Starting phenix.real_space_refine on Sat Jul 4 23:17:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k19_61969/07_2026/9k19_61969.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k19_61969/07_2026/9k19_61969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k19_61969/07_2026/9k19_61969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k19_61969/07_2026/9k19_61969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k19_61969/07_2026/9k19_61969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k19_61969/07_2026/9k19_61969.map" } resolution = 4.06 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 141 5.16 5 C 14630 2.51 5 N 4068 2.21 5 O 4499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23378 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6449 Classifications: {'peptide': 827} Link IDs: {'PTRANS': 27, 'TRANS': 799} Chain breaks: 3 Chain: "B" Number of atoms: 7946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7946 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 37, 'TRANS': 962} Chain breaks: 3 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: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 660 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} 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: 713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 713 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 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: "T" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 222 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "N" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 431 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} 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: "H" 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 15100 SG CYS C 91 81.123 46.447 138.818 1.00117.83 S ATOM 15119 SG CYS C 94 83.141 42.790 138.668 1.00131.81 S ATOM 15158 SG CYS C 100 79.787 43.191 139.295 1.00113.79 S ATOM 20275 SG CYS I 7 26.874 47.146 20.276 1.00 95.06 S ATOM 20460 SG CYS I 29 28.965 49.205 18.871 1.00130.28 S ATOM 20485 SG CYS I 32 29.987 46.028 17.164 1.00111.50 S ATOM 20996 SG CYS J 7 51.278 46.751 119.151 1.00 95.21 S ATOM 21020 SG CYS J 10 50.901 48.381 123.361 1.00107.94 S ATOM 21286 SG CYS J 44 47.848 49.598 120.798 1.00 99.52 S ATOM 21292 SG CYS J 45 48.376 46.372 121.734 1.00 91.25 S ATOM 22397 SG CYS L 12 78.975 19.735 95.627 1.00119.98 S ATOM 22415 SG CYS L 15 78.659 16.462 94.739 1.00108.80 S Time building chain proxies: 4.61, per 1000 atoms: 0.20 Number of scatterers: 23378 At special positions: 0 Unit cell: (118.26, 142.35, 164.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 141 16.00 P 32 15.00 Mg 1 11.99 O 4499 8.00 N 4068 7.00 C 14630 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 900.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 501 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 91 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 501 " - pdb=" SG CYS C 100 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 32 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 7 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 15 " pdb="ZN ZN L 201 " - pdb=" SG CYS L 12 " Number of angles added : 6 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5390 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 34 sheets defined 32.8% alpha, 14.5% beta 5 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 343 through 347 removed outlier: 4.049A pdb=" N HIS A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 359 through 369 removed outlier: 3.872A pdb=" N ASP A 368 " --> pdb=" O GLN A 364 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASN A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.593A pdb=" N LYS A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 492 through 505 removed outlier: 3.502A pdb=" N GLN A 505 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 517 Processing helix chain 'A' and resid 541 through 547 Processing helix chain 'A' and resid 576 through 593 Processing helix chain 'A' and resid 593 through 612 removed outlier: 3.701A pdb=" N ALA A 597 " --> pdb=" O GLY A 593 " (cutoff:3.500A) Proline residue: A 606 - end of helix removed outlier: 3.910A pdb=" N LEU A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 637 removed outlier: 3.607A pdb=" N ASN A 636 " --> pdb=" O GLY A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 642 removed outlier: 3.953A pdb=" N GLU A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 672 removed outlier: 3.599A pdb=" N VAL A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL A 669 " --> pdb=" O LYS A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 683 removed outlier: 3.778A pdb=" N ASN A 682 " --> pdb=" O TYR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.637A pdb=" N GLN A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 693 through 698' Processing helix chain 'A' and resid 715 through 724 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 773 through 786 removed outlier: 3.514A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 845 Proline residue: A 839 - end of helix Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 854 through 863 removed outlier: 3.878A pdb=" N MET A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 859 " --> pdb=" O TRP A 855 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 904 removed outlier: 4.322A pdb=" N VAL A 899 " --> pdb=" O SER A 895 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 903 " --> pdb=" O VAL A 899 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 904 " --> pdb=" O ARG A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 912 Processing helix chain 'A' and resid 942 through 946 Processing helix chain 'A' and resid 953 through 966 removed outlier: 3.792A pdb=" N LEU A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 978 removed outlier: 4.121A pdb=" N ASP A 977 " --> pdb=" O LYS A 974 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE A 978 " --> pdb=" O ALA A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 974 through 978' Processing helix chain 'A' and resid 1009 through 1014 removed outlier: 3.709A pdb=" N ALA A1012 " --> pdb=" O SER A1009 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A1013 " --> pdb=" O TYR A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1027 removed outlier: 3.712A pdb=" N THR A1027 " --> pdb=" O LEU A1024 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1033 Processing helix chain 'A' and resid 1085 through 1095 removed outlier: 3.602A pdb=" N ARG A1089 " --> pdb=" O GLY A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1099 removed outlier: 3.870A pdb=" N LEU A1099 " --> pdb=" O LEU A1096 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1096 through 1099' Processing helix chain 'A' and resid 1111 through 1120 Processing helix chain 'A' and resid 1120 through 1137 removed outlier: 3.634A pdb=" N ALA A1124 " --> pdb=" O GLY A1120 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU A1126 " --> pdb=" O SER A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1155 removed outlier: 3.711A pdb=" N ILE A1148 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1167 No H-bonds generated for 'chain 'A' and resid 1165 through 1167' Processing helix chain 'A' and resid 1168 through 1173 removed outlier: 4.319A pdb=" N LEU A1172 " --> pdb=" O GLY A1168 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR A1173 " --> pdb=" O TYR A1169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1168 through 1173' Processing helix chain 'B' and resid 21 through 41 Processing helix chain 'B' and resid 43 through 61 removed outlier: 4.525A pdb=" N LEU B 58 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLN B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 4.268A pdb=" N ALA B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.544A pdb=" N THR B 182 " --> pdb=" O CYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 282 removed outlier: 3.646A pdb=" N PHE B 280 " --> pdb=" O TRP B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.807A pdb=" N ILE B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 318 removed outlier: 3.993A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER B 306 " --> pdb=" O SER B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 332 through 337 removed outlier: 4.108A pdb=" N LYS B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 351 Processing helix chain 'B' and resid 360 through 380 removed outlier: 3.726A 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 422 Processing helix chain 'B' and resid 423 through 426 removed outlier: 3.732A pdb=" N LEU B 426 " --> pdb=" O GLN B 423 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 423 through 426' Processing helix chain 'B' and resid 441 through 454 Processing helix chain 'B' and resid 480 through 486 Processing helix chain 'B' and resid 544 through 549 removed outlier: 3.957A pdb=" N PHE B 549 " --> pdb=" O VAL B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 582 through 595 Processing helix chain 'B' and resid 635 through 640 removed outlier: 3.559A pdb=" N SER B 639 " --> pdb=" O LYS B 635 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 635 through 640' Processing helix chain 'B' and resid 645 through 652 removed outlier: 3.598A pdb=" N GLN B 652 " --> pdb=" O HIS B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 666 Processing helix chain 'B' and resid 674 through 679 removed outlier: 3.814A pdb=" N GLN B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 694 through 699 removed outlier: 4.352A pdb=" N ILE B 699 " --> pdb=" O VAL B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 706 removed outlier: 3.503A pdb=" N ASP B 706 " --> pdb=" O ALA B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 717 Processing helix chain 'B' and resid 751 through 758 Processing helix chain 'B' and resid 788 through 794 Processing helix chain 'B' and resid 925 through 929 removed outlier: 3.593A pdb=" N PHE B 929 " --> pdb=" O GLN B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 951 removed outlier: 3.739A pdb=" N GLN B 951 " --> pdb=" O PHE B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 967 Processing helix chain 'B' and resid 993 through 1004 removed outlier: 3.634A pdb=" N ILE B 997 " --> pdb=" O SER B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1044 removed outlier: 3.553A pdb=" N LYS B1044 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 removed outlier: 3.612A pdb=" N ALA C 35 " --> pdb=" O ASP C 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 46 " --> pdb=" O MET C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 74 removed outlier: 3.569A pdb=" N LEU C 74 " --> pdb=" O HIS C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.675A pdb=" N ASP C 125 " --> pdb=" O THR C 122 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 126 " --> pdb=" O SER C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.573A pdb=" N SER C 181 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 216 removed outlier: 3.706A pdb=" N LYS C 209 " --> pdb=" O THR C 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 277 through 295 removed outlier: 3.947A pdb=" N LEU C 281 " --> pdb=" O LYS C 277 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 297 No H-bonds generated for 'chain 'C' and resid 296 through 297' Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.036A pdb=" N THR C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 50 removed outlier: 3.696A pdb=" N HIS E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 61 removed outlier: 3.664A pdb=" N LEU E 61 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 Processing helix chain 'E' and resid 78 through 82 removed outlier: 3.894A pdb=" N ILE E 81 " --> pdb=" O ARG E 78 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER E 82 " --> pdb=" O LEU E 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 82' Processing helix chain 'E' and resid 104 through 117 removed outlier: 3.673A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 162 Processing helix chain 'E' and resid 173 through 183 removed outlier: 3.842A pdb=" N PHE E 183 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 190 Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'F' and resid 66 through 82 removed outlier: 3.664A pdb=" N ARG F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 107 removed outlier: 3.529A pdb=" N ILE F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 28 removed outlier: 3.512A pdb=" N TYR J 21 " --> pdb=" O LYS J 17 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 42 through 50 removed outlier: 4.236A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.517A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 51 removed outlier: 3.524A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.762A pdb=" N ALA K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 330 removed outlier: 3.694A pdb=" N GLN A 424 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 326 " --> pdb=" O VAL A 455 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AA3, first strand: chain 'A' and resid 507 through 508 removed outlier: 3.699A pdb=" N TRP A 539 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 529 through 531 removed outlier: 3.544A pdb=" N VAL A 530 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL H 92 " --> pdb=" O VAL A 530 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 556 removed outlier: 4.003A pdb=" N ILE A 561 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 569 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 703 through 704 Processing sheet with id=AA7, first strand: chain 'A' and resid 789 through 791 removed outlier: 7.113A pdb=" N VAL A 797 " --> pdb=" O VAL A 806 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 876 through 880 Processing sheet with id=AA9, first strand: chain 'A' and resid 906 through 907 removed outlier: 7.055A pdb=" N VAL A 906 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1003 through 1007 removed outlier: 4.035A pdb=" N MET A1006 " --> pdb=" O GLY A 937 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLY A 937 " --> pdb=" O MET A1006 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL A 917 " --> pdb=" O TYR I 44 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR I 44 " --> pdb=" O VAL A 917 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1158 through 1159 removed outlier: 6.561A pdb=" N ARG E 192 " --> pdb=" O GLY A1159 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 97 removed outlier: 5.338A pdb=" N PHE B 91 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASP B 131 " --> pdb=" O PHE B 91 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU B 93 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG B 125 " --> pdb=" O ASP B 97 " (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: 6.490A pdb=" N ALA B 215 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN B 529 " --> pdb=" O CYS B 514 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 224 through 225 removed outlier: 3.634A pdb=" N TRP B 225 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 235 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE B 244 " --> pdb=" O TYR B 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 457 through 458 Processing sheet with id=AB9, first strand: chain 'B' and resid 535 through 536 Processing sheet with id=AC1, first strand: chain 'B' and resid 554 through 555 removed outlier: 7.093A pdb=" N VAL B 570 " --> pdb=" O VAL B 577 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL B 579 " --> pdb=" O HIS B 568 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N HIS B 568 " --> pdb=" O VAL B 579 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 628 through 629 removed outlier: 3.887A pdb=" N ALA B 669 " --> pdb=" O HIS B 684 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 738 through 741 Processing sheet with id=AC4, first strand: chain 'B' and resid 738 through 741 removed outlier: 3.856A pdb=" N LYS B 881 " --> pdb=" O SER B 897 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 899 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL B 879 " --> pdb=" O ARG B 899 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.607A pdb=" N GLN B1035 " --> pdb=" O SER B 911 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N PHE B1028 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 942 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE B 784 " --> pdb=" O GLY B 921 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 923 " --> pdb=" O ILE B 784 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N MET B 786 " --> pdb=" O ILE B 923 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 910 through 912 removed outlier: 3.607A pdb=" N GLN B1035 " --> pdb=" O SER B 911 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 12 through 19 removed outlier: 6.694A pdb=" N LYS C 24 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU C 18 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 25 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE C 266 " --> pdb=" O LEU C 27 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 12 through 19 removed outlier: 6.694A pdb=" N LYS C 24 " --> pdb=" O ARG C 16 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU C 18 " --> pdb=" O TYR C 22 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TYR C 22 " --> pdb=" O LEU C 18 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 25 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE C 266 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU C 191 " --> pdb=" O LYS C 262 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 127 through 128 removed outlier: 6.390A pdb=" N GLU C 162 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 58 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LYS C 164 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE C 56 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG C 166 " --> pdb=" O VAL C 54 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VAL C 54 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 168 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 56 " --> pdb=" O VAL L 46 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL L 46 " --> pdb=" O ILE C 56 " (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 221 through 224 removed outlier: 3.601A pdb=" N GLN C 229 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.911A pdb=" N LYS E 94 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU E 124 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N GLY E 123 " --> pdb=" O GLU E 148 " (cutoff:3.500A) removed outlier: 8.877A pdb=" N PHE E 150 " --> pdb=" O GLY E 123 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE E 125 " --> pdb=" O PHE E 150 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 113 through 114 Processing sheet with id=AD5, first strand: chain 'H' and resid 57 through 62 removed outlier: 3.878A pdb=" N PHE H 8 " --> pdb=" O MET H 62 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N GLU H 31 " --> pdb=" O ASP H 15 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP H 44 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU H 120 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N SER H 115 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU H 97 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 14 through 18 Processing sheet with id=AD7, first strand: chain 'K' and resid 21 through 23 709 hydrogen bonds defined for protein. 1938 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 2.50 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: 7273 1.33 - 1.46: 3921 1.46 - 1.58: 12382 1.58 - 1.70: 62 1.70 - 1.82: 218 Bond restraints: 23856 Sorted by residual: bond pdb=" C1' DC N 13 " pdb=" N1 DC N 13 " ideal model delta sigma weight residual 1.468 1.553 -0.085 1.40e-02 5.10e+03 3.73e+01 bond pdb=" C1' DC N 14 " pdb=" N1 DC N 14 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.44e+01 bond pdb=" C1' DG N 12 " pdb=" N9 DG N 12 " ideal model delta sigma weight residual 1.468 1.398 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" C1' DG N 17 " pdb=" N9 DG N 17 " ideal model delta sigma weight residual 1.468 1.404 0.064 1.40e-02 5.10e+03 2.11e+01 bond pdb=" C1' DT N 15 " pdb=" N1 DT N 15 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.48e+01 ... (remaining 23851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 31278 2.21 - 4.42: 925 4.42 - 6.62: 88 6.62 - 8.83: 16 8.83 - 11.04: 2 Bond angle restraints: 32309 Sorted by residual: angle pdb=" O4' DT T 13 " pdb=" C1' DT T 13 " pdb=" N1 DT T 13 " ideal model delta sigma weight residual 108.00 113.35 -5.35 7.00e-01 2.04e+00 5.84e+01 angle pdb=" O4' DA T 7 " pdb=" C4' DA T 7 " pdb=" C3' DA T 7 " ideal model delta sigma weight residual 106.00 102.08 3.92 6.00e-01 2.78e+00 4.26e+01 angle pdb=" CA PHE B 391 " pdb=" C PHE B 391 " pdb=" N ARG B 392 " ideal model delta sigma weight residual 118.42 125.44 -7.02 1.31e+00 5.83e-01 2.87e+01 angle pdb=" N ILE B 435 " pdb=" CA ILE B 435 " pdb=" C ILE B 435 " ideal model delta sigma weight residual 112.12 108.23 3.89 8.40e-01 1.42e+00 2.15e+01 angle pdb=" C4' DT T 13 " pdb=" O4' DT T 13 " pdb=" C1' DT T 13 " ideal model delta sigma weight residual 110.10 105.69 4.41 1.00e+00 1.00e+00 1.95e+01 ... (remaining 32304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.36: 14141 35.36 - 70.71: 290 70.71 - 106.07: 16 106.07 - 141.42: 0 141.42 - 176.78: 2 Dihedral angle restraints: 14449 sinusoidal: 6123 harmonic: 8326 Sorted by residual: dihedral pdb=" CA SER B 561 " pdb=" C SER B 561 " pdb=" N THR B 562 " pdb=" CA THR B 562 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA PHE H 24 " pdb=" C PHE H 24 " pdb=" N ASP H 25 " pdb=" CA ASP H 25 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA ARG A 522 " pdb=" C ARG A 522 " pdb=" N SER A 523 " pdb=" CA SER A 523 " ideal model delta harmonic sigma weight residual 180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 14446 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2644 0.053 - 0.106: 833 0.106 - 0.160: 131 0.160 - 0.213: 12 0.213 - 0.266: 2 Chirality restraints: 3622 Sorted by residual: chirality pdb=" CA ASN A 838 " pdb=" N ASN A 838 " pdb=" C ASN A 838 " pdb=" CB ASN A 838 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU A 945 " pdb=" CB LEU A 945 " pdb=" CD1 LEU A 945 " pdb=" CD2 LEU A 945 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA MET H 112 " pdb=" N MET H 112 " pdb=" C MET H 112 " pdb=" CB MET H 112 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 3619 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG H 144 " 0.019 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C ARG H 144 " -0.063 2.00e-02 2.50e+03 pdb=" O ARG H 144 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS H 145 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 135 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.26e+01 pdb=" C ASP F 135 " -0.061 2.00e-02 2.50e+03 pdb=" O ASP F 135 " 0.023 2.00e-02 2.50e+03 pdb=" N SER F 136 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 799 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" CD GLU B 799 " -0.049 2.00e-02 2.50e+03 pdb=" OE1 GLU B 799 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLU B 799 " 0.018 2.00e-02 2.50e+03 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 42 2.56 - 3.15: 19892 3.15 - 3.73: 34542 3.73 - 4.32: 47553 4.32 - 4.90: 76384 Nonbonded interactions: 178413 Sorted by model distance: nonbonded pdb=" O ILE I 13 " pdb="ZN ZN I 201 " model vdw 1.976 2.230 nonbonded pdb=" C VAL H 92 " pdb="ZN ZN H 201 " model vdw 2.083 2.460 nonbonded pdb=" OG1 THR J 9 " pdb="ZN ZN J 101 " model vdw 2.137 2.230 nonbonded pdb=" C ILE I 13 " pdb="ZN ZN I 201 " model vdw 2.197 2.460 nonbonded pdb=" CZ TYR B 585 " pdb=" OD2 ASP B 589 " model vdw 2.236 3.260 ... (remaining 178408 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 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 : 0.009 0.587 23869 Z= 0.381 Angle : 0.939 32.549 32315 Z= 0.536 Chirality : 0.050 0.266 3622 Planarity : 0.006 0.066 4062 Dihedral : 14.384 176.780 9059 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.86 % Favored : 88.10 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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 are not related in a simple way. whole: -2.94 (0.15), residues: 2832 helix: -0.97 (0.18), residues: 778 sheet: -1.57 (0.26), residues: 382 loop : -2.65 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 80 TYR 0.023 0.002 TYR B 713 PHE 0.029 0.002 PHE E 183 TRP 0.022 0.003 TRP F 126 HIS 0.010 0.002 HIS A 940 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.28 (23856) covalent geometry : angle 0.89217 / 0.53 (32309) hydrogen bonds : bond 0.16052 / 11.02 ( 704) hydrogen bonds : angle 7.09565 / 4.98 ( 1964) metal coordination : bond 0.31361 / 18.88 ( 12) metal coordination : angle 21.45597 / 11.99 ( 6) Misc. bond : bond 0.13756 / 7.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 MET cc_start: 0.6530 (ptt) cc_final: 0.6292 (ptt) REVERT: A 631 MET cc_start: 0.0230 (mmm) cc_final: -0.0411 (mtp) REVERT: A 1006 MET cc_start: 0.6899 (mpp) cc_final: 0.6586 (mpp) REVERT: A 1141 LYS cc_start: 0.7114 (mppt) cc_final: 0.6455 (tptp) REVERT: B 68 MET cc_start: 0.5782 (mpp) cc_final: 0.5439 (mmm) REVERT: B 251 ASN cc_start: 0.5060 (m-40) cc_final: 0.4751 (m-40) REVERT: B 305 ASN cc_start: 0.8625 (m-40) cc_final: 0.8316 (m110) REVERT: B 501 ASP cc_start: 0.6723 (m-30) cc_final: 0.5627 (t0) REVERT: B 1040 MET cc_start: 0.3379 (mtm) cc_final: 0.3163 (mtm) REVERT: C 83 MET cc_start: 0.7669 (mpp) cc_final: 0.7225 (mmm) REVERT: C 85 MET cc_start: 0.7742 (mmm) cc_final: 0.7316 (mmm) REVERT: C 292 LYS cc_start: 0.7888 (mmmt) cc_final: 0.7310 (mmmt) REVERT: F 72 ARG cc_start: 0.6236 (mtm110) cc_final: 0.5539 (ptt180) REVERT: H 91 TYR cc_start: 0.6887 (t80) cc_final: 0.6034 (t80) REVERT: I 4 MET cc_start: 0.5977 (mmm) cc_final: 0.5305 (mmm) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1471 time to fit residues: 53.9223 Evaluate side-chains 173 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.0470 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 overall best weight: 2.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 GLN A 615 GLN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.106926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.088536 restraints weight = 115018.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.089417 restraints weight = 82154.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.090232 restraints weight = 57495.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.090359 restraints weight = 50157.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.090423 restraints weight = 45113.555| |-----------------------------------------------------------------------------| r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.0812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 23869 Z= 0.158 Angle : 0.702 14.959 32315 Z= 0.369 Chirality : 0.047 0.310 3622 Planarity : 0.005 0.061 4062 Dihedral : 12.753 174.943 3457 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.58 % Favored : 88.38 % Rotamer: Outliers : 0.08 % Allowed : 4.35 % Favored : 95.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.15), residues: 2832 helix: -0.57 (0.18), residues: 782 sheet: -1.79 (0.24), residues: 401 loop : -2.50 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1019 TYR 0.014 0.002 TYR A1166 PHE 0.020 0.002 PHE B 321 TRP 0.025 0.002 TRP C 180 HIS 0.008 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (23856) covalent geometry : angle 0.69330 / 0.37 (32309) hydrogen bonds : bond 0.04904 / 3.35 ( 704) hydrogen bonds : angle 5.78481 / 4.02 ( 1964) metal coordination : bond 0.01689 / 0.98 ( 12) metal coordination : angle 7.90409 / 4.48 ( 6) Misc. bond : bond 0.00952 / 0.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.7823 (mp0) cc_final: 0.7487 (tt0) REVERT: A 609 MET cc_start: 0.6620 (ptt) cc_final: 0.6382 (ptt) REVERT: A 631 MET cc_start: 0.0873 (mmm) cc_final: -0.0216 (mtp) REVERT: A 1006 MET cc_start: 0.7482 (mpp) cc_final: 0.7165 (mpp) REVERT: A 1088 TRP cc_start: 0.7590 (t-100) cc_final: 0.7245 (t-100) REVERT: B 68 MET cc_start: 0.5323 (mpp) cc_final: 0.5089 (mmm) REVERT: B 251 ASN cc_start: 0.4736 (m-40) cc_final: 0.4480 (m-40) REVERT: B 305 ASN cc_start: 0.8587 (m-40) cc_final: 0.8232 (m110) REVERT: B 501 ASP cc_start: 0.7036 (m-30) cc_final: 0.6015 (t0) REVERT: B 1023 MET cc_start: 0.5975 (mmp) cc_final: 0.5689 (mmp) REVERT: B 1040 MET cc_start: 0.4022 (mtm) cc_final: 0.3650 (mtm) REVERT: C 83 MET cc_start: 0.7557 (mpp) cc_final: 0.7064 (mmm) REVERT: C 292 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7243 (mmmt) REVERT: F 72 ARG cc_start: 0.6114 (mtm110) cc_final: 0.5565 (ptt180) REVERT: I 4 MET cc_start: 0.5971 (mmm) cc_final: 0.5308 (mmm) outliers start: 2 outliers final: 0 residues processed: 211 average time/residue: 0.1366 time to fit residues: 46.8345 Evaluate side-chains 176 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 161 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 226 optimal weight: 10.0000 chunk 158 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 280 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 239 optimal weight: 0.0470 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 GLN H 35 HIS I 46 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.107936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.089582 restraints weight = 114640.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.090695 restraints weight = 77751.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.091393 restraints weight = 53763.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.091586 restraints weight = 49842.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.091483 restraints weight = 43559.476| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23869 Z= 0.130 Angle : 0.649 11.445 32315 Z= 0.342 Chirality : 0.045 0.316 3622 Planarity : 0.004 0.086 4062 Dihedral : 12.589 176.636 3457 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.45 % Favored : 89.51 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.15), residues: 2832 helix: -0.33 (0.19), residues: 782 sheet: -1.76 (0.25), residues: 398 loop : -2.41 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1019 TYR 0.023 0.001 TYR H 91 PHE 0.020 0.001 PHE C 268 TRP 0.014 0.001 TRP C 180 HIS 0.007 0.001 HIS H 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (23856) covalent geometry : angle 0.64401 / 0.34 (32309) hydrogen bonds : bond 0.04293 / 2.95 ( 704) hydrogen bonds : angle 5.48204 / 3.79 ( 1964) metal coordination : bond 0.01317 / 0.88 ( 12) metal coordination : angle 6.11453 / 3.49 ( 6) Misc. bond : bond 0.00952 / 0.50 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 MET cc_start: 0.6546 (ptt) cc_final: 0.6334 (ptt) REVERT: A 631 MET cc_start: 0.0765 (mmm) cc_final: -0.0297 (mtp) REVERT: A 672 ASN cc_start: 0.4068 (t0) cc_final: 0.3728 (m110) REVERT: B 251 ASN cc_start: 0.4650 (m-40) cc_final: 0.4332 (m-40) REVERT: B 305 ASN cc_start: 0.8535 (m-40) cc_final: 0.8173 (m110) REVERT: B 501 ASP cc_start: 0.7020 (m-30) cc_final: 0.6005 (t0) REVERT: B 1023 MET cc_start: 0.5893 (mmp) cc_final: 0.5473 (mmp) REVERT: B 1040 MET cc_start: 0.4096 (mtm) cc_final: 0.3800 (mtm) REVERT: C 83 MET cc_start: 0.7627 (mpp) cc_final: 0.7070 (mmm) REVERT: C 292 LYS cc_start: 0.7882 (mmmt) cc_final: 0.7345 (mmmt) REVERT: F 72 ARG cc_start: 0.6172 (mtm110) cc_final: 0.5703 (ptt180) REVERT: I 4 MET cc_start: 0.5907 (mmm) cc_final: 0.5228 (mmm) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1456 time to fit residues: 49.7349 Evaluate side-chains 173 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 266 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 268 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 200 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 ASN A 377 GLN ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 163 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 HIS I 46 ASN I 105 ASN ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.104411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.085352 restraints weight = 117818.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.086799 restraints weight = 74380.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.087718 restraints weight = 54582.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.088195 restraints weight = 44558.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.088663 restraints weight = 39654.963| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 23869 Z= 0.250 Angle : 0.809 11.996 32315 Z= 0.425 Chirality : 0.050 0.330 3622 Planarity : 0.006 0.068 4062 Dihedral : 12.819 175.019 3457 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.91 % Favored : 86.05 % Rotamer: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.15), residues: 2832 helix: -0.82 (0.18), residues: 785 sheet: -1.87 (0.24), residues: 401 loop : -2.69 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 415 TYR 0.035 0.003 TYR B1034 PHE 0.030 0.003 PHE B 742 TRP 0.019 0.002 TRP B 510 HIS 0.013 0.002 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.25 (23856) covalent geometry : angle 0.80310 / 0.43 (32309) hydrogen bonds : bond 0.05309 / 3.62 ( 704) hydrogen bonds : angle 5.90932 / 4.11 ( 1964) metal coordination : bond 0.01145 / 0.80 ( 12) metal coordination : angle 7.01529 / 3.82 ( 6) Misc. bond : bond 0.01660 / 0.87 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 GLN cc_start: 0.6507 (mm-40) cc_final: 0.5636 (tm-30) REVERT: A 609 MET cc_start: 0.6708 (ptt) cc_final: 0.6422 (ptt) REVERT: A 631 MET cc_start: 0.1071 (mmm) cc_final: -0.0152 (mtp) REVERT: A 672 ASN cc_start: 0.4504 (t0) cc_final: 0.4234 (m110) REVERT: A 1006 MET cc_start: 0.7492 (mpp) cc_final: 0.7203 (mpp) REVERT: B 68 MET cc_start: 0.5472 (mpp) cc_final: 0.5054 (mmt) REVERT: B 305 ASN cc_start: 0.8542 (m-40) cc_final: 0.8258 (m110) REVERT: B 464 MET cc_start: 0.7929 (tmm) cc_final: 0.7601 (tmm) REVERT: B 501 ASP cc_start: 0.7107 (m-30) cc_final: 0.6148 (t0) REVERT: B 862 GLU cc_start: 0.3965 (tm-30) cc_final: 0.3217 (mp0) REVERT: B 1040 MET cc_start: 0.4314 (mtm) cc_final: 0.3941 (mtm) REVERT: C 83 MET cc_start: 0.7498 (mpp) cc_final: 0.7154 (mmm) REVERT: C 292 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7245 (mmmt) REVERT: F 72 ARG cc_start: 0.6644 (mtm110) cc_final: 0.5965 (ptt180) REVERT: I 4 MET cc_start: 0.5822 (mmm) cc_final: 0.5199 (mmm) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1439 time to fit residues: 49.2105 Evaluate side-chains 164 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 132 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 235 optimal weight: 0.3980 chunk 128 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 240 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 218 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 HIS A 431 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.106913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.087884 restraints weight = 112499.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.089382 restraints weight = 71524.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.090318 restraints weight = 52212.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.090769 restraints weight = 42697.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.091269 restraints weight = 38277.925| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23869 Z= 0.132 Angle : 0.662 12.473 32315 Z= 0.347 Chirality : 0.046 0.317 3622 Planarity : 0.005 0.080 4062 Dihedral : 12.526 176.173 3457 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.42 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.15), residues: 2832 helix: -0.37 (0.18), residues: 787 sheet: -1.78 (0.24), residues: 411 loop : -2.46 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 40 TYR 0.021 0.002 TYR H 91 PHE 0.022 0.001 PHE B 321 TRP 0.020 0.002 TRP B 113 HIS 0.019 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (23856) covalent geometry : angle 0.65684 / 0.35 (32309) hydrogen bonds : bond 0.04030 / 2.73 ( 704) hydrogen bonds : angle 5.43179 / 3.77 ( 1964) metal coordination : bond 0.00761 / 0.52 ( 12) metal coordination : angle 6.00386 / 3.47 ( 6) Misc. bond : bond 0.00170 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8111 (mp0) cc_final: 0.7606 (tt0) REVERT: A 486 GLN cc_start: 0.6506 (mm-40) cc_final: 0.5627 (tm-30) REVERT: A 609 MET cc_start: 0.6383 (ptt) cc_final: 0.6140 (ptt) REVERT: A 631 MET cc_start: 0.1169 (mmm) cc_final: 0.0022 (mtp) REVERT: A 672 ASN cc_start: 0.4474 (t0) cc_final: 0.4266 (m110) REVERT: A 1141 LYS cc_start: 0.7316 (mptt) cc_final: 0.6638 (mmtt) REVERT: B 305 ASN cc_start: 0.8473 (m-40) cc_final: 0.8184 (m110) REVERT: B 501 ASP cc_start: 0.7155 (m-30) cc_final: 0.6191 (t0) REVERT: B 862 GLU cc_start: 0.3625 (tm-30) cc_final: 0.2999 (mp0) REVERT: B 1040 MET cc_start: 0.4419 (mtm) cc_final: 0.4175 (mtm) REVERT: C 83 MET cc_start: 0.7190 (mpp) cc_final: 0.6966 (mmm) REVERT: C 292 LYS cc_start: 0.7834 (mmmt) cc_final: 0.6810 (mmtt) REVERT: H 111 GLU cc_start: 0.3819 (mm-30) cc_final: 0.2804 (mm-30) REVERT: I 4 MET cc_start: 0.5829 (mmm) cc_final: 0.5190 (mmm) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1463 time to fit residues: 50.7632 Evaluate side-chains 170 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 14 optimal weight: 2.9990 chunk 208 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 87 optimal weight: 0.3980 chunk 283 optimal weight: 40.0000 chunk 150 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 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 = 0.4350 r_free = 0.4350 target = 0.106438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.088352 restraints weight = 113776.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.090015 restraints weight = 74340.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.090307 restraints weight = 50427.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.090659 restraints weight = 44222.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.090659 restraints weight = 40433.854| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23869 Z= 0.143 Angle : 0.658 10.321 32315 Z= 0.345 Chirality : 0.046 0.327 3622 Planarity : 0.004 0.060 4062 Dihedral : 12.472 176.830 3457 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.72 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.15), residues: 2832 helix: -0.26 (0.19), residues: 794 sheet: -1.77 (0.24), residues: 393 loop : -2.41 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG H 124 TYR 0.017 0.002 TYR B1034 PHE 0.023 0.002 PHE B 321 TRP 0.016 0.001 TRP B 113 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (23856) covalent geometry : angle 0.65369 / 0.34 (32309) hydrogen bonds : bond 0.03990 / 2.68 ( 704) hydrogen bonds : angle 5.34756 / 3.71 ( 1964) metal coordination : bond 0.00597 / 0.40 ( 12) metal coordination : angle 5.26932 / 3.02 ( 6) Misc. bond : bond 0.00335 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8000 (mp0) cc_final: 0.7777 (tt0) REVERT: A 486 GLN cc_start: 0.6651 (mm-40) cc_final: 0.5740 (tm-30) REVERT: A 609 MET cc_start: 0.6431 (ptt) cc_final: 0.6146 (ptt) REVERT: A 631 MET cc_start: 0.0446 (mmm) cc_final: -0.0519 (mtp) REVERT: A 672 ASN cc_start: 0.4474 (t0) cc_final: 0.4229 (m110) REVERT: B 121 THR cc_start: 0.8090 (m) cc_final: 0.7748 (p) REVERT: B 305 ASN cc_start: 0.8487 (m-40) cc_final: 0.8164 (m110) REVERT: B 464 MET cc_start: 0.7620 (tmm) cc_final: 0.6959 (tmm) REVERT: B 501 ASP cc_start: 0.7021 (m-30) cc_final: 0.6004 (t0) REVERT: B 862 GLU cc_start: 0.3858 (tm-30) cc_final: 0.3202 (mp0) REVERT: C 83 MET cc_start: 0.7266 (mpp) cc_final: 0.7029 (mmm) REVERT: C 292 LYS cc_start: 0.7874 (mmmt) cc_final: 0.7295 (mmmt) REVERT: F 72 ARG cc_start: 0.6572 (mtm110) cc_final: 0.5670 (ptt180) REVERT: I 4 MET cc_start: 0.5697 (mmm) cc_final: 0.5110 (mmm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1429 time to fit residues: 48.0863 Evaluate side-chains 172 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 165 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 153 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.106735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.088461 restraints weight = 116128.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.089798 restraints weight = 77988.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.090165 restraints weight = 54595.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.090435 restraints weight = 50697.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.090498 restraints weight = 46189.469| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23869 Z= 0.134 Angle : 0.648 10.693 32315 Z= 0.339 Chirality : 0.046 0.325 3622 Planarity : 0.004 0.056 4062 Dihedral : 12.397 177.083 3457 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.81 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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 are not related in a simple way. whole: -2.38 (0.15), residues: 2832 helix: -0.19 (0.19), residues: 795 sheet: -1.72 (0.24), residues: 391 loop : -2.36 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 59 TYR 0.028 0.002 TYR H 91 PHE 0.021 0.001 PHE B 321 TRP 0.044 0.002 TRP C 180 HIS 0.015 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (23856) covalent geometry : angle 0.64418 / 0.34 (32309) hydrogen bonds : bond 0.03815 / 2.56 ( 704) hydrogen bonds : angle 5.21699 / 3.62 ( 1964) metal coordination : bond 0.00440 / 0.28 ( 12) metal coordination : angle 5.07299 / 2.92 ( 6) Misc. bond : bond 0.00037 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8355 (mp0) cc_final: 0.7699 (tt0) REVERT: A 486 GLN cc_start: 0.6872 (mm-40) cc_final: 0.5906 (tm-30) REVERT: A 499 LEU cc_start: 0.8478 (mt) cc_final: 0.8183 (mt) REVERT: A 609 MET cc_start: 0.6221 (ptt) cc_final: 0.5940 (ptt) REVERT: A 631 MET cc_start: 0.0248 (mmm) cc_final: -0.0648 (mtp) REVERT: A 672 ASN cc_start: 0.4583 (t0) cc_final: 0.4303 (m110) REVERT: B 120 MET cc_start: 0.4269 (mmp) cc_final: 0.3456 (mtp) REVERT: B 305 ASN cc_start: 0.8477 (m-40) cc_final: 0.8148 (m110) REVERT: B 464 MET cc_start: 0.7624 (tmm) cc_final: 0.6936 (tmm) REVERT: B 501 ASP cc_start: 0.7052 (m-30) cc_final: 0.5994 (t0) REVERT: B 862 GLU cc_start: 0.3861 (tm-30) cc_final: 0.3182 (mp0) REVERT: C 83 MET cc_start: 0.7268 (mpp) cc_final: 0.7050 (mmm) REVERT: C 292 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7348 (mmmt) REVERT: F 72 ARG cc_start: 0.6443 (mtm110) cc_final: 0.5643 (ptt180) REVERT: F 88 MET cc_start: 0.7478 (mmm) cc_final: 0.7108 (mmm) REVERT: I 4 MET cc_start: 0.5473 (mmm) cc_final: 0.4900 (mmm) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1331 time to fit residues: 44.9575 Evaluate side-chains 172 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 96 optimal weight: 0.1980 chunk 255 optimal weight: 4.9990 chunk 268 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 261 optimal weight: 0.3980 chunk 15 optimal weight: 0.0570 chunk 235 optimal weight: 7.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 705 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 410 HIS ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1016 ASN E 42 ASN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.108234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.090109 restraints weight = 116167.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.091274 restraints weight = 76677.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.091876 restraints weight = 53434.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.092017 restraints weight = 48838.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.092114 restraints weight = 44199.079| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23869 Z= 0.114 Angle : 0.631 10.121 32315 Z= 0.327 Chirality : 0.044 0.324 3622 Planarity : 0.004 0.050 4062 Dihedral : 12.259 178.119 3457 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.89 % Favored : 90.08 % Rotamer: Outliers : 0.04 % Allowed : 1.38 % Favored : 98.58 % 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 are not related in a simple way. whole: -2.18 (0.16), residues: 2832 helix: -0.00 (0.19), residues: 797 sheet: -1.65 (0.25), residues: 403 loop : -2.23 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 797 TYR 0.019 0.001 TYR H 91 PHE 0.020 0.001 PHE A 779 TRP 0.028 0.001 TRP C 180 HIS 0.005 0.001 HIS A1147 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (23856) covalent geometry : angle 0.62677 / 0.33 (32309) hydrogen bonds : bond 0.03381 / 2.29 ( 704) hydrogen bonds : angle 4.97712 / 3.44 ( 1964) metal coordination : bond 0.00758 / 0.52 ( 12) metal coordination : angle 5.26477 / 3.06 ( 6) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 215 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8202 (mp0) cc_final: 0.7725 (tt0) REVERT: A 486 GLN cc_start: 0.6866 (mm-40) cc_final: 0.5799 (tm-30) REVERT: A 499 LEU cc_start: 0.8428 (mt) cc_final: 0.8159 (mt) REVERT: A 609 MET cc_start: 0.6137 (ptt) cc_final: 0.5784 (ptt) REVERT: A 612 LEU cc_start: 0.8232 (pt) cc_final: 0.7531 (tp) REVERT: A 631 MET cc_start: 0.0414 (mmm) cc_final: -0.0286 (mmt) REVERT: A 672 ASN cc_start: 0.4651 (t0) cc_final: 0.4358 (m110) REVERT: A 723 GLN cc_start: 0.7886 (pt0) cc_final: 0.7389 (pt0) REVERT: A 779 PHE cc_start: 0.7300 (t80) cc_final: 0.6067 (t80) REVERT: A 783 MET cc_start: 0.4826 (tpp) cc_final: 0.3255 (ptm) REVERT: A 1141 LYS cc_start: 0.7169 (mptt) cc_final: 0.6548 (mmtt) REVERT: A 1155 MET cc_start: 0.3441 (ptt) cc_final: 0.3110 (ptt) REVERT: B 120 MET cc_start: 0.4410 (mmp) cc_final: 0.3102 (ptp) REVERT: B 305 ASN cc_start: 0.8460 (m-40) cc_final: 0.8136 (m-40) REVERT: B 464 MET cc_start: 0.7685 (tmm) cc_final: 0.7132 (tmm) REVERT: B 501 ASP cc_start: 0.7102 (m-30) cc_final: 0.5985 (t0) REVERT: B 862 GLU cc_start: 0.3694 (tm-30) cc_final: 0.3020 (mp0) REVERT: C 83 MET cc_start: 0.7261 (mpp) cc_final: 0.6984 (mmm) REVERT: C 292 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7337 (mmmt) REVERT: F 72 ARG cc_start: 0.6387 (mtm110) cc_final: 0.5590 (ptt180) REVERT: F 88 MET cc_start: 0.7690 (mmm) cc_final: 0.7351 (mmm) REVERT: I 4 MET cc_start: 0.5686 (mmm) cc_final: 0.5076 (mmm) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.1325 time to fit residues: 46.6965 Evaluate side-chains 171 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 212 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 163 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.105841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.087853 restraints weight = 117829.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.088919 restraints weight = 81507.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.089127 restraints weight = 61327.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.089392 restraints weight = 60477.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.089396 restraints weight = 52275.811| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23869 Z= 0.180 Angle : 0.705 10.949 32315 Z= 0.368 Chirality : 0.047 0.337 3622 Planarity : 0.005 0.054 4062 Dihedral : 12.413 177.793 3457 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.83 % Favored : 88.14 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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 are not related in a simple way. whole: -2.39 (0.15), residues: 2832 helix: -0.19 (0.18), residues: 803 sheet: -1.70 (0.25), residues: 381 loop : -2.38 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 395 TYR 0.033 0.002 TYR K 69 PHE 0.026 0.002 PHE C 268 TRP 0.028 0.002 TRP C 180 HIS 0.008 0.002 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (23856) covalent geometry : angle 0.70162 / 0.37 (32309) hydrogen bonds : bond 0.04135 / 2.78 ( 704) hydrogen bonds : angle 5.20898 / 3.61 ( 1964) metal coordination : bond 0.00522 / 0.35 ( 12) metal coordination : angle 5.27080 / 2.93 ( 6) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8168 (mp0) cc_final: 0.7623 (tt0) REVERT: A 609 MET cc_start: 0.6280 (ptt) cc_final: 0.5978 (ptt) REVERT: A 631 MET cc_start: 0.0227 (mmm) cc_final: -0.0242 (mmt) REVERT: A 672 ASN cc_start: 0.4616 (t0) cc_final: 0.4237 (m110) REVERT: B 305 ASN cc_start: 0.8608 (m-40) cc_final: 0.8299 (m110) REVERT: B 464 MET cc_start: 0.7499 (tmm) cc_final: 0.6803 (tmm) REVERT: B 501 ASP cc_start: 0.6979 (m-30) cc_final: 0.5938 (t0) REVERT: B 862 GLU cc_start: 0.3984 (tm-30) cc_final: 0.3107 (mm-30) REVERT: C 83 MET cc_start: 0.7258 (mpp) cc_final: 0.7056 (mmm) REVERT: C 292 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7273 (mmmt) REVERT: F 72 ARG cc_start: 0.6700 (mtm110) cc_final: 0.5773 (ptt180) REVERT: F 88 MET cc_start: 0.7606 (mmm) cc_final: 0.7245 (mmm) REVERT: I 4 MET cc_start: 0.5498 (mmm) cc_final: 0.4934 (mmm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1387 time to fit residues: 46.9809 Evaluate side-chains 171 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 133 optimal weight: 0.0570 chunk 57 optimal weight: 8.9990 chunk 176 optimal weight: 0.0770 overall best weight: 2.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.106618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.088260 restraints weight = 117939.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.089798 restraints weight = 79192.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.090454 restraints weight = 52333.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.090597 restraints weight = 49910.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.090626 restraints weight = 43175.065| |-----------------------------------------------------------------------------| r_work (final): 0.3977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23869 Z= 0.138 Angle : 0.664 11.037 32315 Z= 0.345 Chirality : 0.046 0.329 3622 Planarity : 0.004 0.053 4062 Dihedral : 12.366 178.049 3457 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.66 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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 are not related in a simple way. whole: -2.27 (0.15), residues: 2832 helix: -0.04 (0.19), residues: 798 sheet: -1.79 (0.24), residues: 394 loop : -2.28 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 876 TYR 0.028 0.002 TYR K 69 PHE 0.022 0.001 PHE B 321 TRP 0.027 0.001 TRP C 180 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (23856) covalent geometry : angle 0.65983 / 0.34 (32309) hydrogen bonds : bond 0.03770 / 2.54 ( 704) hydrogen bonds : angle 5.08786 / 3.52 ( 1964) metal coordination : bond 0.00561 / 0.38 ( 12) metal coordination : angle 5.34297 / 3.04 ( 6) Misc. bond : bond 0.00043 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 471 GLU cc_start: 0.8245 (mp0) cc_final: 0.7717 (tt0) REVERT: A 499 LEU cc_start: 0.8472 (mt) cc_final: 0.8180 (mt) REVERT: A 609 MET cc_start: 0.6176 (ptt) cc_final: 0.5867 (ptt) REVERT: A 612 LEU cc_start: 0.8017 (pt) cc_final: 0.7468 (tp) REVERT: A 631 MET cc_start: 0.0026 (mmm) cc_final: -0.0628 (mtp) REVERT: A 672 ASN cc_start: 0.4645 (t0) cc_final: 0.4227 (m110) REVERT: B 120 MET cc_start: 0.3517 (mmm) cc_final: 0.3299 (mtm) REVERT: B 305 ASN cc_start: 0.8499 (m-40) cc_final: 0.8166 (m110) REVERT: B 464 MET cc_start: 0.7637 (tmm) cc_final: 0.6903 (tmm) REVERT: B 501 ASP cc_start: 0.7072 (m-30) cc_final: 0.5949 (t0) REVERT: B 862 GLU cc_start: 0.3693 (tm-30) cc_final: 0.2996 (mp0) REVERT: B 1040 MET cc_start: 0.5181 (mtp) cc_final: 0.4901 (mtm) REVERT: C 83 MET cc_start: 0.7335 (mpp) cc_final: 0.7055 (mmm) REVERT: C 292 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7347 (mmmt) REVERT: F 72 ARG cc_start: 0.6628 (mtm110) cc_final: 0.5788 (ptt180) REVERT: F 88 MET cc_start: 0.7739 (mmm) cc_final: 0.7359 (mmm) REVERT: I 4 MET cc_start: 0.5564 (mmm) cc_final: 0.4973 (mmm) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.1465 time to fit residues: 49.6390 Evaluate side-chains 173 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 64 optimal weight: 20.0000 chunk 284 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 0.3980 chunk 204 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 255 optimal weight: 4.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 940 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 118 GLN B 163 GLN ** B 410 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 780 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.104440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.086494 restraints weight = 118455.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.087899 restraints weight = 80617.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.087898 restraints weight = 54913.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.088227 restraints weight = 53019.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.088443 restraints weight = 47911.820| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6288 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 23869 Z= 0.216 Angle : 0.763 11.835 32315 Z= 0.399 Chirality : 0.049 0.344 3622 Planarity : 0.006 0.059 4062 Dihedral : 12.629 177.502 3457 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 13.21 % Favored : 86.76 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 are not related in a simple way. whole: -2.65 (0.15), residues: 2832 helix: -0.46 (0.18), residues: 800 sheet: -1.86 (0.25), residues: 375 loop : -2.51 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 43 TYR 0.032 0.002 TYR H 91 PHE 0.030 0.002 PHE C 107 TRP 0.024 0.002 TRP C 180 HIS 0.015 0.002 HIS B 634 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (23856) covalent geometry : angle 0.75827 / 0.40 (32309) hydrogen bonds : bond 0.04620 / 3.11 ( 704) hydrogen bonds : angle 5.46023 / 3.79 ( 1964) metal coordination : bond 0.00593 / 0.39 ( 12) metal coordination : angle 5.94313 / 3.29 ( 6) Misc. bond : bond 0.00040 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3647.22 seconds wall clock time: 64 minutes 2.10 seconds (3842.10 seconds total)