Starting phenix.real_space_refine on Mon May 4 20:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k19_61969/05_2026/9k19_61969.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k19_61969/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k19_61969/05_2026/9k19_61969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k19_61969/05_2026/9k19_61969.map" model { file = "/net/cci-nas-00/data/ceres_data/9k19_61969/05_2026/9k19_61969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k19_61969/05_2026/9k19_61969.cif" } 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-2.1rc2-6044/lib/python3.9/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: 5.40, per 1000 atoms: 0.23 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.79 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: 4.93 Time building geometry restraints manager: 2.57 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' DG N 12 " pdb=" N9 DG N 12 " ideal model delta sigma weight residual 1.460 1.398 0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" C1' DG N 17 " pdb=" N9 DG N 17 " ideal model delta sigma weight residual 1.460 1.404 0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" CA ARG B 487 " pdb=" CB ARG B 487 " ideal model delta sigma weight residual 1.527 1.462 0.065 2.48e-02 1.63e+03 6.95e+00 bond pdb=" N LYS H 145 " pdb=" CA LYS H 145 " ideal model delta sigma weight residual 1.458 1.507 -0.049 1.90e-02 2.77e+03 6.59e+00 bond pdb=" C1' DC N 13 " pdb=" N1 DC N 13 " ideal model delta sigma weight residual 1.490 1.553 -0.063 3.00e-02 1.11e+03 4.47e+00 ... (remaining 23851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 31311 2.21 - 4.42: 892 4.42 - 6.62: 88 6.62 - 8.83: 16 8.83 - 11.04: 2 Bond angle restraints: 32309 Sorted by residual: 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=" N VAL A 666 " pdb=" CA VAL A 666 " pdb=" C VAL A 666 " ideal model delta sigma weight residual 112.96 108.62 4.34 1.00e+00 1.00e+00 1.88e+01 angle pdb=" N ILE B 335 " pdb=" CA ILE B 335 " pdb=" C ILE B 335 " ideal model delta sigma weight residual 111.67 107.56 4.11 9.50e-01 1.11e+00 1.87e+01 angle pdb=" C THR B 338 " pdb=" N LYS B 339 " pdb=" CA LYS B 339 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+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: 2658 0.053 - 0.106: 824 0.106 - 0.160: 127 0.160 - 0.213: 11 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: 2.320 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5790 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= 0.352 Angle : 0.931 32.549 32315 Z= 0.508 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 covalent geometry : bond 0.00515 (23856) covalent geometry : angle 0.88408 (32309) hydrogen bonds : bond 0.16052 ( 704) hydrogen bonds : angle 7.09565 ( 1964) metal coordination : bond 0.31361 ( 12) metal coordination : angle 21.45597 ( 6) Misc. bond : bond 0.13756 ( 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 : 0.871 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: 0.1541 time to fit residues: 56.2194 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 : 0.766 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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** C 149 GLN E 182 GLN I 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.106910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.088454 restraints weight = 115477.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.089309 restraints weight = 85436.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.090161 restraints weight = 59244.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.090294 restraints weight = 50513.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.090380 restraints weight = 46030.111| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23869 Z= 0.154 Angle : 0.677 14.076 32315 Z= 0.356 Chirality : 0.045 0.227 3622 Planarity : 0.005 0.062 4062 Dihedral : 12.701 177.472 3457 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.41 % Favored : 88.56 % Rotamer: Outliers : 0.08 % Allowed : 4.90 % Favored : 95.02 % 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: -2.65 (0.15), residues: 2832 helix: -0.50 (0.18), residues: 778 sheet: -1.82 (0.25), residues: 388 loop : -2.48 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1019 TYR 0.016 0.002 TYR A1166 PHE 0.017 0.002 PHE B 321 TRP 0.020 0.002 TRP C 180 HIS 0.008 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00341 (23856) covalent geometry : angle 0.66880 (32309) hydrogen bonds : bond 0.04474 ( 704) hydrogen bonds : angle 5.66969 ( 1964) metal coordination : bond 0.01069 ( 12) metal coordination : angle 7.53320 ( 6) Misc. bond : bond 0.00822 ( 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 210 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LYS cc_start: 0.6952 (mptt) cc_final: 0.6737 (mmpt) REVERT: A 609 MET cc_start: 0.6663 (ptt) cc_final: 0.6409 (ptt) REVERT: A 631 MET cc_start: 0.0982 (mmm) cc_final: -0.0170 (mtp) REVERT: A 1006 MET cc_start: 0.7444 (mpp) cc_final: 0.7234 (mpp) REVERT: A 1088 TRP cc_start: 0.7596 (t-100) cc_final: 0.7222 (t-100) REVERT: A 1141 LYS cc_start: 0.6731 (mppt) cc_final: 0.6277 (tptp) REVERT: B 68 MET cc_start: 0.5357 (mpp) cc_final: 0.5108 (mmm) REVERT: B 251 ASN cc_start: 0.4626 (m-40) cc_final: 0.4387 (m-40) REVERT: B 305 ASN cc_start: 0.8561 (m-40) cc_final: 0.8244 (m110) REVERT: B 501 ASP cc_start: 0.7029 (m-30) cc_final: 0.6074 (t0) REVERT: B 1023 MET cc_start: 0.6052 (mmp) cc_final: 0.5778 (mmp) REVERT: B 1040 MET cc_start: 0.4064 (mtm) cc_final: 0.3738 (mtm) REVERT: C 83 MET cc_start: 0.7503 (mpp) cc_final: 0.7016 (mmm) REVERT: C 292 LYS cc_start: 0.7755 (mmmt) cc_final: 0.7283 (mmmt) REVERT: F 72 ARG cc_start: 0.6258 (mtm110) cc_final: 0.5757 (ptt180) REVERT: I 4 MET cc_start: 0.5923 (mmm) cc_final: 0.5265 (mmm) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.1466 time to fit residues: 50.0066 Evaluate side-chains 175 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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: 0.2980 chunk 29 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 280 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 239 optimal weight: 9.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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** I 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.106478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.088368 restraints weight = 115107.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.089258 restraints weight = 78976.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.089734 restraints weight = 55930.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.089977 restraints weight = 51555.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.089951 restraints weight = 46993.329| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23869 Z= 0.166 Angle : 0.672 10.146 32315 Z= 0.354 Chirality : 0.045 0.220 3622 Planarity : 0.005 0.064 4062 Dihedral : 12.598 178.162 3457 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.62 % Favored : 88.35 % Rotamer: Outliers : 0.04 % Allowed : 5.30 % Favored : 94.66 % 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: -2.60 (0.15), residues: 2832 helix: -0.43 (0.18), residues: 789 sheet: -1.71 (0.25), residues: 395 loop : -2.50 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 20 TYR 0.028 0.002 TYR H 91 PHE 0.020 0.002 PHE C 268 TRP 0.012 0.001 TRP B 113 HIS 0.008 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00365 (23856) covalent geometry : angle 0.66756 (32309) hydrogen bonds : bond 0.04353 ( 704) hydrogen bonds : angle 5.51406 ( 1964) metal coordination : bond 0.00755 ( 12) metal coordination : angle 5.88955 ( 6) Misc. bond : bond 0.00031 ( 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 210 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 LYS cc_start: 0.6996 (mptt) cc_final: 0.6771 (mmpt) REVERT: A 503 MET cc_start: 0.7502 (tpt) cc_final: 0.7283 (tpt) REVERT: A 609 MET cc_start: 0.6544 (ptt) cc_final: 0.6309 (ptt) REVERT: A 631 MET cc_start: 0.0840 (mmm) cc_final: -0.0170 (mtp) REVERT: A 672 ASN cc_start: 0.3985 (t0) cc_final: 0.3715 (m110) REVERT: B 68 MET cc_start: 0.5233 (mpp) cc_final: 0.4953 (mmm) REVERT: B 251 ASN cc_start: 0.4740 (m-40) cc_final: 0.4534 (m-40) REVERT: B 305 ASN cc_start: 0.8499 (m-40) cc_final: 0.8173 (m110) REVERT: B 501 ASP cc_start: 0.7032 (m-30) cc_final: 0.6074 (t0) REVERT: B 1023 MET cc_start: 0.5451 (mmp) cc_final: 0.5228 (mmp) REVERT: B 1040 MET cc_start: 0.4060 (mtm) cc_final: 0.3771 (mtm) REVERT: C 83 MET cc_start: 0.7596 (mpp) cc_final: 0.7062 (mmm) REVERT: C 292 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7300 (mmmt) REVERT: I 4 MET cc_start: 0.5903 (mmm) cc_final: 0.5244 (mmm) REVERT: J 48 MET cc_start: 0.6353 (mmm) cc_final: 0.6014 (mmt) outliers start: 1 outliers final: 1 residues processed: 210 average time/residue: 0.1410 time to fit residues: 48.9368 Evaluate side-chains 172 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 171 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 10.0000 chunk 259 optimal weight: 9.9990 chunk 268 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 200 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 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 163 GLN ** B 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 ASN ** K 40 HIS ** 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 = 0.4336 r_free = 0.4336 target = 0.105775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.086641 restraints weight = 116886.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.088129 restraints weight = 73255.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.089017 restraints weight = 53445.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.089672 restraints weight = 43798.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.090077 restraints weight = 38421.805| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23869 Z= 0.196 Angle : 0.715 10.095 32315 Z= 0.375 Chirality : 0.047 0.253 3622 Planarity : 0.005 0.059 4062 Dihedral : 12.621 177.945 3457 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.39 % Favored : 87.57 % Rotamer: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % 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: -2.74 (0.15), residues: 2832 helix: -0.54 (0.18), residues: 785 sheet: -1.85 (0.24), residues: 407 loop : -2.57 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1060 TYR 0.031 0.002 TYR B1034 PHE 0.026 0.002 PHE B 321 TRP 0.014 0.002 TRP B 510 HIS 0.010 0.002 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00447 (23856) covalent geometry : angle 0.70976 (32309) hydrogen bonds : bond 0.04568 ( 704) hydrogen bonds : angle 5.65908 ( 1964) metal coordination : bond 0.00563 ( 12) metal coordination : angle 6.29962 ( 6) Misc. bond : bond 0.00351 ( 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 212 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 MET cc_start: 0.7703 (tpt) cc_final: 0.7405 (tpt) REVERT: A 609 MET cc_start: 0.6577 (ptt) cc_final: 0.6333 (ptt) REVERT: A 631 MET cc_start: 0.0960 (mmm) cc_final: -0.0213 (mtp) REVERT: A 672 ASN cc_start: 0.4578 (t0) cc_final: 0.4320 (m110) REVERT: A 783 MET cc_start: 0.5811 (tpt) cc_final: 0.5597 (tpp) REVERT: B 68 MET cc_start: 0.5205 (mpp) cc_final: 0.4961 (mmm) REVERT: B 305 ASN cc_start: 0.8534 (m-40) cc_final: 0.8216 (m110) REVERT: B 501 ASP cc_start: 0.7081 (m-30) cc_final: 0.6047 (t0) REVERT: B 1040 MET cc_start: 0.4279 (mtm) cc_final: 0.3980 (mtm) REVERT: C 83 MET cc_start: 0.7522 (mpp) cc_final: 0.7181 (mmm) REVERT: C 292 LYS cc_start: 0.7899 (mmmt) cc_final: 0.7276 (mmmt) REVERT: F 88 MET cc_start: 0.7622 (mmm) cc_final: 0.7278 (mmm) REVERT: I 4 MET cc_start: 0.5659 (mmm) cc_final: 0.5021 (mmm) REVERT: J 48 MET cc_start: 0.6393 (mmm) cc_final: 0.5993 (mmt) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1550 time to fit residues: 52.6137 Evaluate side-chains 165 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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: 0.0020 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 chunk 234 optimal weight: 0.0270 chunk 240 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 218 optimal weight: 0.0870 chunk 35 optimal weight: 10.0000 overall best weight: 0.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 HIS A 431 HIS ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 51 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 GLN ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.107843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.089828 restraints weight = 114364.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.091142 restraints weight = 74351.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.091605 restraints weight = 50136.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.091801 restraints weight = 48157.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.091841 restraints weight = 42485.858| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23869 Z= 0.120 Angle : 0.631 12.514 32315 Z= 0.327 Chirality : 0.044 0.236 3622 Planarity : 0.004 0.072 4062 Dihedral : 12.334 179.939 3457 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.43 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -2.35 (0.15), residues: 2832 helix: -0.16 (0.19), residues: 794 sheet: -1.72 (0.24), residues: 406 loop : -2.33 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 80 TYR 0.026 0.001 TYR H 76 PHE 0.045 0.001 PHE H 40 TRP 0.022 0.001 TRP B 113 HIS 0.016 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00248 (23856) covalent geometry : angle 0.62486 (32309) hydrogen bonds : bond 0.03555 ( 704) hydrogen bonds : angle 5.17636 ( 1964) metal coordination : bond 0.01517 ( 12) metal coordination : angle 6.24247 ( 6) Misc. bond : bond 0.00065 ( 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 221 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.8361 (mt) cc_final: 0.8064 (mt) REVERT: A 503 MET cc_start: 0.7394 (tpt) cc_final: 0.7134 (tpt) REVERT: A 609 MET cc_start: 0.6269 (ptt) cc_final: 0.5902 (ptt) REVERT: A 612 LEU cc_start: 0.8180 (pt) cc_final: 0.7620 (tp) REVERT: A 631 MET cc_start: 0.0710 (mmm) cc_final: -0.0287 (mtp) REVERT: A 672 ASN cc_start: 0.4624 (t0) cc_final: 0.4349 (m110) REVERT: B 305 ASN cc_start: 0.8443 (m-40) cc_final: 0.8137 (m110) REVERT: B 464 MET cc_start: 0.7399 (tmm) cc_final: 0.6760 (tmm) REVERT: B 501 ASP cc_start: 0.7069 (m-30) cc_final: 0.6090 (t0) REVERT: C 83 MET cc_start: 0.7127 (mpp) cc_final: 0.6903 (mmm) REVERT: C 292 LYS cc_start: 0.7807 (mmmt) cc_final: 0.7222 (mmmt) REVERT: H 39 MET cc_start: 0.5187 (mmm) cc_final: 0.4377 (mmm) REVERT: I 4 MET cc_start: 0.5729 (mmm) cc_final: 0.5093 (mmm) REVERT: J 48 MET cc_start: 0.5985 (mmm) cc_final: 0.5708 (mmm) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1433 time to fit residues: 51.5340 Evaluate side-chains 175 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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: 4.9990 chunk 208 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 87 optimal weight: 0.0170 chunk 283 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 250 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 GLN ** 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** 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 = 0.4330 r_free = 0.4330 target = 0.105611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.086465 restraints weight = 115019.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.087960 restraints weight = 72052.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.088860 restraints weight = 52387.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.089527 restraints weight = 42770.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.089782 restraints weight = 37516.252| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23869 Z= 0.186 Angle : 0.704 11.948 32315 Z= 0.367 Chirality : 0.047 0.239 3622 Planarity : 0.005 0.061 4062 Dihedral : 12.465 179.380 3457 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.25 % Favored : 87.71 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -2.50 (0.15), residues: 2832 helix: -0.32 (0.18), residues: 799 sheet: -1.78 (0.24), residues: 393 loop : -2.42 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 797 TYR 0.025 0.002 TYR B1034 PHE 0.027 0.002 PHE C 268 TRP 0.036 0.002 TRP C 180 HIS 0.011 0.002 HIS C 177 Details of bonding type rmsd covalent geometry : bond 0.00423 (23856) covalent geometry : angle 0.69898 (32309) hydrogen bonds : bond 0.04243 ( 704) hydrogen bonds : angle 5.39278 ( 1964) metal coordination : bond 0.00663 ( 12) metal coordination : angle 6.20438 ( 6) Misc. bond : bond 0.00067 ( 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 202 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.967 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 503 MET cc_start: 0.7712 (tpt) cc_final: 0.7408 (tpt) REVERT: A 609 MET cc_start: 0.6475 (ptt) cc_final: 0.6216 (ptt) REVERT: A 631 MET cc_start: 0.0553 (mmm) cc_final: -0.0455 (mtp) REVERT: A 672 ASN cc_start: 0.4677 (t0) cc_final: 0.4373 (m110) REVERT: B 305 ASN cc_start: 0.8536 (m-40) cc_final: 0.8232 (m110) REVERT: B 501 ASP cc_start: 0.7157 (m-30) cc_final: 0.6104 (t0) REVERT: C 83 MET cc_start: 0.7309 (mpp) cc_final: 0.7101 (mmm) REVERT: C 292 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7274 (mmmt) REVERT: F 88 MET cc_start: 0.7594 (mmm) cc_final: 0.7255 (mmm) REVERT: H 39 MET cc_start: 0.5665 (mmm) cc_final: 0.4929 (mmm) REVERT: I 4 MET cc_start: 0.5146 (mmm) cc_final: 0.4612 (mmm) REVERT: J 48 MET cc_start: 0.6481 (mmm) cc_final: 0.6049 (mmt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1437 time to fit residues: 47.8090 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 : 0.818 ------------------------------------------------------------------------------- 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: 5.9990 chunk 151 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 259 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 201 optimal weight: 0.6980 chunk 144 optimal weight: 8.9990 chunk 153 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 922 GLN ** 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** ** C 177 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.106317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.088346 restraints weight = 116517.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.089627 restraints weight = 77790.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.090005 restraints weight = 54594.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.090228 restraints weight = 49083.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.090261 restraints weight = 44952.163| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6192 moved from start: 0.2451 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= 0.142 Angle : 0.655 10.846 32315 Z= 0.341 Chirality : 0.045 0.232 3622 Planarity : 0.004 0.059 4062 Dihedral : 12.382 179.546 3457 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.59 % Favored : 89.37 % 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: -2.35 (0.15), residues: 2832 helix: -0.13 (0.19), residues: 795 sheet: -1.73 (0.25), residues: 394 loop : -2.35 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 70 TYR 0.025 0.002 TYR H 91 PHE 0.021 0.002 PHE B 321 TRP 0.025 0.001 TRP C 180 HIS 0.006 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00315 (23856) covalent geometry : angle 0.65117 (32309) hydrogen bonds : bond 0.03822 ( 704) hydrogen bonds : angle 5.19712 ( 1964) metal coordination : bond 0.00645 ( 12) metal coordination : angle 5.46568 ( 6) Misc. bond : bond 0.00035 ( 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 215 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.901 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 499 LEU cc_start: 0.8518 (mt) cc_final: 0.8246 (mt) REVERT: A 503 MET cc_start: 0.7770 (tpt) cc_final: 0.7467 (tpt) REVERT: A 609 MET cc_start: 0.6354 (ptt) cc_final: 0.6114 (ptt) REVERT: A 631 MET cc_start: -0.0100 (mmm) cc_final: -0.0657 (mtp) REVERT: A 672 ASN cc_start: 0.4683 (t0) cc_final: 0.4303 (m110) REVERT: B 68 MET cc_start: 0.5110 (mpp) cc_final: 0.4845 (mmt) REVERT: B 305 ASN cc_start: 0.8472 (m-40) cc_final: 0.8147 (m110) REVERT: B 464 MET cc_start: 0.7620 (tmm) cc_final: 0.6854 (tmm) REVERT: B 501 ASP cc_start: 0.7079 (m-30) cc_final: 0.6029 (t0) REVERT: B 862 GLU cc_start: 0.3834 (tm-30) cc_final: 0.3096 (mp0) REVERT: B 1023 MET cc_start: 0.5424 (mmp) cc_final: 0.5064 (mmp) REVERT: C 83 MET cc_start: 0.7304 (mpp) cc_final: 0.7080 (mmm) REVERT: C 292 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7289 (mmmt) REVERT: F 88 MET cc_start: 0.7653 (mmm) cc_final: 0.7317 (mmm) REVERT: H 39 MET cc_start: 0.5829 (mmm) cc_final: 0.4919 (mmm) REVERT: I 4 MET cc_start: 0.5106 (mmm) cc_final: 0.4643 (mmm) REVERT: J 48 MET cc_start: 0.6383 (mmm) cc_final: 0.5970 (mmt) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1448 time to fit residues: 51.2163 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 : 0.908 ------------------------------------------------------------------------------- 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: 0.0010 chunk 255 optimal weight: 0.9990 chunk 268 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 178 optimal weight: 0.6980 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 235 optimal weight: 7.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 GLN ** B 114 HIS ** 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** I 105 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.108278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.090046 restraints weight = 116523.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.091460 restraints weight = 77528.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.091637 restraints weight = 51971.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.091970 restraints weight = 50701.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.092078 restraints weight = 45364.617| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23869 Z= 0.115 Angle : 0.622 11.627 32315 Z= 0.321 Chirality : 0.043 0.233 3622 Planarity : 0.004 0.053 4062 Dihedral : 12.213 177.268 3457 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.68 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -2.14 (0.16), residues: 2832 helix: 0.10 (0.19), residues: 798 sheet: -1.64 (0.25), residues: 397 loop : -2.24 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 797 TYR 0.027 0.001 TYR K 69 PHE 0.023 0.001 PHE B 742 TRP 0.026 0.001 TRP C 180 HIS 0.008 0.001 HIS H 42 Details of bonding type rmsd covalent geometry : bond 0.00243 (23856) covalent geometry : angle 0.61922 (32309) hydrogen bonds : bond 0.03313 ( 704) hydrogen bonds : angle 4.91094 ( 1964) metal coordination : bond 0.00762 ( 12) metal coordination : angle 4.63937 ( 6) Misc. bond : bond 0.00015 ( 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: 0 poor density : 216 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 MET cc_start: 0.6151 (ptt) cc_final: 0.5828 (ptt) REVERT: A 612 LEU cc_start: 0.8230 (pt) cc_final: 0.7563 (tp) REVERT: A 631 MET cc_start: 0.0370 (mmm) cc_final: -0.0143 (mmt) REVERT: A 672 ASN cc_start: 0.4783 (t0) cc_final: 0.4403 (m110) REVERT: A 1141 LYS cc_start: 0.7219 (mptt) cc_final: 0.6615 (mmtt) REVERT: B 68 MET cc_start: 0.4908 (mpp) cc_final: 0.4633 (mmt) REVERT: B 121 THR cc_start: 0.7846 (m) cc_final: 0.7549 (p) REVERT: B 305 ASN cc_start: 0.8442 (m-40) cc_final: 0.8120 (m110) REVERT: B 464 MET cc_start: 0.7608 (tmm) cc_final: 0.6914 (tmm) REVERT: B 501 ASP cc_start: 0.7073 (m-30) cc_final: 0.5930 (t0) REVERT: B 862 GLU cc_start: 0.3684 (tm-30) cc_final: 0.2991 (mp0) REVERT: B 1023 MET cc_start: 0.5657 (mmp) cc_final: 0.5207 (mmp) REVERT: C 83 MET cc_start: 0.7297 (mpp) cc_final: 0.6988 (mmm) REVERT: C 292 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7317 (mmmt) REVERT: F 65 MET cc_start: 0.5513 (tmm) cc_final: 0.5195 (tmm) REVERT: F 88 MET cc_start: 0.7816 (mmm) cc_final: 0.7511 (mmm) REVERT: H 39 MET cc_start: 0.5800 (mmm) cc_final: 0.4965 (mmm) REVERT: I 4 MET cc_start: 0.5054 (mmm) cc_final: 0.4603 (mmm) REVERT: I 21 GLU cc_start: 0.7157 (pm20) cc_final: 0.6896 (mm-30) REVERT: J 48 MET cc_start: 0.6194 (mmm) cc_final: 0.5782 (mmt) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1396 time to fit residues: 49.9556 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 : 0.908 ------------------------------------------------------------------------------- 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: 2.9990 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 124 optimal weight: 0.2980 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 219 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 177 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.105813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.087282 restraints weight = 115427.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.089161 restraints weight = 75213.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.089009 restraints weight = 51029.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.089521 restraints weight = 49687.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.089634 restraints weight = 42616.105| |-----------------------------------------------------------------------------| r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23869 Z= 0.167 Angle : 0.692 11.119 32315 Z= 0.359 Chirality : 0.046 0.227 3622 Planarity : 0.005 0.078 4062 Dihedral : 12.374 177.953 3457 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.72 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % 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: -0.06 (0.18), residues: 798 sheet: -1.66 (0.26), residues: 379 loop : -2.31 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 876 TYR 0.027 0.002 TYR H 91 PHE 0.025 0.002 PHE B 321 TRP 0.019 0.002 TRP C 180 HIS 0.009 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00378 (23856) covalent geometry : angle 0.68697 (32309) hydrogen bonds : bond 0.04033 ( 704) hydrogen bonds : angle 5.10880 ( 1964) metal coordination : bond 0.00666 ( 12) metal coordination : angle 5.90396 ( 6) Misc. bond : bond 0.00079 ( 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 202 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.889 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 503 MET cc_start: 0.7649 (tpt) cc_final: 0.7419 (tpt) REVERT: A 609 MET cc_start: 0.6295 (ptt) cc_final: 0.6046 (ptt) REVERT: A 631 MET cc_start: 0.0021 (mmm) cc_final: -0.0244 (mmt) REVERT: A 672 ASN cc_start: 0.4641 (t0) cc_final: 0.4236 (m110) REVERT: B 68 MET cc_start: 0.5105 (mpp) cc_final: 0.4839 (mmt) REVERT: B 305 ASN cc_start: 0.8615 (m-40) cc_final: 0.8276 (m110) REVERT: B 464 MET cc_start: 0.7775 (tmm) cc_final: 0.6993 (tmm) REVERT: B 501 ASP cc_start: 0.7081 (m-30) cc_final: 0.6022 (t0) REVERT: B 862 GLU cc_start: 0.4059 (tm-30) cc_final: 0.3294 (mp0) REVERT: B 1023 MET cc_start: 0.5256 (mmp) cc_final: 0.4972 (mmp) REVERT: C 83 MET cc_start: 0.7401 (mpp) cc_final: 0.7108 (mmm) REVERT: C 292 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7341 (mmmt) REVERT: E 201 ARG cc_start: 0.7791 (mpt180) cc_final: 0.5806 (mmt180) REVERT: F 88 MET cc_start: 0.7889 (mmm) cc_final: 0.7562 (mmm) REVERT: I 4 MET cc_start: 0.5092 (mmm) cc_final: 0.4535 (mmm) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1436 time to fit residues: 47.5650 Evaluate side-chains 169 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 9.9990 chunk 264 optimal weight: 7.9990 chunk 130 optimal weight: 0.0970 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 124 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 546 GLN ** 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 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** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.106286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.088855 restraints weight = 116835.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.089845 restraints weight = 78700.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.090531 restraints weight = 56447.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.090716 restraints weight = 49293.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.090742 restraints weight = 44040.109| |-----------------------------------------------------------------------------| r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.2884 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 : 0.651 10.918 32315 Z= 0.336 Chirality : 0.044 0.218 3622 Planarity : 0.004 0.067 4062 Dihedral : 12.302 176.432 3457 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.28 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.08 (0.19), residues: 797 sheet: -1.72 (0.26), residues: 365 loop : -2.26 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 18 TYR 0.031 0.001 TYR A 810 PHE 0.021 0.001 PHE B 321 TRP 0.020 0.002 TRP C 180 HIS 0.008 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00288 (23856) covalent geometry : angle 0.64687 (32309) hydrogen bonds : bond 0.03570 ( 704) hydrogen bonds : angle 4.93514 ( 1964) metal coordination : bond 0.00746 ( 12) metal coordination : angle 5.64561 ( 6) Misc. bond : bond 0.00033 ( 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 203 residues out of total 2533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 LEU cc_start: 0.8441 (mt) cc_final: 0.8197 (mt) REVERT: A 503 MET cc_start: 0.7382 (tpt) cc_final: 0.7157 (tpt) REVERT: A 609 MET cc_start: 0.6228 (ptt) cc_final: 0.5946 (ptt) REVERT: A 631 MET cc_start: 0.0235 (mmm) cc_final: -0.0377 (mmt) REVERT: A 672 ASN cc_start: 0.4613 (t0) cc_final: 0.4240 (m110) REVERT: B 68 MET cc_start: 0.5003 (mpp) cc_final: 0.4719 (mmt) REVERT: B 210 GLU cc_start: 0.6829 (mp0) cc_final: 0.6448 (mt-10) REVERT: B 305 ASN cc_start: 0.8449 (m-40) cc_final: 0.8152 (m110) REVERT: B 464 MET cc_start: 0.7509 (tmm) cc_final: 0.6801 (tmm) REVERT: B 501 ASP cc_start: 0.7105 (m-30) cc_final: 0.6252 (t70) REVERT: B 862 GLU cc_start: 0.3934 (tm-30) cc_final: 0.3142 (mp0) REVERT: B 1023 MET cc_start: 0.5664 (mmp) cc_final: 0.5358 (mmp) REVERT: C 83 MET cc_start: 0.7301 (mpp) cc_final: 0.7002 (mmm) REVERT: C 292 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7303 (mmmt) REVERT: E 201 ARG cc_start: 0.7770 (mpt180) cc_final: 0.5734 (mmt180) REVERT: F 65 MET cc_start: 0.5896 (tmm) cc_final: 0.5670 (tmm) REVERT: F 88 MET cc_start: 0.7842 (mmm) cc_final: 0.7547 (mmm) REVERT: I 4 MET cc_start: 0.4972 (mmm) cc_final: 0.4457 (mmm) REVERT: L 38 TYR cc_start: 0.4817 (m-80) cc_final: 0.4575 (m-10) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1459 time to fit residues: 48.2789 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 : 0.866 ------------------------------------------------------------------------------- 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: 7.9990 chunk 6 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 238 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 255 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 514 GLN ** 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** ** C 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** 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 = 0.4318 r_free = 0.4318 target = 0.104438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.087016 restraints weight = 117438.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.087857 restraints weight = 80944.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.088438 restraints weight = 60274.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.088735 restraints weight = 51169.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.088806 restraints weight = 46096.808| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23869 Z= 0.176 Angle : 0.717 10.906 32315 Z= 0.371 Chirality : 0.046 0.220 3622 Planarity : 0.005 0.058 4062 Dihedral : 12.497 176.500 3457 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.43 % Favored : 87.54 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.15), residues: 2832 helix: -0.22 (0.18), residues: 803 sheet: -1.67 (0.25), residues: 384 loop : -2.46 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 392 TYR 0.026 0.002 TYR H 91 PHE 0.029 0.002 PHE C 107 TRP 0.018 0.002 TRP B 276 HIS 0.011 0.002 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00399 (23856) covalent geometry : angle 0.71106 (32309) hydrogen bonds : bond 0.04209 ( 704) hydrogen bonds : angle 5.20103 ( 1964) metal coordination : bond 0.00717 ( 12) metal coordination : angle 6.81475 ( 6) Misc. bond : bond 0.00090 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3880.67 seconds wall clock time: 68 minutes 6.08 seconds (4086.08 seconds total)