 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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: 0.0470 chunk 163 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 328 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 306 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 chunk 212 optimal weight: 1.9990 chunk 276 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C 889 HIS C1006 HIS C1100 GLN ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 GLN ** M 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.132135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.099802 restraints weight = 67130.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097496 restraints weight = 77868.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099135 restraints weight = 68850.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098962 restraints weight = 47052.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.099380 restraints weight = 39771.483| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28809 Z= 0.139 Angle : 0.595 12.178 39217 Z= 0.310 Chirality : 0.044 0.206 4429 Planarity : 0.005 0.057 4938 Dihedral : 13.536 118.196 4398 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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 are not related in a simple way. whole: -0.83 (0.14), residues: 3395 helix: 0.62 (0.14), residues: 1243 sheet: -1.14 (0.23), residues: 520 loop : -1.24 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D1197 TYR 0.028 0.001 TYR D 432 PHE 0.017 0.001 PHE M 646 TRP 0.020 0.002 TRP D 21 HIS 0.005 0.001 HIS C1006 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (28805) covalent geometry : angle 0.59333 / 0.31 (39211) hydrogen bonds : bond 0.04739 / 3.20 ( 1248) hydrogen bonds : angle 4.72732 / 3.31 ( 3400) metal coordination : bond 0.00762 / 0.39 ( 4) metal coordination : angle 3.93233 / 1.91 ( 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 298 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 1.028 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 30 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7232 (ptm-80) REVERT: A 124 ASN cc_start: 0.8645 (p0) cc_final: 0.8265 (p0) REVERT: A 192 LEU cc_start: 0.8222 (mt) cc_final: 0.7855 (mt) REVERT: B 47 SER cc_start: 0.8753 (m) cc_final: 0.8372 (t) REVERT: C 67 ASP cc_start: 0.8559 (t0) cc_final: 0.8261 (t70) REVERT: C 293 PHE cc_start: 0.4800 (t80) cc_final: 0.4014 (t80) REVERT: C 374 ASN cc_start: 0.7654 (t0) cc_final: 0.7010 (m-40) REVERT: C 402 SER cc_start: 0.9176 (p) cc_final: 0.8821 (p) REVERT: C 1002 GLU cc_start: 0.8257 (mp0) cc_final: 0.7934 (mm-30) REVERT: D 45 PHE cc_start: 0.7564 (m-80) cc_final: 0.7332 (m-80) REVERT: D 159 ARG cc_start: 0.9202 (ptm160) cc_final: 0.8999 (ptm160) REVERT: D 456 MET cc_start: 0.8321 (mtt) cc_final: 0.7953 (mtt) REVERT: D 463 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8584 (tp-100) REVERT: D 527 MET cc_start: 0.7383 (ptm) cc_final: 0.6942 (ppp) REVERT: D 615 ARG cc_start: 0.7872 (mtp180) cc_final: 0.6692 (tmt170) REVERT: D 763 MET cc_start: 0.8943 (mtm) cc_final: 0.8597 (mtm) REVERT: E 90 GLU cc_start: 0.8673 (pm20) cc_final: 0.8349 (tp30) REVERT: M 363 LEU cc_start: 0.8727 (tp) cc_final: 0.8427 (tp) REVERT: M 464 MET cc_start: 0.1048 (mmt) cc_final: 0.0034 (mmt) REVERT: M 740 GLN cc_start: 0.8320 (tp40) cc_final: 0.8086 (tp40) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1716 time to fit residues: 84.8431 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 : 1.045 ------------------------------------------------------------------------------- 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: 4.9990 chunk 80 optimal weight: 20.0000 chunk 295 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 341 optimal weight: 60.0000 chunk 122 optimal weight: 0.0570 chunk 298 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 241 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN C 320 HIS C 829 GLN C 889 HIS C1006 HIS D 101 HIS D 507 ASN ** D 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 744 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.133819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.102295 restraints weight = 68039.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.100103 restraints weight = 81547.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.101278 restraints weight = 68723.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102023 restraints weight = 44324.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.102306 restraints weight = 39977.858| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3917 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= 0.119 Angle : 0.595 10.547 39217 Z= 0.308 Chirality : 0.044 0.272 4429 Planarity : 0.005 0.061 4938 Dihedral : 13.473 117.821 4398 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % 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 are not related in a simple way. whole: -0.71 (0.14), residues: 3395 helix: 0.71 (0.15), residues: 1243 sheet: -0.99 (0.23), residues: 510 loop : -1.19 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1197 TYR 0.017 0.001 TYR D1198 PHE 0.023 0.001 PHE C 191 TRP 0.018 0.002 TRP C1038 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (28805) covalent geometry : angle 0.59290 / 0.31 (39211) hydrogen bonds : bond 0.04555 / 3.08 ( 1248) hydrogen bonds : angle 4.63004 / 3.24 ( 3400) metal coordination : bond 0.00532 / 0.27 ( 4) metal coordination : angle 3.87425 / 1.91 ( 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 305 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7227 (ptm-80) REVERT: A 72 LYS cc_start: 0.8906 (tttt) cc_final: 0.8374 (tptt) REVERT: A 124 ASN cc_start: 0.8650 (p0) cc_final: 0.8286 (p0) REVERT: A 192 LEU cc_start: 0.8169 (mt) cc_final: 0.7853 (mt) REVERT: B 47 SER cc_start: 0.8758 (m) cc_final: 0.8372 (t) REVERT: C 67 ASP cc_start: 0.8463 (t0) cc_final: 0.8153 (t70) REVERT: C 293 PHE cc_start: 0.4605 (t80) cc_final: 0.3820 (t80) REVERT: C 374 ASN cc_start: 0.7668 (t0) cc_final: 0.6900 (m-40) REVERT: C 402 SER cc_start: 0.9163 (p) cc_final: 0.8740 (p) REVERT: C 564 MET cc_start: 0.7610 (mtm) cc_final: 0.7146 (ttm) REVERT: C 796 GLU cc_start: 0.7319 (pt0) cc_final: 0.6823 (pm20) REVERT: C 1002 GLU cc_start: 0.8151 (mp0) cc_final: 0.7822 (mm-30) REVERT: C 1036 GLU cc_start: 0.8131 (mp0) cc_final: 0.7678 (mm-30) REVERT: D 159 ARG cc_start: 0.9098 (ptm160) cc_final: 0.8891 (ptm160) REVERT: D 463 GLN cc_start: 0.8992 (tp-100) cc_final: 0.8524 (tp-100) REVERT: D 527 MET cc_start: 0.7331 (ptm) cc_final: 0.6871 (ppp) REVERT: D 615 ARG cc_start: 0.7782 (mtp180) cc_final: 0.6611 (tmt170) REVERT: D 763 MET cc_start: 0.8873 (mtm) cc_final: 0.8479 (mtm) REVERT: M 363 LEU cc_start: 0.8613 (tp) cc_final: 0.8326 (tp) REVERT: M 464 MET cc_start: 0.0842 (mmt) cc_final: -0.0162 (mmt) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.1749 time to fit residues: 87.3388 Evaluate side-chains 232 residues out of total 2899 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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: 8.9990 chunk 110 optimal weight: 0.7980 chunk 323 optimal weight: 20.0000 chunk 239 optimal weight: 2.9990 chunk 327 optimal weight: 8.9990 chunk 197 optimal weight: 0.9980 chunk 268 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 GLN C 889 HIS C1006 HIS ** D 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 516 GLN ** 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 = 0.3928 r_free = 0.3928 target = 0.133538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102245 restraints weight = 67647.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.099933 restraints weight = 77783.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101654 restraints weight = 69367.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.101353 restraints weight = 47248.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102178 restraints weight = 40708.227| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4021 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= 0.120 Angle : 0.590 11.156 39217 Z= 0.305 Chirality : 0.044 0.265 4429 Planarity : 0.005 0.057 4938 Dihedral : 13.425 117.867 4398 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 are not related in a simple way. whole: -0.65 (0.14), residues: 3395 helix: 0.75 (0.15), residues: 1238 sheet: -0.96 (0.23), residues: 510 loop : -1.14 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 793 TYR 0.025 0.001 TYR D 432 PHE 0.016 0.001 PHE M 646 TRP 0.031 0.002 TRP C1038 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (28805) covalent geometry : angle 0.58870 / 0.31 (39211) hydrogen bonds : bond 0.04464 / 3.02 ( 1248) hydrogen bonds : angle 4.59049 / 3.22 ( 3400) metal coordination : bond 0.00596 / 0.30 ( 4) metal coordination : angle 3.75684 / 1.81 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4266.83 seconds wall clock time: 74 minutes 52.89 seconds (4492.89 seconds total)