Starting phenix.real_space_refine on Sun Aug 24 21:16:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hil_34820/08_2025/8hil_34820.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hil_34820/08_2025/8hil_34820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hil_34820/08_2025/8hil_34820.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hil_34820/08_2025/8hil_34820.map" model { file = "/net/cci-nas-00/data/ceres_data/8hil_34820/08_2025/8hil_34820.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hil_34820/08_2025/8hil_34820.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 Mg 1 5.21 5 S 142 5.16 5 C 14579 2.51 5 N 4028 2.21 5 O 4378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23134 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6724 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 27, 'TRANS': 832} Chain breaks: 1 Chain: "B" Number of atoms: 8002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 8002 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 37, 'TRANS': 970} Chain breaks: 2 Chain: "C" Number of atoms: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2340 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 10, 'TRANS': 289} Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1698 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 653 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 4, 'TRANS': 74} Chain: "H" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1135 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "I" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 799 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain breaks: 1 Chain: "J" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 514 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "K" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 887 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 375 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15431 SG CYS C 91 76.731 55.598 147.524 1.00 75.40 S ATOM 15450 SG CYS C 94 77.587 53.560 144.645 1.00 96.75 S ATOM 15489 SG CYS C 100 75.271 51.423 147.930 1.00 66.88 S ATOM 20599 SG CYS I 7 44.922 48.221 22.285 1.00 87.40 S ATOM 20784 SG CYS I 29 48.546 49.829 22.974 1.00 90.52 S ATOM 20809 SG CYS I 32 48.085 46.690 19.452 1.00 97.38 S ATOM 21430 SG CYS J 10 50.155 57.966 126.372 1.00 27.07 S ATOM 21696 SG CYS J 44 48.206 59.128 123.553 1.00 29.38 S ATOM 22807 SG CYS L 12 79.164 24.060 106.723 1.00 83.08 S ATOM 22825 SG CYS L 15 78.550 20.137 106.948 1.00 81.63 S ATOM 22927 SG CYS L 29 82.023 21.779 107.275 1.00 89.69 S ATOM 22953 SG CYS L 32 80.662 20.377 104.003 1.00 30.00 S Time building chain proxies: 4.41, per 1000 atoms: 0.19 Number of scatterers: 23134 At special positions: 0 Unit cell: (121.545, 141.255, 164.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 142 16.00 Mg 1 11.99 O 4378 8.00 N 4028 7.00 C 14579 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 978.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2101 " pdb="ZN ZN A2101 " - pdb=" ND1 HIS A 938 " pdb="ZN ZN A2101 " - pdb=" NE2 HIS A 940 " pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 91 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 29 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 12 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 32 " Number of angles added : 6 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5482 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 37 sheets defined 32.4% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 359 through 369 removed outlier: 4.152A pdb=" N GLU A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.503A pdb=" N CYS A 443 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY A 444 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.607A pdb=" N LEU A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 removed outlier: 3.558A pdb=" N ALA A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 576 through 593 removed outlier: 3.954A pdb=" N ASN A 582 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 586 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 610 removed outlier: 3.827A pdb=" N ALA A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A 599 " --> pdb=" O LYS A 595 " (cutoff:3.500A) Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 620 through 625 removed outlier: 4.173A pdb=" N LEU A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 642 through 650 removed outlier: 3.692A pdb=" N ARG A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 674 removed outlier: 3.784A pdb=" N VAL A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 673 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N MET A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 684 removed outlier: 3.675A pdb=" N LEU A 683 " --> pdb=" O SER A 679 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 679 through 684' Processing helix chain 'A' and resid 692 through 697 removed outlier: 3.819A pdb=" N VAL A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 724 removed outlier: 3.704A pdb=" N VAL A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 750 through 770 Processing helix chain 'A' and resid 772 through 784 removed outlier: 3.907A pdb=" N GLY A 776 " --> pdb=" O LEU A 772 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 780 " --> pdb=" O GLY A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 845 removed outlier: 3.512A pdb=" N THR A 834 " --> pdb=" O VAL A 830 " (cutoff:3.500A) Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 854 removed outlier: 3.930A pdb=" N SER A 854 " --> pdb=" O ASN A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.867A pdb=" N LYS A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 904 removed outlier: 4.214A pdb=" N VAL A 899 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 949 removed outlier: 3.543A pdb=" N LEU A 946 " --> pdb=" O ASN A 942 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 969 removed outlier: 3.557A pdb=" N ALA A 963 " --> pdb=" O ARG A 959 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 968 " --> pdb=" O ILE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1023 removed outlier: 3.617A pdb=" N VAL A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1028 through 1034 Processing helix chain 'A' and resid 1085 through 1093 removed outlier: 3.756A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1099 removed outlier: 3.603A pdb=" N LEU A1099 " --> pdb=" O LEU A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1119 Processing helix chain 'A' and resid 1120 through 1141 removed outlier: 3.617A pdb=" N GLU A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL A1139 " --> pdb=" O SER A1135 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A1140 " --> pdb=" O VAL A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1156 removed outlier: 4.096A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1170 removed outlier: 3.733A pdb=" N LYS A1170 " --> pdb=" O SER A1166 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.591A pdb=" N SER B 27 " --> pdb=" O PRO B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.671A pdb=" N PHE B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 63 " --> pdb=" O GLN B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.622A pdb=" N LEU B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.990A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER B 316 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 347 through 353 removed outlier: 3.662A pdb=" N LEU B 352 " --> pdb=" O CYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 380 removed outlier: 4.143A pdb=" N ARG B 366 " --> pdb=" O THR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 398 through 423 removed outlier: 3.667A pdb=" N GLN B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 441 through 455 removed outlier: 3.562A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 487 removed outlier: 3.940A pdb=" N LEU B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.968A pdb=" N TRP B 510 " --> pdb=" O PRO B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.587A pdb=" N LEU B 548 " --> pdb=" O VAL B 545 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP B 550 " --> pdb=" O GLU B 547 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 551 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 552 " --> pdb=" O PHE B 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 545 through 552' Processing helix chain 'B' and resid 582 through 596 removed outlier: 4.010A pdb=" N ALA B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.961A pdb=" N GLN B 638 " --> pdb=" O HIS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 650 Processing helix chain 'B' and resid 659 through 664 removed outlier: 3.794A pdb=" N GLU B 664 " --> pdb=" O ILE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 removed outlier: 4.390A pdb=" N GLN B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.584A pdb=" N LEU B 693 " --> pdb=" O SER B 690 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 717 through 722 Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.622A pdb=" N LEU B 762 " --> pdb=" O LYS B 759 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 763 " --> pdb=" O ASP B 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 759 through 763' Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.609A pdb=" N ASN B 928 " --> pdb=" O GLU B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.720A pdb=" N ARG B 950 " --> pdb=" O ALA B 946 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 946 through 951' Processing helix chain 'B' and resid 953 through 967 removed outlier: 3.623A pdb=" N CYS B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1004 Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.592A pdb=" N ALA C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 removed outlier: 3.777A pdb=" N LEU C 74 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.875A pdb=" N CYS C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.544A pdb=" N ASP C 125 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.660A pdb=" N TRP C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.735A pdb=" N ALA C 237 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 277 through 295 Processing helix chain 'E' and resid 30 through 50 removed outlier: 3.688A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA E 39 " --> pdb=" O ARG E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.613A pdb=" N VAL E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.702A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.674A pdb=" N GLU E 119 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 removed outlier: 3.664A pdb=" N LYS E 135 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA E 136 " --> pdb=" O THR E 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 136' Processing helix chain 'E' and resid 151 through 155 removed outlier: 3.500A pdb=" N ASP E 154 " --> pdb=" O GLN E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 183 removed outlier: 3.829A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 removed outlier: 3.698A pdb=" N GLN E 189 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 190 " --> pdb=" O GLU E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 190' Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'F' and resid 66 through 82 removed outlier: 4.221A pdb=" N GLY F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.981A pdb=" N LYS F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU F 104 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.951A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.748A pdb=" N ARG J 46 " --> pdb=" O ARG J 42 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR J 51 " --> pdb=" O ARG J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.500A pdb=" N LEU J 59 " --> pdb=" O LEU J 55 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.611A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.900A pdb=" N ALA K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA2, first strand: chain 'A' and resid 338 through 342 removed outlier: 4.173A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 412 " --> pdb=" O GLN A 424 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 351 through 354 Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 508 Processing sheet with id=AA5, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.626A pdb=" N VAL H 92 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE H 8 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU H 17 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ARG H 29 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE H 40 " --> pdb=" O ARG H 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU H 111 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE H 100 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N TYR H 113 " --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.648A pdb=" N ILE A 561 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 703 through 704 removed outlier: 3.610A pdb=" N GLY A 703 " --> pdb=" O VAL A 741 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 789 through 791 removed outlier: 3.525A pdb=" N VAL A 790 " --> pdb=" O ARG A 798 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A 798 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N VAL A 797 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 876 through 880 removed outlier: 6.591A pdb=" N VAL A1071 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A1048 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASP A1073 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A1046 " --> pdb=" O ASP A1073 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A1075 " --> pdb=" O ALA A1044 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 916 through 918 removed outlier: 6.927A pdb=" N VAL A 917 " --> pdb=" O VAL I 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AB3, first strand: chain 'B' and resid 94 through 96 removed outlier: 3.537A pdb=" N MET B 126 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLY B 168 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 128 " --> pdb=" O PRO B 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AB5, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AB6, first strand: chain 'B' and resid 394 through 397 removed outlier: 6.819A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB8, first strand: chain 'B' and resid 263 through 264 Processing sheet with id=AB9, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AC1, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AC2, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AC3, first strand: chain 'B' and resid 576 through 580 removed outlier: 5.712A pdb=" N TRP B 576 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 572 " --> pdb=" O TRP B 576 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY B 578 " --> pdb=" O VAL B 570 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 570 " --> pdb=" O GLY B 578 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LYS B 569 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE B 616 " --> pdb=" O LYS B 569 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 571 " --> pdb=" O ILE B 616 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 738 through 741 removed outlier: 3.840A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) removed outlier: 9.261A pdb=" N VAL B 901 " --> pdb=" O GLY B 877 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N GLY B 877 " --> pdb=" O VAL B 901 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 766 through 772 removed outlier: 7.799A pdb=" N MET B 786 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ILE B 923 " --> pdb=" O MET B 786 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 855 through 857 removed outlier: 3.612A pdb=" N ILE B 857 " --> pdb=" O VAL B 869 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1011 through 1012 Processing sheet with id=AC8, first strand: chain 'C' and resid 15 through 19 removed outlier: 6.671A pdb=" N LYS C 24 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU C 18 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE C 25 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.765A pdb=" N GLU C 162 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASN C 59 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 164 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ARG C 170 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE C 51 " --> pdb=" O ARG C 170 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLY C 172 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N VAL C 49 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AD2, first strand: chain 'C' and resid 192 through 194 Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 224 Processing sheet with id=AD4, first strand: chain 'E' and resid 84 through 86 removed outlier: 3.684A pdb=" N VAL E 93 " --> pdb=" O HIS E 85 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS E 92 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU E 124 " --> pdb=" O LYS E 92 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS E 94 " --> pdb=" O LEU E 124 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU E 126 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 96 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD6, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AD7, first strand: chain 'I' and resid 15 through 17 removed outlier: 3.782A pdb=" N LEU I 26 " --> pdb=" O LYS I 17 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 88 through 89 Processing sheet with id=AD9, first strand: chain 'K' and resid 19 through 20 removed outlier: 6.717A pdb=" N ILE K 72 " --> pdb=" O TYR K 61 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR K 61 " --> pdb=" O ILE K 72 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ARG K 74 " --> pdb=" O ALA K 59 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA K 59 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N HIS K 76 " --> pdb=" O LEU K 57 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 11 697 hydrogen bonds defined for protein. 1926 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.20 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5673 1.33 - 1.45: 4830 1.45 - 1.58: 12824 1.58 - 1.70: 0 1.70 - 1.82: 219 Bond restraints: 23546 Sorted by residual: bond pdb=" N VAL A 428 " pdb=" CA VAL A 428 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.27e-02 6.20e+03 9.39e+00 bond pdb=" N LEU B 248 " pdb=" CA LEU B 248 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.29e-02 6.01e+03 8.51e+00 bond pdb=" N SER B 783 " pdb=" CA SER B 783 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.47e+00 bond pdb=" N CYS A 886 " pdb=" CA CYS A 886 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.41e+00 bond pdb=" CA ASN B 180 " pdb=" C ASN B 180 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.56e-02 4.11e+03 8.39e+00 ... (remaining 23541 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 29639 2.04 - 4.09: 1793 4.09 - 6.13: 226 6.13 - 8.17: 73 8.17 - 10.22: 22 Bond angle restraints: 31753 Sorted by residual: angle pdb=" N LEU H 37 " pdb=" CA LEU H 37 " pdb=" C LEU H 37 " ideal model delta sigma weight residual 114.56 105.74 8.82 1.27e+00 6.20e-01 4.82e+01 angle pdb=" N VAL I 48 " pdb=" CA VAL I 48 " pdb=" C VAL I 48 " ideal model delta sigma weight residual 110.23 115.86 -5.63 1.04e+00 9.25e-01 2.93e+01 angle pdb=" C LYS A 889 " pdb=" N TYR A 890 " pdb=" CA TYR A 890 " ideal model delta sigma weight residual 123.93 132.16 -8.23 1.54e+00 4.22e-01 2.86e+01 angle pdb=" N GLU B 332 " pdb=" CA GLU B 332 " pdb=" C GLU B 332 " ideal model delta sigma weight residual 114.62 108.59 6.03 1.14e+00 7.69e-01 2.80e+01 angle pdb=" N SER A1061 " pdb=" CA SER A1061 " pdb=" C SER A1061 " ideal model delta sigma weight residual 113.88 107.53 6.35 1.23e+00 6.61e-01 2.66e+01 ... (remaining 31748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 13425 16.39 - 32.77: 755 32.77 - 49.16: 152 49.16 - 65.55: 17 65.55 - 81.93: 13 Dihedral angle restraints: 14362 sinusoidal: 5891 harmonic: 8471 Sorted by residual: dihedral pdb=" CA THR B 265 " pdb=" C THR B 265 " pdb=" N VAL B 266 " pdb=" CA VAL B 266 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA ASP A 750 " pdb=" C ASP A 750 " pdb=" N PRO A 751 " pdb=" CA PRO A 751 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA VAL B 233 " pdb=" C VAL B 233 " pdb=" N SER B 234 " pdb=" CA SER B 234 " ideal model delta harmonic sigma weight residual 180.00 -150.73 -29.27 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 14359 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3056 0.089 - 0.178: 460 0.178 - 0.268: 34 0.268 - 0.357: 2 0.357 - 0.446: 2 Chirality restraints: 3554 Sorted by residual: chirality pdb=" CB ILE B 167 " pdb=" CA ILE B 167 " pdb=" CG1 ILE B 167 " pdb=" CG2 ILE B 167 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 chirality pdb=" CB ILE H 5 " pdb=" CA ILE H 5 " pdb=" CG1 ILE H 5 " pdb=" CG2 ILE H 5 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.62e+00 chirality pdb=" CB VAL A 759 " pdb=" CA VAL A 759 " pdb=" CG1 VAL A 759 " pdb=" CG2 VAL A 759 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3551 not shown) Planarity restraints: 4099 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 560 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C THR B 560 " 0.057 2.00e-02 2.50e+03 pdb=" O THR B 560 " -0.022 2.00e-02 2.50e+03 pdb=" N SER B 561 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1034 " -0.022 2.00e-02 2.50e+03 2.32e-02 1.07e+01 pdb=" CG TYR B1034 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B1034 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B1034 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B1034 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B1034 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B1034 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B1034 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP E 27 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.77e+00 pdb=" N PRO E 28 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 28 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 28 " -0.042 5.00e-02 4.00e+02 ... (remaining 4096 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 518 2.66 - 3.22: 20841 3.22 - 3.78: 33842 3.78 - 4.34: 46456 4.34 - 4.90: 75949 Nonbonded interactions: 177606 Sorted by model distance: nonbonded pdb=" O ASP A 449 " pdb="MG MG A2102 " model vdw 2.105 2.170 nonbonded pdb=" OD2 ASP A 453 " pdb="MG MG A2102 " model vdw 2.194 2.170 nonbonded pdb=" N LYS I 78 " pdb="ZN ZN I 202 " model vdw 2.200 2.310 nonbonded pdb=" O GLN B 333 " pdb=" OG1 THR B 338 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 360 " pdb=" OE1 GLN B 363 " model vdw 2.258 3.040 ... (remaining 177601 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.200 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.010 0.558 23560 Z= 0.407 Angle : 1.146 38.551 31759 Z= 0.642 Chirality : 0.062 0.446 3554 Planarity : 0.007 0.074 4099 Dihedral : 11.196 81.934 8880 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.31 % Favored : 86.38 % Rotamer: Outliers : 1.12 % Allowed : 4.69 % Favored : 94.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.62 (0.12), residues: 2886 helix: -3.15 (0.12), residues: 831 sheet: -2.53 (0.24), residues: 386 loop : -3.28 (0.13), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 40 TYR 0.055 0.003 TYR B1034 PHE 0.042 0.004 PHE B 391 TRP 0.032 0.004 TRP F 126 HIS 0.012 0.002 HIS A 940 Details of bonding type rmsd covalent geometry : bond 0.00742 (23546) covalent geometry : angle 1.11822 (31753) hydrogen bonds : bond 0.21518 ( 695) hydrogen bonds : angle 7.92188 ( 1926) metal coordination : bond 0.26777 ( 14) metal coordination : angle 18.27365 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 358 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.7300 (m-30) cc_final: 0.6829 (p0) REVERT: A 1006 MET cc_start: 0.6686 (mtm) cc_final: 0.6007 (tmm) REVERT: A 1024 LEU cc_start: 0.8598 (mm) cc_final: 0.8382 (mt) REVERT: A 1229 LEU cc_start: 0.7027 (tp) cc_final: 0.6822 (pt) REVERT: B 557 MET cc_start: 0.7058 (mmm) cc_final: 0.6605 (mpp) REVERT: B 585 TYR cc_start: 0.7981 (t80) cc_final: 0.7706 (t80) REVERT: B 1040 MET cc_start: 0.6156 (mtm) cc_final: 0.5562 (mtt) REVERT: F 98 LEU cc_start: 0.9044 (tt) cc_final: 0.8826 (mp) REVERT: H 7 MET cc_start: 0.6770 (mtt) cc_final: 0.6479 (mtt) REVERT: H 11 ILE cc_start: 0.8457 (tt) cc_final: 0.8109 (mp) REVERT: H 68 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6777 (pp) REVERT: H 97 LEU cc_start: 0.8245 (tt) cc_final: 0.8006 (tt) REVERT: I 97 MET cc_start: 0.5364 (mpt) cc_final: 0.4869 (mmt) REVERT: I 113 ARG cc_start: 0.6853 (ttt90) cc_final: 0.4961 (tpt90) outliers start: 29 outliers final: 8 residues processed: 377 average time/residue: 0.1937 time to fit residues: 107.0077 Evaluate side-chains 208 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 576 TRP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 144 ARG Chi-restraints excluded: chain I residue 72 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 0.0170 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.0870 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.4980 chunk 111 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 HIS A 635 HIS A 705 GLN A 747 HIS A 892 GLN A 894 ASN A 901 ASN A 923 GLN A1011 ASN ** A1063 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1154 ASN ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 187 ASN B 334 GLN B 425 HIS ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 HIS B 652 GLN B 985 HIS C 229 GLN C 254 GLN E 91 ASN E 158 ASN H 36 ASN I 31 ASN I 41 ASN I 81 HIS I 110 HIS K 51 HIS K 65 HIS ** K 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.108368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085010 restraints weight = 56645.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084607 restraints weight = 42645.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085135 restraints weight = 33819.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085414 restraints weight = 29880.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085534 restraints weight = 28678.630| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 23560 Z= 0.114 Angle : 0.641 16.496 31759 Z= 0.333 Chirality : 0.044 0.176 3554 Planarity : 0.005 0.057 4099 Dihedral : 6.818 59.618 3187 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.05 % Favored : 89.81 % Rotamer: Outliers : 1.82 % Allowed : 7.37 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.14), residues: 2886 helix: -1.44 (0.16), residues: 843 sheet: -1.92 (0.25), residues: 405 loop : -2.81 (0.14), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 424 TYR 0.021 0.001 TYR A 362 PHE 0.022 0.001 PHE A 322 TRP 0.027 0.002 TRP A1058 HIS 0.011 0.001 HIS A1063 Details of bonding type rmsd covalent geometry : bond 0.00233 (23546) covalent geometry : angle 0.62374 (31753) hydrogen bonds : bond 0.04027 ( 695) hydrogen bonds : angle 5.28964 ( 1926) metal coordination : bond 0.00970 ( 14) metal coordination : angle 10.61002 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 264 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 645 MET cc_start: 0.6012 (ttt) cc_final: 0.5713 (tpp) REVERT: A 764 VAL cc_start: 0.8720 (t) cc_final: 0.8488 (t) REVERT: A 1006 MET cc_start: 0.6437 (mtm) cc_final: 0.5826 (tmm) REVERT: A 1024 LEU cc_start: 0.8484 (mm) cc_final: 0.8284 (mt) REVERT: A 1058 TRP cc_start: 0.5859 (p-90) cc_final: 0.5567 (p90) REVERT: B 90 LYS cc_start: 0.8005 (ptpt) cc_final: 0.7710 (mttm) REVERT: B 338 THR cc_start: 0.6636 (OUTLIER) cc_final: 0.6158 (m) REVERT: B 557 MET cc_start: 0.6991 (mmm) cc_final: 0.6542 (mpp) REVERT: C 117 GLN cc_start: 0.7035 (tp-100) cc_final: 0.6821 (tp-100) REVERT: F 67 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7692 (pttp) REVERT: F 98 LEU cc_start: 0.9007 (tt) cc_final: 0.8780 (mp) REVERT: H 11 ILE cc_start: 0.8404 (tt) cc_final: 0.7973 (mp) REVERT: H 68 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6681 (pp) REVERT: I 40 ASP cc_start: 0.6016 (t0) cc_final: 0.5805 (t70) REVERT: I 72 LYS cc_start: 0.1877 (OUTLIER) cc_final: 0.0761 (tttt) REVERT: I 97 MET cc_start: 0.5973 (mpt) cc_final: 0.5099 (mmt) REVERT: I 113 ARG cc_start: 0.6652 (ttt90) cc_final: 0.5086 (tpt90) outliers start: 47 outliers final: 21 residues processed: 302 average time/residue: 0.1690 time to fit residues: 77.7161 Evaluate side-chains 223 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 23 optimal weight: 9.9990 chunk 282 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 0.0270 chunk 168 optimal weight: 2.9990 overall best weight: 1.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN A 922 GLN A1063 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 HIS B 764 ASN C 177 HIS E 42 ASN ** E 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS K 76 HIS L 19 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.105525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082274 restraints weight = 57111.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.082357 restraints weight = 44674.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082591 restraints weight = 38194.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082974 restraints weight = 32117.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083130 restraints weight = 29382.721| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23560 Z= 0.164 Angle : 0.647 11.523 31759 Z= 0.336 Chirality : 0.045 0.166 3554 Planarity : 0.005 0.050 4099 Dihedral : 6.290 59.817 3177 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.37 % Favored : 88.46 % Rotamer: Outliers : 2.33 % Allowed : 9.35 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.15), residues: 2886 helix: -0.71 (0.18), residues: 838 sheet: -1.54 (0.26), residues: 399 loop : -2.63 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 424 TYR 0.025 0.002 TYR B 585 PHE 0.019 0.002 PHE B 321 TRP 0.025 0.002 TRP B 84 HIS 0.011 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00378 (23546) covalent geometry : angle 0.63607 (31753) hydrogen bonds : bond 0.04287 ( 695) hydrogen bonds : angle 4.96854 ( 1926) metal coordination : bond 0.00568 ( 14) metal coordination : angle 8.50427 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 207 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 809 LYS cc_start: 0.6845 (OUTLIER) cc_final: 0.6579 (ttpp) REVERT: A 1024 LEU cc_start: 0.8467 (mm) cc_final: 0.8232 (mt) REVERT: B 338 THR cc_start: 0.6494 (OUTLIER) cc_final: 0.6040 (m) REVERT: B 557 MET cc_start: 0.6971 (mmm) cc_final: 0.6702 (mpp) REVERT: B 585 TYR cc_start: 0.7939 (t80) cc_final: 0.7667 (t80) REVERT: B 895 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8012 (p) REVERT: C 117 GLN cc_start: 0.7284 (tp-100) cc_final: 0.7028 (tp-100) REVERT: E 121 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6382 (pp) REVERT: F 60 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6156 (pttt) REVERT: F 98 LEU cc_start: 0.9024 (tt) cc_final: 0.8791 (mp) REVERT: H 68 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6563 (pp) REVERT: I 15 TYR cc_start: 0.6172 (m-80) cc_final: 0.5730 (m-10) REVERT: I 33 ASP cc_start: 0.6628 (p0) cc_final: 0.6353 (p0) REVERT: I 72 LYS cc_start: 0.1943 (OUTLIER) cc_final: 0.0768 (tttt) REVERT: I 97 MET cc_start: 0.5955 (mpt) cc_final: 0.5233 (mmt) REVERT: I 113 ARG cc_start: 0.6710 (ttt90) cc_final: 0.5141 (tpt90) outliers start: 60 outliers final: 32 residues processed: 257 average time/residue: 0.1596 time to fit residues: 63.1859 Evaluate side-chains 225 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 809 LYS Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 146 optimal weight: 0.0170 chunk 239 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 257 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 248 optimal weight: 0.7980 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 ASN K 89 GLN L 19 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.107652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084127 restraints weight = 56646.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083697 restraints weight = 41943.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084217 restraints weight = 35923.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084516 restraints weight = 30391.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084689 restraints weight = 28883.713| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.469 23560 Z= 0.336 Angle : 0.576 11.469 31759 Z= 0.298 Chirality : 0.043 0.180 3554 Planarity : 0.004 0.052 4099 Dihedral : 5.832 59.818 3177 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.88 % Favored : 90.06 % Rotamer: Outliers : 2.52 % Allowed : 10.24 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.15), residues: 2886 helix: -0.16 (0.18), residues: 832 sheet: -1.33 (0.26), residues: 393 loop : -2.43 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 424 TYR 0.020 0.001 TYR B 585 PHE 0.017 0.001 PHE A 322 TRP 0.030 0.001 TRP B 84 HIS 0.008 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00225 (23546) covalent geometry : angle 0.56635 (31753) hydrogen bonds : bond 0.03334 ( 695) hydrogen bonds : angle 4.58445 ( 1926) metal coordination : bond 0.39274 ( 14) metal coordination : angle 7.56479 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 764 VAL cc_start: 0.8738 (t) cc_final: 0.8509 (t) REVERT: A 858 MET cc_start: 0.7631 (mtm) cc_final: 0.7270 (mtm) REVERT: A 1006 MET cc_start: 0.6639 (tmm) cc_final: 0.6125 (tmm) REVERT: A 1024 LEU cc_start: 0.8409 (mm) cc_final: 0.8185 (mt) REVERT: B 422 MET cc_start: 0.6988 (mmm) cc_final: 0.6756 (mmm) REVERT: B 557 MET cc_start: 0.7003 (mmm) cc_final: 0.6665 (mpp) REVERT: B 585 TYR cc_start: 0.7826 (t80) cc_final: 0.7540 (t80) REVERT: B 895 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8044 (p) REVERT: B 950 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.7239 (mtp180) REVERT: C 99 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7666 (tm-30) REVERT: C 194 ILE cc_start: 0.7742 (mt) cc_final: 0.7480 (tt) REVERT: E 121 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6453 (pp) REVERT: F 60 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.6158 (pttt) REVERT: H 68 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6634 (pp) REVERT: I 33 ASP cc_start: 0.6775 (p0) cc_final: 0.6498 (p0) REVERT: I 72 LYS cc_start: 0.1823 (OUTLIER) cc_final: 0.0659 (tttt) REVERT: I 97 MET cc_start: 0.6033 (mpt) cc_final: 0.5319 (mmt) REVERT: I 113 ARG cc_start: 0.6607 (ttt90) cc_final: 0.4984 (tpt90) REVERT: J 31 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: K 7 TYR cc_start: 0.5655 (OUTLIER) cc_final: 0.5087 (m-80) outliers start: 65 outliers final: 32 residues processed: 279 average time/residue: 0.1730 time to fit residues: 74.8937 Evaluate side-chains 237 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 41 optimal weight: 0.5980 chunk 186 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 272 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 228 optimal weight: 7.9990 chunk 202 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN H 129 HIS ** L 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.107345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.083599 restraints weight = 56542.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083568 restraints weight = 41603.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083887 restraints weight = 34279.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084234 restraints weight = 30180.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084360 restraints weight = 28550.823| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 23560 Z= 0.111 Angle : 0.580 11.636 31759 Z= 0.297 Chirality : 0.043 0.202 3554 Planarity : 0.004 0.091 4099 Dihedral : 5.673 58.115 3177 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.22 % Favored : 89.74 % Rotamer: Outliers : 2.52 % Allowed : 10.82 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.15), residues: 2886 helix: 0.08 (0.19), residues: 829 sheet: -1.23 (0.26), residues: 395 loop : -2.34 (0.14), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 424 TYR 0.017 0.001 TYR B 585 PHE 0.015 0.001 PHE A 322 TRP 0.029 0.001 TRP B 84 HIS 0.006 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00248 (23546) covalent geometry : angle 0.57067 (31753) hydrogen bonds : bond 0.03308 ( 695) hydrogen bonds : angle 4.48456 ( 1926) metal coordination : bond 0.00634 ( 14) metal coordination : angle 7.51201 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1006 MET cc_start: 0.6695 (tmm) cc_final: 0.6186 (tmm) REVERT: B 338 THR cc_start: 0.6449 (OUTLIER) cc_final: 0.5903 (m) REVERT: B 541 MET cc_start: 0.7940 (mmm) cc_final: 0.7709 (mmm) REVERT: B 557 MET cc_start: 0.7080 (mmm) cc_final: 0.6755 (mpp) REVERT: B 585 TYR cc_start: 0.7801 (t80) cc_final: 0.7453 (t80) REVERT: B 895 THR cc_start: 0.8396 (OUTLIER) cc_final: 0.8044 (p) REVERT: C 99 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 121 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6507 (pp) REVERT: F 60 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6205 (pttt) REVERT: H 11 ILE cc_start: 0.8411 (tt) cc_final: 0.7952 (mp) REVERT: H 68 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6521 (pp) REVERT: H 89 TYR cc_start: 0.5424 (m-10) cc_final: 0.4986 (m-10) REVERT: I 33 ASP cc_start: 0.6823 (p0) cc_final: 0.6551 (p0) REVERT: I 72 LYS cc_start: 0.1836 (OUTLIER) cc_final: 0.0648 (tttt) REVERT: I 97 MET cc_start: 0.6042 (mpt) cc_final: 0.5358 (mmt) REVERT: I 113 ARG cc_start: 0.6576 (ttt90) cc_final: 0.4995 (tpt90) REVERT: J 1 MET cc_start: 0.8356 (mmt) cc_final: 0.8134 (mmt) REVERT: J 31 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: K 7 TYR cc_start: 0.5569 (OUTLIER) cc_final: 0.4978 (m-80) outliers start: 65 outliers final: 39 residues processed: 264 average time/residue: 0.1882 time to fit residues: 76.4737 Evaluate side-chains 238 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 809 ASP Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 281 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 chunk 65 optimal weight: 0.0020 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 224 optimal weight: 5.9990 chunk 66 optimal weight: 0.0020 chunk 275 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 HIS ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1032 ASN L 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.107216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.083590 restraints weight = 56766.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083935 restraints weight = 43100.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084257 restraints weight = 34423.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084554 restraints weight = 30308.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084642 restraints weight = 28422.866| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23560 Z= 0.115 Angle : 0.578 12.021 31759 Z= 0.296 Chirality : 0.043 0.227 3554 Planarity : 0.004 0.086 4099 Dihedral : 5.577 58.354 3177 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.57 % Favored : 89.40 % Rotamer: Outliers : 2.25 % Allowed : 11.79 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.00 (0.15), residues: 2886 helix: 0.21 (0.19), residues: 835 sheet: -1.14 (0.26), residues: 392 loop : -2.30 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 144 TYR 0.016 0.001 TYR A 653 PHE 0.021 0.001 PHE E 183 TRP 0.024 0.001 TRP A1058 HIS 0.006 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00258 (23546) covalent geometry : angle 0.56973 (31753) hydrogen bonds : bond 0.03276 ( 695) hydrogen bonds : angle 4.43457 ( 1926) metal coordination : bond 0.00402 ( 14) metal coordination : angle 6.98413 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 858 MET cc_start: 0.7634 (mtm) cc_final: 0.7278 (mtm) REVERT: B 338 THR cc_start: 0.6450 (OUTLIER) cc_final: 0.5908 (m) REVERT: B 541 MET cc_start: 0.7922 (mmm) cc_final: 0.7688 (mmm) REVERT: B 557 MET cc_start: 0.7043 (mmm) cc_final: 0.6777 (mpp) REVERT: B 585 TYR cc_start: 0.7848 (t80) cc_final: 0.7468 (t80) REVERT: B 895 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.8064 (p) REVERT: C 99 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7918 (tm-30) REVERT: E 121 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6621 (pp) REVERT: F 60 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6292 (pttt) REVERT: H 11 ILE cc_start: 0.8430 (tt) cc_final: 0.7965 (mp) REVERT: H 39 MET cc_start: 0.5376 (mmm) cc_final: 0.5153 (mmm) REVERT: H 68 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6490 (pp) REVERT: I 33 ASP cc_start: 0.6740 (p0) cc_final: 0.6472 (p0) REVERT: I 72 LYS cc_start: 0.1882 (OUTLIER) cc_final: 0.0693 (tttt) REVERT: I 97 MET cc_start: 0.6031 (mpt) cc_final: 0.5393 (mmt) REVERT: I 113 ARG cc_start: 0.6615 (ttt90) cc_final: 0.5031 (tpt90) REVERT: J 1 MET cc_start: 0.8259 (mmt) cc_final: 0.7958 (mmt) REVERT: J 31 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7959 (mt-10) REVERT: K 7 TYR cc_start: 0.5579 (OUTLIER) cc_final: 0.4970 (m-80) REVERT: K 97 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8020 (tp30) outliers start: 58 outliers final: 41 residues processed: 253 average time/residue: 0.1792 time to fit residues: 70.5931 Evaluate side-chains 241 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 48 optimal weight: 7.9990 chunk 260 optimal weight: 6.9990 chunk 173 optimal weight: 0.0370 chunk 180 optimal weight: 8.9990 chunk 284 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS L 19 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.106947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.083221 restraints weight = 56660.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083157 restraints weight = 41769.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.083633 restraints weight = 35218.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.083892 restraints weight = 30044.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083990 restraints weight = 28091.082| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23560 Z= 0.120 Angle : 0.576 11.877 31759 Z= 0.295 Chirality : 0.043 0.178 3554 Planarity : 0.004 0.071 4099 Dihedral : 5.429 58.039 3175 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 2.75 % Allowed : 11.91 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.15), residues: 2886 helix: 0.29 (0.19), residues: 836 sheet: -1.11 (0.26), residues: 399 loop : -2.27 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 424 TYR 0.024 0.001 TYR A 653 PHE 0.018 0.001 PHE E 183 TRP 0.017 0.001 TRP A1058 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00270 (23546) covalent geometry : angle 0.56826 (31753) hydrogen bonds : bond 0.03340 ( 695) hydrogen bonds : angle 4.42803 ( 1926) metal coordination : bond 0.00520 ( 14) metal coordination : angle 6.76875 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 202 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6734 (ttp) REVERT: A 858 MET cc_start: 0.7597 (mtm) cc_final: 0.7293 (mtm) REVERT: B 338 THR cc_start: 0.6518 (OUTLIER) cc_final: 0.5982 (m) REVERT: B 541 MET cc_start: 0.7941 (mmm) cc_final: 0.7706 (mmm) REVERT: B 585 TYR cc_start: 0.7800 (t80) cc_final: 0.7447 (t80) REVERT: B 851 HIS cc_start: 0.7073 (m-70) cc_final: 0.6870 (m170) REVERT: B 895 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8043 (p) REVERT: C 99 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7927 (tm-30) REVERT: E 121 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6648 (pp) REVERT: F 60 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.5930 (ptmt) REVERT: H 11 ILE cc_start: 0.8352 (tt) cc_final: 0.7888 (mp) REVERT: H 68 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6471 (pp) REVERT: I 33 ASP cc_start: 0.6741 (p0) cc_final: 0.6489 (p0) REVERT: I 72 LYS cc_start: 0.1926 (OUTLIER) cc_final: 0.0705 (tttt) REVERT: I 97 MET cc_start: 0.6238 (mpt) cc_final: 0.5491 (mmt) REVERT: I 113 ARG cc_start: 0.6654 (ttt90) cc_final: 0.5010 (tpt90) REVERT: J 1 MET cc_start: 0.8277 (mmt) cc_final: 0.7990 (mmt) REVERT: J 31 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: K 7 TYR cc_start: 0.5588 (OUTLIER) cc_final: 0.4949 (m-80) REVERT: K 97 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8044 (tp30) outliers start: 71 outliers final: 45 residues processed: 260 average time/residue: 0.1809 time to fit residues: 73.5812 Evaluate side-chains 237 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 972 LYS Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 17 LYS Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 227 optimal weight: 0.5980 chunk 266 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 459 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 GLN H 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.083100 restraints weight = 56558.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083488 restraints weight = 40989.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083765 restraints weight = 32099.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084111 restraints weight = 29590.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084200 restraints weight = 28557.614| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23560 Z= 0.115 Angle : 0.576 12.073 31759 Z= 0.295 Chirality : 0.043 0.169 3554 Planarity : 0.004 0.072 4099 Dihedral : 5.338 57.656 3175 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 2.56 % Allowed : 12.22 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.16), residues: 2886 helix: 0.37 (0.19), residues: 836 sheet: -1.08 (0.26), residues: 402 loop : -2.20 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 424 TYR 0.025 0.001 TYR A 653 PHE 0.023 0.001 PHE H 8 TRP 0.028 0.001 TRP A1058 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00258 (23546) covalent geometry : angle 0.56968 (31753) hydrogen bonds : bond 0.03266 ( 695) hydrogen bonds : angle 4.38507 ( 1926) metal coordination : bond 0.00452 ( 14) metal coordination : angle 6.28678 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 1.049 Fit side-chains REVERT: A 858 MET cc_start: 0.7586 (mtm) cc_final: 0.7295 (mtm) REVERT: B 338 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6045 (m) REVERT: B 436 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5842 (mm-30) REVERT: B 541 MET cc_start: 0.7891 (mmm) cc_final: 0.7685 (mmm) REVERT: B 585 TYR cc_start: 0.7830 (t80) cc_final: 0.7458 (t80) REVERT: B 895 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8067 (p) REVERT: C 99 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7917 (tm-30) REVERT: E 121 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6631 (pp) REVERT: F 60 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.5906 (ptmt) REVERT: H 11 ILE cc_start: 0.8347 (tt) cc_final: 0.7870 (mp) REVERT: H 39 MET cc_start: 0.5365 (mmm) cc_final: 0.4941 (mmm) REVERT: H 68 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6302 (pp) REVERT: I 33 ASP cc_start: 0.6722 (p0) cc_final: 0.6463 (p0) REVERT: I 72 LYS cc_start: 0.1896 (OUTLIER) cc_final: 0.0682 (tttt) REVERT: I 97 MET cc_start: 0.6224 (mpt) cc_final: 0.5511 (mmt) REVERT: I 113 ARG cc_start: 0.6554 (ttt90) cc_final: 0.4913 (tpt90) REVERT: J 1 MET cc_start: 0.8206 (mmt) cc_final: 0.7879 (mmt) REVERT: J 31 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: K 7 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.4968 (m-80) REVERT: K 97 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8088 (tp30) REVERT: K 111 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8149 (tppp) REVERT: L 51 ARG cc_start: 0.6808 (mtt-85) cc_final: 0.6100 (mtp180) outliers start: 66 outliers final: 42 residues processed: 246 average time/residue: 0.1752 time to fit residues: 68.6781 Evaluate side-chains 228 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 999 ASP Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 141 LEU Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 223 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 92 optimal weight: 0.0870 chunk 115 optimal weight: 0.3980 chunk 234 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 202 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 2 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 459 HIS ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 851 HIS E 151 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.108008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.084110 restraints weight = 56706.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.084326 restraints weight = 41523.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084718 restraints weight = 33323.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084994 restraints weight = 29716.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085104 restraints weight = 27957.746| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23560 Z= 0.101 Angle : 0.570 12.193 31759 Z= 0.290 Chirality : 0.043 0.368 3554 Planarity : 0.004 0.064 4099 Dihedral : 5.121 56.677 3173 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 1.94 % Allowed : 13.34 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.16), residues: 2886 helix: 0.51 (0.19), residues: 833 sheet: -1.01 (0.27), residues: 403 loop : -2.15 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 424 TYR 0.022 0.001 TYR A 752 PHE 0.036 0.001 PHE H 8 TRP 0.024 0.001 TRP A1058 HIS 0.007 0.001 HIS A 938 Details of bonding type rmsd covalent geometry : bond 0.00221 (23546) covalent geometry : angle 0.56419 (31753) hydrogen bonds : bond 0.03017 ( 695) hydrogen bonds : angle 4.25811 ( 1926) metal coordination : bond 0.00444 ( 14) metal coordination : angle 5.84919 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 199 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 764 VAL cc_start: 0.8719 (t) cc_final: 0.8466 (t) REVERT: A 858 MET cc_start: 0.7627 (mtm) cc_final: 0.7344 (mtm) REVERT: B 436 GLU cc_start: 0.5827 (mm-30) cc_final: 0.5626 (mm-30) REVERT: B 541 MET cc_start: 0.7916 (mmm) cc_final: 0.7707 (mmm) REVERT: B 585 TYR cc_start: 0.7812 (t80) cc_final: 0.7463 (t80) REVERT: B 895 THR cc_start: 0.8416 (OUTLIER) cc_final: 0.8059 (p) REVERT: C 99 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7863 (tm-30) REVERT: E 121 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6709 (pp) REVERT: F 60 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.5977 (ptmt) REVERT: F 83 MET cc_start: 0.8398 (mmm) cc_final: 0.8103 (mmm) REVERT: H 7 MET cc_start: 0.6642 (mtt) cc_final: 0.6329 (mtt) REVERT: H 39 MET cc_start: 0.5180 (mmm) cc_final: 0.4862 (mmm) REVERT: H 68 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6306 (pp) REVERT: I 33 ASP cc_start: 0.6810 (p0) cc_final: 0.6599 (p0) REVERT: I 72 LYS cc_start: 0.1839 (OUTLIER) cc_final: 0.0688 (tttt) REVERT: I 97 MET cc_start: 0.6154 (mpt) cc_final: 0.5438 (mmt) REVERT: I 113 ARG cc_start: 0.6606 (ttt90) cc_final: 0.5044 (tpt90) REVERT: J 1 MET cc_start: 0.8148 (mmt) cc_final: 0.7792 (mmt) REVERT: J 31 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: K 7 TYR cc_start: 0.5553 (OUTLIER) cc_final: 0.4963 (m-80) REVERT: K 97 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8079 (tp30) REVERT: K 111 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8136 (tppp) outliers start: 50 outliers final: 39 residues processed: 242 average time/residue: 0.1714 time to fit residues: 66.2054 Evaluate side-chains 231 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 184 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 145 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 232 optimal weight: 0.0030 chunk 203 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 236 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.107047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.083136 restraints weight = 56712.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083413 restraints weight = 41682.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083791 restraints weight = 33098.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084072 restraints weight = 29828.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084136 restraints weight = 28084.428| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23560 Z= 0.126 Angle : 0.592 11.836 31759 Z= 0.301 Chirality : 0.044 0.401 3554 Planarity : 0.004 0.068 4099 Dihedral : 5.199 56.754 3173 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 1.98 % Allowed : 13.34 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.16), residues: 2886 helix: 0.50 (0.19), residues: 832 sheet: -0.98 (0.27), residues: 400 loop : -2.13 (0.15), residues: 1654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 424 TYR 0.026 0.002 TYR H 91 PHE 0.015 0.001 PHE I 87 TRP 0.022 0.001 TRP A1058 HIS 0.006 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00288 (23546) covalent geometry : angle 0.58659 (31753) hydrogen bonds : bond 0.03300 ( 695) hydrogen bonds : angle 4.31958 ( 1926) metal coordination : bond 0.00435 ( 14) metal coordination : angle 5.96308 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5772 Ramachandran restraints generated. 2886 Oldfield, 0 Emsley, 2886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 190 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 1006 MET cc_start: 0.6957 (tmm) cc_final: 0.6440 (tmm) REVERT: B 541 MET cc_start: 0.7867 (mmm) cc_final: 0.7644 (mmm) REVERT: B 585 TYR cc_start: 0.7818 (t80) cc_final: 0.7504 (t80) REVERT: B 895 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8059 (p) REVERT: C 99 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7938 (tm-30) REVERT: E 121 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6700 (pp) REVERT: F 60 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.5938 (ptmt) REVERT: F 83 MET cc_start: 0.8400 (mmm) cc_final: 0.8110 (mmm) REVERT: H 7 MET cc_start: 0.6536 (mtt) cc_final: 0.6233 (mtt) REVERT: H 68 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6256 (pp) REVERT: I 33 ASP cc_start: 0.6816 (p0) cc_final: 0.6607 (p0) REVERT: I 72 LYS cc_start: 0.1964 (OUTLIER) cc_final: 0.0760 (tttt) REVERT: I 97 MET cc_start: 0.6164 (mpt) cc_final: 0.5470 (mmt) REVERT: I 113 ARG cc_start: 0.6591 (ttt90) cc_final: 0.5054 (tpt90) REVERT: J 1 MET cc_start: 0.8155 (mmt) cc_final: 0.7840 (mmt) REVERT: J 31 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: K 7 TYR cc_start: 0.5596 (OUTLIER) cc_final: 0.4982 (m-80) REVERT: K 111 LYS cc_start: 0.8404 (mmmt) cc_final: 0.8142 (tppp) outliers start: 51 outliers final: 42 residues processed: 233 average time/residue: 0.1623 time to fit residues: 60.4298 Evaluate side-chains 230 residues out of total 2578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 917 VAL Chi-restraints excluded: chain A residue 1031 VAL Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 334 GLN Chi-restraints excluded: chain B residue 391 PHE Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 852 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 950 ARG Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 14 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain K residue 7 TYR Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 71 ILE Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 73 optimal weight: 0.0980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS K 40 HIS L 28 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.107136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083493 restraints weight = 56496.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084056 restraints weight = 41914.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084398 restraints weight = 32758.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084668 restraints weight = 29076.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084733 restraints weight = 27330.624| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23560 Z= 0.121 Angle : 0.601 11.846 31759 Z= 0.305 Chirality : 0.044 0.397 3554 Planarity : 0.004 0.065 4099 Dihedral : 5.211 57.033 3173 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 1.90 % Allowed : 13.69 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.16), residues: 2886 helix: 0.50 (0.19), residues: 836 sheet: -0.97 (0.27), residues: 400 loop : -2.14 (0.15), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 424 TYR 0.029 0.001 TYR H 91 PHE 0.039 0.001 PHE H 8 TRP 0.020 0.001 TRP A1058 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00278 (23546) covalent geometry : angle 0.59516 (31753) hydrogen bonds : bond 0.03265 ( 695) hydrogen bonds : angle 4.31015 ( 1926) metal coordination : bond 0.00424 ( 14) metal coordination : angle 6.04794 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3408.37 seconds wall clock time: 60 minutes 9.63 seconds (3609.63 seconds total)