Starting phenix.real_space_refine on Sun Jun 7 00:19:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h50_51872/06_2026/9h50_51872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h50_51872/06_2026/9h50_51872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h50_51872/06_2026/9h50_51872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h50_51872/06_2026/9h50_51872.map" model { file = "/net/cci-nas-00/data/ceres_data/9h50_51872/06_2026/9h50_51872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h50_51872/06_2026/9h50_51872.cif" } resolution = 2.72 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17847 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 Mg 2 5.21 5 S 56 5.16 5 C 11526 2.51 5 N 2971 2.21 5 O 3385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17941 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 9032 Classifications: {'peptide': 1108} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1068} Chain breaks: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 12, 'ASN:plan1': 2, 'ASP:plan': 4, 'HIS:plan': 2, 'PHE:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 8825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8825 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 1064} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 348 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 297 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 13, 'GLN:plan1': 5, 'ASN:plan1': 9, 'GLU:plan': 14, 'HIS:plan': 3, 'TYR:plan': 6, 'PHE:plan': 3, 'ARG:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 241 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' MG': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Time building chain proxies: 4.00, per 1000 atoms: 0.22 Number of scatterers: 17941 At special positions: 0 Unit cell: (116.234, 182.187, 98.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 1 15.00 Mg 2 11.99 O 3385 8.00 N 2971 7.00 C 11526 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 796.8 milliseconds 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4254 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 18 sheets defined 55.0% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.837A pdb=" N LYS A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 59 through 66 Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 113 through 131 removed outlier: 6.265A pdb=" N ASP A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 161 through 165 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.648A pdb=" N LEU A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 239 through 249 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.949A pdb=" N ALA A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.664A pdb=" N ASP A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 355 through 359 Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 399 through 412 removed outlier: 4.052A pdb=" N PHE A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 470 through 488 Processing helix chain 'A' and resid 492 through 506 removed outlier: 3.515A pdb=" N GLY A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 530 Processing helix chain 'A' and resid 531 through 536 removed outlier: 3.726A pdb=" N ARG A 534 " --> pdb=" O THR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 Processing helix chain 'A' and resid 551 through 560 removed outlier: 3.579A pdb=" N GLN A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.944A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 607 Processing helix chain 'A' and resid 609 through 633 removed outlier: 4.793A pdb=" N TYR A 614 " --> pdb=" O ASN A 610 " (cutoff:3.500A) Proline residue: A 615 - end of helix Processing helix chain 'A' and resid 637 through 670 removed outlier: 4.007A pdb=" N VAL A 651 " --> pdb=" O ASN A 647 " (cutoff:3.500A) Proline residue: A 657 - end of helix Processing helix chain 'A' and resid 680 through 696 removed outlier: 3.805A pdb=" N LEU A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 686 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 713 through 716 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 736 through 744 Processing helix chain 'A' and resid 747 through 755 Processing helix chain 'A' and resid 756 through 762 removed outlier: 3.684A pdb=" N SER A 760 " --> pdb=" O GLU A 757 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 762 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.666A pdb=" N ASN A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 808 removed outlier: 3.763A pdb=" N LYS A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N MET A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 838 Processing helix chain 'A' and resid 869 through 872 removed outlier: 4.012A pdb=" N PHE A 872 " --> pdb=" O ASN A 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 869 through 872' Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.606A pdb=" N PHE A 877 " --> pdb=" O PHE A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 922 Processing helix chain 'A' and resid 928 through 946 Processing helix chain 'A' and resid 950 through 956 Processing helix chain 'A' and resid 957 through 960 Processing helix chain 'A' and resid 978 through 984 Processing helix chain 'A' and resid 987 through 993 Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1006 through 1018 removed outlier: 4.596A pdb=" N LYS A1018 " --> pdb=" O ASN A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1071 Processing helix chain 'B' and resid 13 through 25 Processing helix chain 'B' and resid 38 through 49 Processing helix chain 'B' and resid 59 through 66 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.664A pdb=" N ALA B 106 " --> pdb=" O ILE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 removed outlier: 5.994A pdb=" N ASP B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE B 127 " --> pdb=" O ARG B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 161 through 166 removed outlier: 3.872A pdb=" N ALA B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 205 through 211 removed outlier: 4.124A pdb=" N SER B 209 " --> pdb=" O GLY B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 235 through 238 Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 264 through 271 removed outlier: 4.073A pdb=" N ASN B 269 " --> pdb=" O GLU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.828A pdb=" N ASP B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 324 through 334 Processing helix chain 'B' and resid 341 through 353 Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.712A pdb=" N LYS B 357 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 399 through 412 removed outlier: 4.012A pdb=" N PHE B 403 " --> pdb=" O PRO B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 455 through 468 Processing helix chain 'B' and resid 470 through 488 Processing helix chain 'B' and resid 492 through 505 Processing helix chain 'B' and resid 518 through 530 Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 579 through 585 removed outlier: 3.526A pdb=" N LEU B 585 " --> pdb=" O VAL B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 607 Processing helix chain 'B' and resid 609 through 633 removed outlier: 4.840A pdb=" N TYR B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) Proline residue: B 615 - end of helix Processing helix chain 'B' and resid 637 through 669 removed outlier: 3.876A pdb=" N VAL B 651 " --> pdb=" O ASN B 647 " (cutoff:3.500A) Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 680 through 696 removed outlier: 3.917A pdb=" N LEU B 684 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 712 Processing helix chain 'B' and resid 713 through 716 Processing helix chain 'B' and resid 721 through 726 Processing helix chain 'B' and resid 736 through 744 Processing helix chain 'B' and resid 747 through 755 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 771 through 781 Processing helix chain 'B' and resid 782 through 808 removed outlier: 4.131A pdb=" N LYS B 798 " --> pdb=" O ALA B 794 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N MET B 799 " --> pdb=" O GLU B 795 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 800 " --> pdb=" O LYS B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 838 Processing helix chain 'B' and resid 869 through 872 removed outlier: 4.027A pdb=" N PHE B 872 " --> pdb=" O ASN B 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 869 through 872' Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.850A pdb=" N PHE B 877 " --> pdb=" O PHE B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 923 removed outlier: 3.656A pdb=" N ALA B 923 " --> pdb=" O GLU B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 946 Processing helix chain 'B' and resid 950 through 956 Processing helix chain 'B' and resid 957 through 960 Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 997 through 1004 Processing helix chain 'B' and resid 1006 through 1018 removed outlier: 4.505A pdb=" N LYS B1018 " --> pdb=" O ASN B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1042 removed outlier: 3.964A pdb=" N GLN B1041 " --> pdb=" O PRO B1038 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B1042 " --> pdb=" O LEU B1039 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1038 through 1042' Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 56 removed outlier: 8.410A pdb=" N THR A 55 " --> pdb=" O CYS A 32 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TRP A 34 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP A 4 " --> pdb=" O TRP A 33 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL A 35 " --> pdb=" O TRP A 4 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE A 6 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR A 3 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N VAL A 73 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 5 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 91 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU A 135 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN A 93 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE A 157 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N PHE A 134 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 removed outlier: 5.960A pdb=" N THR A 191 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE A 275 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 193 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE A 293 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL A 322 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG A 295 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 540 removed outlier: 8.503A pdb=" N TYR A 539 " --> pdb=" O VAL A 509 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET A 511 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A 381 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALA A 510 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N HIS A 383 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA A 512 " --> pdb=" O HIS A 383 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N PHE A 385 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N LYS A 380 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N TRP A 568 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 382 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N HIS A 570 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 384 " --> pdb=" O HIS A 570 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY A 572 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N GLN A 588 " --> pdb=" O SER A 566 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TRP A 568 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ALA A 590 " --> pdb=" O TRP A 568 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A 570 " --> pdb=" O ALA A 590 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 392 through 394 Processing sheet with id=AA5, first strand: chain 'A' and resid 700 through 704 removed outlier: 6.410A pdb=" N THR A 673 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL A 817 " --> pdb=" O THR A 673 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TYR A 675 " --> pdb=" O VAL A 817 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TYR A 846 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE A 816 " --> pdb=" O TYR A 846 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 820 through 821 removed outlier: 3.914A pdb=" N GLY A 821 " --> pdb=" O ARG A 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 891 Processing sheet with id=AA8, first strand: chain 'A' and resid 1082 through 1085 Processing sheet with id=AA9, first strand: chain 'A' and resid 1087 through 1090 removed outlier: 3.610A pdb=" N ALA A1087 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 54 through 56 removed outlier: 6.818A pdb=" N TRP B 4 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL B 35 " --> pdb=" O TRP B 4 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE B 6 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 71 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR B 72 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N THR B 94 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR B 74 " --> pdb=" O THR B 94 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL B 91 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU B 135 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN B 93 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE B 157 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N PHE B 134 " --> pdb=" O ILE B 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 255 through 257 removed outlier: 5.872A pdb=" N PHE B 228 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 192 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 193 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 296 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE B 293 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N VAL B 322 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG B 295 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 538 through 540 removed outlier: 8.391A pdb=" N TYR B 539 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N MET B 511 " --> pdb=" O TYR B 539 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 382 " --> pdb=" O THR B 569 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR B 571 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 384 " --> pdb=" O TYR B 571 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY B 572 " --> pdb=" O ALA B 590 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 392 through 394 Processing sheet with id=AB5, first strand: chain 'B' and resid 700 through 704 removed outlier: 3.749A pdb=" N ILE B 677 " --> pdb=" O VAL B 817 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL B 859 " --> pdb=" O ASN B 843 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 820 through 821 removed outlier: 3.839A pdb=" N GLY B 821 " --> pdb=" O ARG B 849 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 888 through 890 Processing sheet with id=AB8, first strand: chain 'B' and resid 1082 through 1085 Processing sheet with id=AB9, first strand: chain 'B' and resid 1087 through 1090 removed outlier: 3.706A pdb=" N ALA B1087 " --> pdb=" O LEU B1099 " (cutoff:3.500A) 810 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5719 1.34 - 1.46: 4051 1.46 - 1.58: 8432 1.58 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 18300 Sorted by residual: bond pdb=" O3 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.90e+00 bond pdb=" O4 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" O2 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.24e+00 bond pdb=" O1 PO4 B1201 " pdb=" P PO4 B1201 " ideal model delta sigma weight residual 1.565 1.509 0.056 2.00e-02 2.50e+03 7.78e+00 bond pdb=" N VAL A 0 " pdb=" CA VAL A 0 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 18295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 24136 1.06 - 2.12: 553 2.12 - 3.18: 54 3.18 - 4.24: 62 4.24 - 5.30: 4 Bond angle restraints: 24809 Sorted by residual: angle pdb=" N ILE B 771 " pdb=" CA ILE B 771 " pdb=" C ILE B 771 " ideal model delta sigma weight residual 111.62 107.85 3.77 7.90e-01 1.60e+00 2.28e+01 angle pdb=" N ILE B 281 " pdb=" CA ILE B 281 " pdb=" C ILE B 281 " ideal model delta sigma weight residual 112.76 108.98 3.78 1.27e+00 6.20e-01 8.84e+00 angle pdb=" C GLU B 104 " pdb=" CA GLU B 104 " pdb=" CB GLU B 104 " ideal model delta sigma weight residual 110.42 115.72 -5.30 1.99e+00 2.53e-01 7.08e+00 angle pdb=" N GLU A 308 " pdb=" CA GLU A 308 " pdb=" CB GLU A 308 " ideal model delta sigma weight residual 113.65 110.29 3.36 1.47e+00 4.63e-01 5.24e+00 angle pdb=" C ASP A 306 " pdb=" N LEU A 307 " pdb=" CA LEU A 307 " ideal model delta sigma weight residual 121.54 125.45 -3.91 1.91e+00 2.74e-01 4.19e+00 ... (remaining 24804 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 10280 14.52 - 29.04: 497 29.04 - 43.56: 97 43.56 - 58.09: 11 58.09 - 72.61: 4 Dihedral angle restraints: 10889 sinusoidal: 4292 harmonic: 6597 Sorted by residual: dihedral pdb=" CA PHE B 870 " pdb=" C PHE B 870 " pdb=" N SER B 871 " pdb=" CA SER B 871 " ideal model delta harmonic sigma weight residual 180.00 161.87 18.13 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ILE B 492 " pdb=" C ILE B 492 " pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta harmonic sigma weight residual -180.00 -163.43 -16.57 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ILE A 492 " pdb=" C ILE A 492 " pdb=" N GLN A 493 " pdb=" CA GLN A 493 " ideal model delta harmonic sigma weight residual -180.00 -163.84 -16.16 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 10886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1745 0.029 - 0.058: 621 0.058 - 0.087: 168 0.087 - 0.116: 126 0.116 - 0.145: 35 Chirality restraints: 2695 Sorted by residual: chirality pdb=" CA ILE A 339 " pdb=" N ILE A 339 " pdb=" C ILE A 339 " pdb=" CB ILE A 339 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE B 276 " pdb=" N ILE B 276 " pdb=" C ILE B 276 " pdb=" CB ILE B 276 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 255 " pdb=" N ILE A 255 " pdb=" C ILE A 255 " pdb=" CB ILE A 255 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 2692 not shown) Planarity restraints: 3178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 648 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.79e+00 pdb=" C TYR A 648 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR A 648 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 649 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 648 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" C TYR B 648 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR B 648 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 649 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 953 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C ILE A 953 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 953 " 0.009 2.00e-02 2.50e+03 pdb=" N CYS A 954 " 0.008 2.00e-02 2.50e+03 ... (remaining 3175 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 178 2.53 - 3.12: 14561 3.12 - 3.72: 27249 3.72 - 4.31: 39904 4.31 - 4.90: 67430 Nonbonded interactions: 149322 Sorted by model distance: nonbonded pdb=" OH TYR B 921 " pdb=" OD1 ASP B 933 " model vdw 1.939 3.040 nonbonded pdb=" OH TYR A 921 " pdb=" OD1 ASP A 933 " model vdw 1.950 3.040 nonbonded pdb=" OE1 GLN A 632 " pdb=" O HOH A1301 " model vdw 2.007 3.040 nonbonded pdb=" OG SER A 987 " pdb=" OE1 GLU A 990 " model vdw 2.019 3.040 nonbonded pdb=" OG SER B1003 " pdb=" OH TYR B1025 " model vdw 2.031 3.040 ... (remaining 149317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 0 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 11 or (resid 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26 through 51 or (resid 52 and (na \ me N or name CA or name C or name O or name CB )) or resid 53 through 59 or (res \ id 60 and (name N or name CA or name C or name O or name CB )) or resid 61 throu \ gh 67 or (resid 68 through 69 and (name N or name CA or name C or name O or name \ CB )) or resid 70 through 102 or (resid 103 and (name N or name CA or name C or \ name O or name CB )) or resid 104 through 168 or (resid 169 through 170 and (na \ me N or name CA or name C or name O or name CB )) or resid 171 through 174 or (r \ esid 175 through 176 and (name N or name CA or name C or name O or name CB )) or \ resid 177 or (resid 178 and (name N or name CA or name C or name O or name CB ) \ ) or resid 179 or (resid 180 and (name N or name CA or name C or name O or name \ CB )) or resid 188 through 197 or (resid 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 211 or (resid 212 through 216 and \ (name N or name CA or name C or name O or name CB )) or resid 217 or (resid 218 \ through 219 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 20 through 221 or (resid 222 through 225 and (name N or name CA or name C or nam \ e O or name CB )) or resid 226 through 238 or (resid 239 through 241 and (name N \ or name CA or name C or name O or name CB )) or resid 242 through 248 or (resid \ 249 through 251 and (name N or name CA or name C or name O or name CB )) or res \ id 252 through 253 or (resid 254 and (name N or name CA or name C or name O or n \ ame CB )) or resid 255 through 261 or (resid 262 and (name N or name CA or name \ C or name O or name CB )) or resid 263 through 278 or (resid 279 and (name N or \ name CA or name C or name O or name CB )) or resid 280 through 298 or (resid 299 \ and (name N or name CA or name C or name O or name CB )) or resid 300 or (resid \ 301 through 302 and (name N or name CA or name C or name O or name CB )) or res \ id 303 through 306 or (resid 307 through 308 and (name N or name CA or name C or \ name O or name CB )) or resid 309 through 311 or (resid 312 and (name N or name \ CA or name C or name O or name CB )) or resid 313 through 319 or (resid 320 thr \ ough 321 and (name N or name CA or name C or name O or name CB )) or resid 322 t \ hrough 323 or (resid 324 through 327 and (name N or name CA or name C or name O \ or name CB )) or resid 328 or (resid 329 through 330 and (name N or name CA or n \ ame C or name O or name CB )) or resid 331 or (resid 332 through 335 and (name N \ or name CA or name C or name O or name CB )) or resid 336 through 341 or (resid \ 342 through 343 and (name N or name CA or name C or name O or name CB )) or res \ id 344 through 345 or (resid 346 and (name N or name CA or name C or name O or n \ ame CB )) or resid 347 through 349 or (resid 350 and (name N or name CA or name \ C or name O or name CB )) or resid 351 through 725 or (resid 726 through 727 and \ (name N or name CA or name C or name O or name CB )) or resid 728 through 735 o \ r (resid 736 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 37 or (resid 738 and (name N or name CA or name C or name O or name CB )) or res \ id 739 through 741 or (resid 742 through 743 and (name N or name CA or name C or \ name O or name CB )) or resid 744 through 761 or (resid 762 through 766 and (na \ me N or name CA or name C or name O or name CB )) or resid 767 through 885 or (r \ esid 886 through 887 and (name N or name CA or name C or name O or name CB )) or \ resid 888 through 894 or (resid 895 and (name N or name CA or name C or name O \ or name CB )) or resid 896 through 1115)) selection = (chain 'B' and ((resid 0 through 2 and (name N or name CA or name C or name O or \ name CB )) or resid 3 through 111 or (resid 112 and (name N or name CA or name \ C or name O or name CB )) or resid 113 through 152 or (resid 153 and (name N or \ name CA or name C or name O or name CB )) or resid 154 through 206 or (resid 207 \ and (name N or name CA or name C or name O or name CB )) or resid 208 through 2 \ 64 or (resid 265 and (name N or name CA or name C or name O or name CB )) or res \ id 266 through 296 or (resid 297 and (name N or name CA or name C or name O or n \ ame CB )) or resid 298 through 355 or (resid 356 through 360 and (name N or name \ CA or name C or name O or name CB )) or resid 361 through 747 or (resid 748 and \ (name N or name CA or name C or name O or name CB )) or resid 749 through 759 o \ r (resid 760 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 61 through 765 or (resid 766 and (name N or name CA or name C or name O or name \ CB )) or resid 767 through 776 or (resid 777 and (name N or name CA or name C or \ name O or name CB )) or resid 778 through 891 or (resid 892 and (name N or name \ CA or name C or name O or name CB )) or resid 893 through 962 or resid 971 thro \ ugh 992 or (resid 993 and (name N or name CA or name C or name O or name CB )) o \ r resid 994 through 1115)) } 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 individual isotropic 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: 4.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.030 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 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:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.003 0.060 18300 Z= 0.153 Angle : 0.433 5.296 24809 Z= 0.244 Chirality : 0.039 0.145 2695 Planarity : 0.003 0.029 3178 Dihedral : 9.043 72.608 6635 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 0.21 % Allowed : 2.19 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 2201 helix: 1.67 (0.17), residues: 1026 sheet: 0.15 (0.32), residues: 297 loop : 0.14 (0.23), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 712 TYR 0.011 0.001 TYR B 648 PHE 0.012 0.001 PHE A 939 TRP 0.005 0.001 TRP B 820 HIS 0.002 0.000 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18300) covalent geometry : angle 0.43260 / 0.24 (24809) hydrogen bonds : bond 0.15065 / 9.61 ( 810) hydrogen bonds : angle 6.09495 / 4.37 ( 2283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 197 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 726 TRP cc_start: 0.8304 (t-100) cc_final: 0.7941 (t-100) REVERT: B 6 PHE cc_start: 0.8520 (m-80) cc_final: 0.8112 (m-80) REVERT: B 22 MET cc_start: 0.4505 (mmp) cc_final: 0.3759 (mmm) REVERT: B 95 TRP cc_start: 0.6626 (t-100) cc_final: 0.6205 (t-100) REVERT: B 164 ASN cc_start: 0.7167 (m-40) cc_final: 0.6911 (p0) REVERT: B 193 LEU cc_start: 0.9242 (tp) cc_final: 0.8662 (pp) REVERT: B 273 LEU cc_start: 0.8602 (tp) cc_final: 0.8114 (tm) outliers start: 4 outliers final: 3 residues processed: 200 average time/residue: 0.6196 time to fit residues: 137.9839 Evaluate side-chains 111 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain B residue 38 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 0.9990 overall best weight: 2.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 68 HIS A1058 ASN B 466 ASN B 493 GLN ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.119238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077528 restraints weight = 37015.043| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.98 r_work: 0.3039 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18300 Z= 0.170 Angle : 0.531 7.432 24809 Z= 0.283 Chirality : 0.043 0.182 2695 Planarity : 0.004 0.039 3178 Dihedral : 4.541 112.271 2448 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.05 % Rotamer: Outliers : 1.02 % Allowed : 7.54 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 2201 helix: 1.52 (0.16), residues: 1038 sheet: 0.08 (0.32), residues: 293 loop : -0.14 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1031 TYR 0.017 0.001 TYR A 313 PHE 0.021 0.001 PHE A 325 TRP 0.008 0.001 TRP A 726 HIS 0.012 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (18300) covalent geometry : angle 0.53103 / 0.28 (24809) hydrogen bonds : bond 0.04624 / 2.97 ( 810) hydrogen bonds : angle 5.10630 / 3.67 ( 2283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7824 (mp0) REVERT: A 846 TYR cc_start: 0.8195 (m-80) cc_final: 0.7970 (m-80) REVERT: A 887 ASP cc_start: 0.8010 (p0) cc_final: 0.7636 (t70) REVERT: A 942 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 22 MET cc_start: 0.3145 (mmp) cc_final: 0.2632 (mmm) REVERT: B 95 TRP cc_start: 0.6586 (t-100) cc_final: 0.6138 (t-100) REVERT: B 193 LEU cc_start: 0.8994 (tp) cc_final: 0.8645 (pp) REVERT: B 229 ILE cc_start: 0.6406 (mp) cc_final: 0.6017 (tp) REVERT: B 273 LEU cc_start: 0.8232 (tp) cc_final: 0.7697 (tm) REVERT: B 511 MET cc_start: 0.8967 (mtm) cc_final: 0.8655 (mtm) REVERT: B 564 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7688 (pm20) outliers start: 19 outliers final: 3 residues processed: 136 average time/residue: 0.5327 time to fit residues: 82.9163 Evaluate side-chains 111 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 107 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 564 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 213 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 125 optimal weight: 40.0000 chunk 31 optimal weight: 6.9990 chunk 140 optimal weight: 30.0000 chunk 152 optimal weight: 0.9980 chunk 131 optimal weight: 50.0000 chunk 40 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS B 466 ASN ** B 826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.118254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.076240 restraints weight = 37925.647| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.02 r_work: 0.3010 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18300 Z= 0.208 Angle : 0.536 7.293 24809 Z= 0.285 Chirality : 0.044 0.176 2695 Planarity : 0.004 0.045 3178 Dihedral : 4.012 17.754 2444 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 1.12 % Allowed : 8.34 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2201 helix: 1.35 (0.16), residues: 1032 sheet: 0.06 (0.31), residues: 290 loop : -0.20 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1031 TYR 0.016 0.001 TYR A 347 PHE 0.017 0.002 PHE A 325 TRP 0.009 0.001 TRP B 661 HIS 0.004 0.001 HIS A 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (18300) covalent geometry : angle 0.53558 / 0.28 (24809) hydrogen bonds : bond 0.04377 / 2.83 ( 810) hydrogen bonds : angle 5.01907 / 3.61 ( 2283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7834 (mtp) REVERT: A 68 HIS cc_start: 0.8525 (t70) cc_final: 0.8219 (t-90) REVERT: A 101 LYS cc_start: 0.8158 (mmmt) cc_final: 0.7930 (mmmt) REVERT: A 734 MET cc_start: 0.4940 (OUTLIER) cc_final: 0.4423 (pmm) REVERT: A 818 GLU cc_start: 0.8545 (mm-30) cc_final: 0.7963 (mp0) REVERT: A 846 TYR cc_start: 0.8268 (m-80) cc_final: 0.8009 (m-80) REVERT: A 887 ASP cc_start: 0.7905 (p0) cc_final: 0.7495 (t70) REVERT: A 942 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 6 PHE cc_start: 0.7468 (m-80) cc_final: 0.6873 (m-80) REVERT: B 22 MET cc_start: 0.3287 (mmp) cc_final: 0.2583 (mmm) REVERT: B 95 TRP cc_start: 0.6460 (t-100) cc_final: 0.6164 (t-100) REVERT: B 229 ILE cc_start: 0.6474 (mp) cc_final: 0.6044 (tp) REVERT: B 564 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: B 852 THR cc_start: 0.9067 (m) cc_final: 0.8764 (p) REVERT: B 993 LYS cc_start: 0.9285 (tptp) cc_final: 0.8913 (ttpp) outliers start: 21 outliers final: 8 residues processed: 126 average time/residue: 0.5237 time to fit residues: 75.6574 Evaluate side-chains 117 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 564 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 203 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 167 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 213 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** B 826 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 = 0.3932 r_free = 0.3932 target = 0.121550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079684 restraints weight = 37210.985| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.01 r_work: 0.3085 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 18300 Z= 0.096 Angle : 0.470 6.944 24809 Z= 0.248 Chirality : 0.041 0.167 2695 Planarity : 0.003 0.049 3178 Dihedral : 3.824 18.222 2444 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.55 % Rotamer: Outliers : 0.96 % Allowed : 9.19 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.18), residues: 2201 helix: 1.59 (0.16), residues: 1027 sheet: -0.05 (0.31), residues: 307 loop : -0.14 (0.22), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1031 TYR 0.017 0.001 TYR A 313 PHE 0.015 0.001 PHE A 939 TRP 0.007 0.001 TRP B 661 HIS 0.002 0.000 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (18300) covalent geometry : angle 0.46952 / 0.25 (24809) hydrogen bonds : bond 0.03468 / 2.24 ( 810) hydrogen bonds : angle 4.74864 / 3.43 ( 2283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7812 (mtp) REVERT: A 68 HIS cc_start: 0.8444 (t70) cc_final: 0.8042 (t-90) REVERT: A 192 ILE cc_start: 0.6916 (mm) cc_final: 0.6693 (pt) REVERT: A 708 ARG cc_start: 0.8526 (mtt180) cc_final: 0.7819 (ttt-90) REVERT: A 734 MET cc_start: 0.4714 (OUTLIER) cc_final: 0.4285 (pmm) REVERT: A 818 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8011 (mp0) REVERT: A 846 TYR cc_start: 0.8167 (m-80) cc_final: 0.7936 (m-80) REVERT: A 887 ASP cc_start: 0.7894 (p0) cc_final: 0.7468 (t70) REVERT: A 942 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 22 MET cc_start: 0.3246 (mmp) cc_final: 0.2512 (tmm) REVERT: B 193 LEU cc_start: 0.9028 (tp) cc_final: 0.8759 (pp) REVERT: B 229 ILE cc_start: 0.6512 (mp) cc_final: 0.6177 (tp) REVERT: B 564 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: B 852 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8948 (p) REVERT: B 1078 LYS cc_start: 0.8473 (tppt) cc_final: 0.8265 (mmmm) outliers start: 18 outliers final: 3 residues processed: 128 average time/residue: 0.5382 time to fit residues: 78.8915 Evaluate side-chains 114 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 90 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 826 GLN ** 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 = 0.3870 r_free = 0.3870 target = 0.117311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.075556 restraints weight = 37845.460| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.95 r_work: 0.2999 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 18300 Z= 0.268 Angle : 0.563 6.325 24809 Z= 0.300 Chirality : 0.044 0.157 2695 Planarity : 0.004 0.044 3178 Dihedral : 4.049 17.904 2442 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.28 % Allowed : 10.48 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2201 helix: 1.34 (0.16), residues: 1027 sheet: -0.16 (0.31), residues: 299 loop : -0.26 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1031 TYR 0.017 0.001 TYR B 648 PHE 0.020 0.002 PHE B 500 TRP 0.010 0.001 TRP B 95 HIS 0.004 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.27 (18300) covalent geometry : angle 0.56256 / 0.30 (24809) hydrogen bonds : bond 0.04463 / 2.88 ( 810) hydrogen bonds : angle 4.96901 / 3.56 ( 2283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (mtp) REVERT: A 68 HIS cc_start: 0.8533 (t70) cc_final: 0.8140 (t-90) REVERT: A 192 ILE cc_start: 0.6935 (mm) cc_final: 0.6724 (pt) REVERT: A 233 HIS cc_start: 0.7965 (t70) cc_final: 0.7735 (t70) REVERT: A 708 ARG cc_start: 0.8573 (mtt180) cc_final: 0.8198 (ttt180) REVERT: A 734 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.4528 (pmm) REVERT: A 818 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8035 (mp0) REVERT: A 942 GLN cc_start: 0.8888 (tm-30) cc_final: 0.8633 (tm-30) REVERT: B 6 PHE cc_start: 0.7556 (m-80) cc_final: 0.6927 (m-80) REVERT: B 22 MET cc_start: 0.3296 (mmp) cc_final: 0.2462 (tmm) REVERT: B 229 ILE cc_start: 0.6705 (mp) cc_final: 0.6273 (tp) REVERT: B 273 LEU cc_start: 0.7549 (mm) cc_final: 0.7049 (tm) REVERT: B 561 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8175 (pp) REVERT: B 564 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: B 852 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8780 (p) outliers start: 24 outliers final: 6 residues processed: 119 average time/residue: 0.5266 time to fit residues: 71.4232 Evaluate side-chains 112 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 90 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 204 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 826 GLN ** 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 = 0.3908 r_free = 0.3908 target = 0.119956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.078387 restraints weight = 37311.669| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.93 r_work: 0.3066 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18300 Z= 0.120 Angle : 0.480 6.469 24809 Z= 0.255 Chirality : 0.041 0.160 2695 Planarity : 0.003 0.044 3178 Dihedral : 3.877 18.132 2442 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.54 % Favored : 96.41 % Rotamer: Outliers : 1.02 % Allowed : 11.01 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2201 helix: 1.53 (0.16), residues: 1026 sheet: -0.12 (0.31), residues: 307 loop : -0.22 (0.22), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1031 TYR 0.011 0.001 TYR A 347 PHE 0.015 0.001 PHE A 939 TRP 0.017 0.001 TRP B 95 HIS 0.002 0.000 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (18300) covalent geometry : angle 0.48024 / 0.25 (24809) hydrogen bonds : bond 0.03636 / 2.36 ( 810) hydrogen bonds : angle 4.75670 / 3.43 ( 2283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7952 (mtp) REVERT: A 68 HIS cc_start: 0.8492 (t70) cc_final: 0.8068 (t-90) REVERT: A 192 ILE cc_start: 0.6901 (mm) cc_final: 0.6683 (pt) REVERT: A 233 HIS cc_start: 0.7970 (t70) cc_final: 0.7739 (t70) REVERT: A 708 ARG cc_start: 0.8556 (mtt180) cc_final: 0.8307 (ttt180) REVERT: A 734 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.4218 (pmm) REVERT: A 818 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8050 (mp0) REVERT: A 846 TYR cc_start: 0.8222 (m-80) cc_final: 0.7982 (m-80) REVERT: A 887 ASP cc_start: 0.7989 (p0) cc_final: 0.7510 (t70) REVERT: A 942 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8494 (tm-30) REVERT: B 6 PHE cc_start: 0.7598 (m-80) cc_final: 0.6957 (m-80) REVERT: B 22 MET cc_start: 0.3165 (mmp) cc_final: 0.2469 (tmm) REVERT: B 229 ILE cc_start: 0.6717 (mp) cc_final: 0.6297 (tp) REVERT: B 273 LEU cc_start: 0.7587 (mm) cc_final: 0.7080 (tm) REVERT: B 564 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: B 852 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8848 (p) outliers start: 19 outliers final: 5 residues processed: 118 average time/residue: 0.5521 time to fit residues: 74.8032 Evaluate side-chains 110 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 151 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 142 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 chunk 205 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 826 GLN ** 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 = 0.3902 r_free = 0.3902 target = 0.119475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.077794 restraints weight = 37671.545| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.98 r_work: 0.3044 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18300 Z= 0.148 Angle : 0.491 7.960 24809 Z= 0.260 Chirality : 0.042 0.153 2695 Planarity : 0.004 0.044 3178 Dihedral : 3.859 17.621 2442 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.86 % Favored : 96.09 % Rotamer: Outliers : 1.12 % Allowed : 10.96 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2201 helix: 1.51 (0.16), residues: 1027 sheet: -0.04 (0.32), residues: 297 loop : -0.23 (0.22), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1031 TYR 0.017 0.001 TYR A 313 PHE 0.015 0.001 PHE A 939 TRP 0.016 0.001 TRP B 95 HIS 0.002 0.000 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (18300) covalent geometry : angle 0.49144 / 0.26 (24809) hydrogen bonds : bond 0.03748 / 2.42 ( 810) hydrogen bonds : angle 4.73780 / 3.42 ( 2283) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7936 (mtp) REVERT: A 68 HIS cc_start: 0.8530 (t70) cc_final: 0.8091 (t-90) REVERT: A 192 ILE cc_start: 0.6921 (mm) cc_final: 0.6669 (pp) REVERT: A 233 HIS cc_start: 0.8001 (t70) cc_final: 0.7744 (t70) REVERT: A 708 ARG cc_start: 0.8573 (mtt180) cc_final: 0.8322 (ttt180) REVERT: A 734 MET cc_start: 0.4488 (OUTLIER) cc_final: 0.4118 (pmm) REVERT: A 818 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7973 (mp0) REVERT: A 846 TYR cc_start: 0.8239 (m-80) cc_final: 0.7982 (m-80) REVERT: A 887 ASP cc_start: 0.7961 (p0) cc_final: 0.7454 (t70) REVERT: A 942 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 6 PHE cc_start: 0.7634 (m-80) cc_final: 0.7427 (m-80) REVERT: B 22 MET cc_start: 0.3150 (mmp) cc_final: 0.2467 (tmm) REVERT: B 229 ILE cc_start: 0.6764 (mp) cc_final: 0.6331 (tp) REVERT: B 273 LEU cc_start: 0.7553 (mm) cc_final: 0.7042 (tm) REVERT: B 561 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8128 (pp) REVERT: B 564 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: B 852 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8904 (p) outliers start: 21 outliers final: 8 residues processed: 118 average time/residue: 0.5328 time to fit residues: 72.5202 Evaluate side-chains 116 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 726 TRP Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 852 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 94 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 213 optimal weight: 0.0470 chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 218 optimal weight: 0.0570 chunk 114 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 826 GLN ** 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 = 0.3931 r_free = 0.3931 target = 0.121618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080280 restraints weight = 37188.474| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.96 r_work: 0.3085 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18300 Z= 0.098 Angle : 0.468 8.072 24809 Z= 0.246 Chirality : 0.041 0.153 2695 Planarity : 0.003 0.044 3178 Dihedral : 3.722 17.611 2442 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.59 % Favored : 96.37 % Rotamer: Outliers : 0.86 % Allowed : 11.33 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 2201 helix: 1.63 (0.16), residues: 1034 sheet: -0.10 (0.31), residues: 307 loop : -0.23 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1031 TYR 0.016 0.001 TYR A 313 PHE 0.014 0.001 PHE A 939 TRP 0.021 0.001 TRP B 95 HIS 0.002 0.000 HIS A 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (18300) covalent geometry : angle 0.46793 / 0.25 (24809) hydrogen bonds : bond 0.03222 / 2.10 ( 810) hydrogen bonds : angle 4.59344 / 3.32 ( 2283) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7867 (mtp) REVERT: A 68 HIS cc_start: 0.8532 (t70) cc_final: 0.8091 (t-90) REVERT: A 192 ILE cc_start: 0.6914 (mm) cc_final: 0.6704 (pp) REVERT: A 233 HIS cc_start: 0.7971 (t70) cc_final: 0.7714 (t70) REVERT: A 708 ARG cc_start: 0.8523 (mtt180) cc_final: 0.8239 (ttt180) REVERT: A 734 MET cc_start: 0.4202 (OUTLIER) cc_final: 0.3832 (pmm) REVERT: A 818 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7956 (mp0) REVERT: A 846 TYR cc_start: 0.8191 (m-80) cc_final: 0.7971 (m-80) REVERT: A 887 ASP cc_start: 0.7971 (p0) cc_final: 0.7505 (t70) REVERT: A 942 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8504 (tm-30) REVERT: B 6 PHE cc_start: 0.7606 (m-80) cc_final: 0.7371 (m-80) REVERT: B 22 MET cc_start: 0.3086 (mmp) cc_final: 0.2425 (tmm) REVERT: B 229 ILE cc_start: 0.6750 (mp) cc_final: 0.6333 (tp) REVERT: B 273 LEU cc_start: 0.7480 (mm) cc_final: 0.6966 (tm) outliers start: 16 outliers final: 7 residues processed: 127 average time/residue: 0.5087 time to fit residues: 74.5642 Evaluate side-chains 112 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 564 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 97 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 120 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 826 GLN ** 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 = 0.3892 r_free = 0.3892 target = 0.118910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077004 restraints weight = 37373.840| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.98 r_work: 0.3026 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18300 Z= 0.191 Angle : 0.522 7.297 24809 Z= 0.276 Chirality : 0.043 0.151 2695 Planarity : 0.004 0.044 3178 Dihedral : 3.864 17.749 2442 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.82 % Rotamer: Outliers : 0.80 % Allowed : 11.49 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 2201 helix: 1.51 (0.16), residues: 1034 sheet: -0.10 (0.32), residues: 297 loop : -0.29 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1031 TYR 0.018 0.001 TYR A 347 PHE 0.016 0.002 PHE B 500 TRP 0.016 0.001 TRP B 95 HIS 0.003 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (18300) covalent geometry : angle 0.52178 / 0.28 (24809) hydrogen bonds : bond 0.03925 / 2.54 ( 810) hydrogen bonds : angle 4.75660 / 3.43 ( 2283) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7947 (mtp) REVERT: A 68 HIS cc_start: 0.8577 (t70) cc_final: 0.8149 (t-90) REVERT: A 109 MET cc_start: 0.7894 (ttp) cc_final: 0.7666 (ttm) REVERT: A 233 HIS cc_start: 0.8032 (t70) cc_final: 0.7765 (t70) REVERT: A 708 ARG cc_start: 0.8555 (mtt180) cc_final: 0.8197 (ttt180) REVERT: A 734 MET cc_start: 0.4359 (OUTLIER) cc_final: 0.4111 (mpt) REVERT: A 818 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7929 (mp0) REVERT: A 887 ASP cc_start: 0.7945 (p0) cc_final: 0.7462 (t70) REVERT: A 942 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8609 (tm-30) REVERT: B 6 PHE cc_start: 0.7656 (m-80) cc_final: 0.7414 (m-80) REVERT: B 22 MET cc_start: 0.3114 (mmp) cc_final: 0.2500 (mmm) REVERT: B 229 ILE cc_start: 0.6922 (mp) cc_final: 0.6476 (tp) REVERT: B 273 LEU cc_start: 0.7571 (mm) cc_final: 0.7057 (tm) REVERT: B 564 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7725 (pm20) outliers start: 15 outliers final: 6 residues processed: 113 average time/residue: 0.5233 time to fit residues: 68.0597 Evaluate side-chains 108 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 564 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 26 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 193 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 165 optimal weight: 0.0670 chunk 24 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 826 GLN ** 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 = 0.3914 r_free = 0.3914 target = 0.120483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.078969 restraints weight = 37114.843| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.94 r_work: 0.3063 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18300 Z= 0.115 Angle : 0.496 9.978 24809 Z= 0.260 Chirality : 0.041 0.151 2695 Planarity : 0.003 0.044 3178 Dihedral : 3.790 17.962 2442 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.77 % Favored : 96.18 % Rotamer: Outliers : 0.48 % Allowed : 12.08 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2201 helix: 1.62 (0.16), residues: 1027 sheet: -0.14 (0.31), residues: 301 loop : -0.25 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1031 TYR 0.016 0.001 TYR A 347 PHE 0.014 0.001 PHE A 939 TRP 0.021 0.001 TRP A 726 HIS 0.002 0.000 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (18300) covalent geometry : angle 0.49637 / 0.26 (24809) hydrogen bonds : bond 0.03501 / 2.28 ( 810) hydrogen bonds : angle 4.67778 / 3.38 ( 2283) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4402 Ramachandran restraints generated. 2201 Oldfield, 0 Emsley, 2201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7917 (mtp) REVERT: A 68 HIS cc_start: 0.8574 (t70) cc_final: 0.8152 (t-90) REVERT: A 233 HIS cc_start: 0.8037 (t70) cc_final: 0.7776 (t70) REVERT: A 708 ARG cc_start: 0.8508 (mtt180) cc_final: 0.8237 (ttt180) REVERT: A 818 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7945 (mp0) REVERT: A 846 TYR cc_start: 0.8216 (m-80) cc_final: 0.7983 (m-80) REVERT: A 887 ASP cc_start: 0.7969 (p0) cc_final: 0.7497 (t70) REVERT: A 942 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8527 (tm-30) REVERT: B 6 PHE cc_start: 0.7650 (m-80) cc_final: 0.7403 (m-80) REVERT: B 22 MET cc_start: 0.3126 (mmp) cc_final: 0.2465 (tmm) REVERT: B 229 ILE cc_start: 0.6919 (mp) cc_final: 0.6473 (tp) REVERT: B 273 LEU cc_start: 0.7501 (mm) cc_final: 0.6999 (tm) REVERT: B 564 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7587 (pm20) outliers start: 9 outliers final: 5 residues processed: 107 average time/residue: 0.5205 time to fit residues: 64.0801 Evaluate side-chains 106 residues out of total 1999 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 THR Chi-restraints excluded: chain A residue 22 MET Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 564 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 145 optimal weight: 0.4980 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 88 optimal weight: 0.0050 chunk 73 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 938 GLN ** B 826 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 = 0.3922 r_free = 0.3922 target = 0.120940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079284 restraints weight = 37288.718| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 3.01 r_work: 0.3072 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18300 Z= 0.109 Angle : 0.486 9.121 24809 Z= 0.254 Chirality : 0.041 0.153 2695 Planarity : 0.003 0.044 3178 Dihedral : 3.743 18.022 2442 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 0.53 % Allowed : 11.97 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 2201 helix: 1.70 (0.16), residues: 1020 sheet: -0.01 (0.32), residues: 291 loop : -0.26 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1031 TYR 0.035 0.001 TYR A 351 PHE 0.022 0.001 PHE B 755 TRP 0.022 0.001 TRP A 726 HIS 0.002 0.000 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (18300) covalent geometry : angle 0.48601 / 0.25 (24809) hydrogen bonds : bond 0.03359 / 2.18 ( 810) hydrogen bonds : angle 4.64355 / 3.36 ( 2283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5937.62 seconds wall clock time: 102 minutes 13.54 seconds (6133.54 seconds total)