Starting phenix.real_space_refine on Fri Aug 7 22:46:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xwg_67335/08_2026/9xwg_67335.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xwg_67335/08_2026/9xwg_67335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xwg_67335/08_2026/9xwg_67335.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xwg_67335/08_2026/9xwg_67335.map" model { file = "/net/cci-nas-00/data/ceres_data/9xwg_67335/08_2026/9xwg_67335.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xwg_67335/08_2026/9xwg_67335.cif" } resolution = 3.38 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= 0.003 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 15378 2.51 5 N 4092 2.21 5 O 4281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23832 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7944 Classifications: {'peptide': 1019} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 970} Chain: "B" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7944 Classifications: {'peptide': 1019} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 970} Chain: "C" Number of atoms: 7944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1019, 7944 Classifications: {'peptide': 1019} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 970} Time building chain proxies: 5.65, per 1000 atoms: 0.24 Number of scatterers: 23832 At special positions: 0 Unit cell: (118.656, 115.36, 154.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 4281 8.00 N 4092 7.00 C 15378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 966.7 milliseconds 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5682 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 25 sheets defined 60.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 Processing helix chain 'A' and resid 12 through 34 removed outlier: 4.280A pdb=" N SER A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 65 through 74 Processing helix chain 'A' and resid 105 through 120 removed outlier: 3.626A pdb=" N ILE A 120 " --> pdb=" O LYS A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 170 removed outlier: 3.532A pdb=" N MET A 157 " --> pdb=" O ASP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.906A pdb=" N GLU A 212 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 removed outlier: 3.646A pdb=" N ARG A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 294 through 311 removed outlier: 3.720A pdb=" N LEU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 356 Processing helix chain 'A' and resid 356 through 365 removed outlier: 3.984A pdb=" N VAL A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 382 Processing helix chain 'A' and resid 386 through 418 removed outlier: 4.440A pdb=" N GLY A 398 " --> pdb=" O VAL A 394 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU A 399 " --> pdb=" O LEU A 395 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.004A pdb=" N ALA A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TRP A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 447 removed outlier: 4.263A pdb=" N PHE A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 455 through 461 Processing helix chain 'A' and resid 462 through 479 removed outlier: 3.520A pdb=" N GLN A 466 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ILE A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 removed outlier: 3.733A pdb=" N LYS A 489 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.792A pdb=" N LYS A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 513 removed outlier: 3.809A pdb=" N ALA A 513 " --> pdb=" O ASP A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 513' Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 530 through 549 Processing helix chain 'A' and resid 576 through 592 Processing helix chain 'A' and resid 633 through 652 removed outlier: 3.974A pdb=" N ASN A 649 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLU A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 698 removed outlier: 3.819A pdb=" N ASN A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 removed outlier: 3.812A pdb=" N ALA A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 743 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 773 through 777 removed outlier: 3.575A pdb=" N LEU A 777 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 793 Processing helix chain 'A' and resid 824 through 833 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 852 through 866 removed outlier: 3.563A pdb=" N GLU A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 885 Processing helix chain 'A' and resid 886 through 896 removed outlier: 3.649A pdb=" N THR A 896 " --> pdb=" O MET A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 899 No H-bonds generated for 'chain 'A' and resid 897 through 899' Processing helix chain 'A' and resid 900 through 911 removed outlier: 3.854A pdb=" N VAL A 904 " --> pdb=" O GLY A 900 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 907 " --> pdb=" O GLY A 903 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 909 " --> pdb=" O THR A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 948 removed outlier: 3.624A pdb=" N GLY A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 962 removed outlier: 3.578A pdb=" N ARG A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 975 removed outlier: 3.603A pdb=" N LEU A 975 " --> pdb=" O LEU A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 983 removed outlier: 4.073A pdb=" N LEU A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 983 " --> pdb=" O PRO A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1004 removed outlier: 3.905A pdb=" N VAL A1002 " --> pdb=" O ILE A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1017 removed outlier: 3.604A pdb=" N ALA A1010 " --> pdb=" O LEU A1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 12 through 32 removed outlier: 4.338A pdb=" N SER B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 102 through 104 No H-bonds generated for 'chain 'B' and resid 102 through 104' Processing helix chain 'B' and resid 105 through 120 removed outlier: 3.652A pdb=" N ILE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 240 through 245 removed outlier: 3.968A pdb=" N ARG B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 261 Processing helix chain 'B' and resid 295 through 311 removed outlier: 4.251A pdb=" N GLN B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 356 Processing helix chain 'B' and resid 356 through 382 removed outlier: 4.230A pdb=" N VAL B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 386 through 418 removed outlier: 4.463A pdb=" N GLY B 398 " --> pdb=" O VAL B 394 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 399 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 431 removed outlier: 4.176A pdb=" N ALA B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 447 removed outlier: 4.239A pdb=" N PHE B 447 " --> pdb=" O THR B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 455 through 461 Processing helix chain 'B' and resid 461 through 479 removed outlier: 4.615A pdb=" N PHE B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE B 470 " --> pdb=" O GLN B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 removed outlier: 3.987A pdb=" N LYS B 489 " --> pdb=" O TYR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 503 removed outlier: 3.537A pdb=" N LYS B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 513 removed outlier: 3.790A pdb=" N ALA B 513 " --> pdb=" O ASP B 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 513' Processing helix chain 'B' and resid 514 through 530 Processing helix chain 'B' and resid 530 through 549 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 576 through 592 Processing helix chain 'B' and resid 633 through 652 removed outlier: 3.643A pdb=" N ASN B 649 " --> pdb=" O ILE B 645 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU B 650 " --> pdb=" O GLU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 697 Processing helix chain 'B' and resid 721 through 727 Processing helix chain 'B' and resid 730 through 743 removed outlier: 3.637A pdb=" N LEU B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 769 removed outlier: 3.522A pdb=" N ARG B 768 " --> pdb=" O THR B 764 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 769 " --> pdb=" O GLU B 765 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 764 through 769' Processing helix chain 'B' and resid 773 through 777 removed outlier: 3.596A pdb=" N LEU B 777 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 793 Processing helix chain 'B' and resid 824 through 833 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 852 through 867 removed outlier: 3.567A pdb=" N GLU B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 857 " --> pdb=" O GLY B 853 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 867 " --> pdb=" O SER B 863 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 885 removed outlier: 3.745A pdb=" N LEU B 877 " --> pdb=" O ILE B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 896 removed outlier: 3.550A pdb=" N THR B 896 " --> pdb=" O MET B 892 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 899 No H-bonds generated for 'chain 'B' and resid 897 through 899' Processing helix chain 'B' and resid 900 through 911 removed outlier: 3.974A pdb=" N VAL B 904 " --> pdb=" O GLY B 900 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 909 " --> pdb=" O THR B 905 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 948 removed outlier: 4.039A pdb=" N GLY B 922 " --> pdb=" O VAL B 918 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY B 928 " --> pdb=" O ILE B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 962 Processing helix chain 'B' and resid 962 through 975 removed outlier: 3.562A pdb=" N ILE B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 975 " --> pdb=" O LEU B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 removed outlier: 3.843A pdb=" N ARG B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 983 " --> pdb=" O PRO B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 1006 removed outlier: 3.880A pdb=" N VAL B1002 " --> pdb=" O ILE B 998 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1017 removed outlier: 3.677A pdb=" N ALA B1010 " --> pdb=" O LEU B1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 12 Processing helix chain 'C' and resid 12 through 34 removed outlier: 4.241A pdb=" N SER C 32 " --> pdb=" O ALA C 28 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 65 Processing helix chain 'C' and resid 65 through 74 Processing helix chain 'C' and resid 105 through 120 removed outlier: 3.640A pdb=" N ILE C 120 " --> pdb=" O LYS C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 170 Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 240 through 245 Processing helix chain 'C' and resid 257 through 261 Processing helix chain 'C' and resid 294 through 311 removed outlier: 4.381A pdb=" N GLN C 311 " --> pdb=" O ALA C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 356 Processing helix chain 'C' and resid 356 through 382 removed outlier: 4.112A pdb=" N VAL C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL C 363 " --> pdb=" O THR C 359 " (cutoff:3.500A) Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 386 through 418 removed outlier: 4.429A pdb=" N GLY C 398 " --> pdb=" O VAL C 394 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU C 399 " --> pdb=" O LEU C 395 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 431 removed outlier: 4.161A pdb=" N ALA C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N TRP C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR C 430 " --> pdb=" O SER C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 447 removed outlier: 4.160A pdb=" N PHE C 447 " --> pdb=" O THR C 443 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 452 Processing helix chain 'C' and resid 455 through 461 Processing helix chain 'C' and resid 461 through 479 removed outlier: 4.679A pdb=" N PHE C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE C 470 " --> pdb=" O GLN C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 removed outlier: 3.905A pdb=" N LYS C 489 " --> pdb=" O TYR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 503 removed outlier: 3.596A pdb=" N LYS C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 513 removed outlier: 3.829A pdb=" N ALA C 513 " --> pdb=" O ASP C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 510 through 513' Processing helix chain 'C' and resid 514 through 530 Processing helix chain 'C' and resid 530 through 549 Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 576 through 592 Processing helix chain 'C' and resid 633 through 652 removed outlier: 3.622A pdb=" N ASN C 649 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C 650 " --> pdb=" O GLU C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 697 Processing helix chain 'C' and resid 720 through 727 removed outlier: 3.588A pdb=" N ALA C 724 " --> pdb=" O ASP C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 743 removed outlier: 3.598A pdb=" N LEU C 742 " --> pdb=" O LEU C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 764 through 769 removed outlier: 3.707A pdb=" N ARG C 769 " --> pdb=" O GLU C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 777 removed outlier: 3.552A pdb=" N SER C 776 " --> pdb=" O LEU C 773 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 777 " --> pdb=" O LEU C 774 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 773 through 777' Processing helix chain 'C' and resid 788 through 792 Processing helix chain 'C' and resid 824 through 833 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 852 through 867 removed outlier: 3.925A pdb=" N GLU C 856 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 885 Processing helix chain 'C' and resid 886 through 896 removed outlier: 3.541A pdb=" N THR C 896 " --> pdb=" O MET C 892 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 899 No H-bonds generated for 'chain 'C' and resid 897 through 899' Processing helix chain 'C' and resid 900 through 911 removed outlier: 3.795A pdb=" N VAL C 904 " --> pdb=" O GLY C 900 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 909 " --> pdb=" O THR C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 948 removed outlier: 4.063A pdb=" N GLY C 922 " --> pdb=" O VAL C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 960 removed outlier: 3.529A pdb=" N VAL C 960 " --> pdb=" O ILE C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 974 Processing helix chain 'C' and resid 976 through 983 removed outlier: 4.077A pdb=" N LEU C 980 " --> pdb=" O ALA C 976 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER C 983 " --> pdb=" O PRO C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 1004 removed outlier: 3.822A pdb=" N VAL C1002 " --> pdb=" O ILE C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1017 removed outlier: 3.619A pdb=" N ALA C1010 " --> pdb=" O LEU C1006 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 134 removed outlier: 5.602A pdb=" N GLY A 130 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASN A 52 " --> pdb=" O GLY A 130 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 48 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 96 " --> pdb=" O ARG A 81 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG A 81 " --> pdb=" O MET A 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 180 removed outlier: 5.750A pdb=" N ALA A 288 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 177 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA A 286 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 179 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY A 284 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 143 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET A 289 " --> pdb=" O TYR A 141 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N TYR A 141 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N GLY A 142 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP A 324 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE A 144 " --> pdb=" O VAL A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 180 removed outlier: 5.750A pdb=" N ALA A 288 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL A 177 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA A 286 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU A 179 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLY A 284 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET A 275 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN A 599 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 569 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 568 " --> pdb=" O ARG A 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 266 removed outlier: 6.296A pdb=" N ILE A 187 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 750 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 748 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A 761 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS A 746 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA6, first strand: chain 'A' and resid 247 through 250 removed outlier: 3.737A pdb=" N ARG A 253 " --> pdb=" O VAL A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 702 through 706 removed outlier: 5.184A pdb=" N ASN A 703 " --> pdb=" O ASP A 818 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP A 818 " --> pdb=" O ASN A 703 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 672 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 712 through 717 Processing sheet with id=AA9, first strand: chain 'B' and resid 129 through 134 removed outlier: 5.571A pdb=" N GLY B 130 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN B 52 " --> pdb=" O GLY B 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL B 48 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B 96 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG B 81 " --> pdb=" O MET B 96 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 174 through 180 removed outlier: 5.974A pdb=" N ALA B 288 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 177 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B 286 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 179 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 284 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASP B 281 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 149 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N MET B 289 " --> pdb=" O TYR B 141 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N TYR B 141 " --> pdb=" O MET B 289 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLY B 142 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP B 324 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE B 144 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 174 through 180 removed outlier: 5.974A pdb=" N ALA B 288 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 177 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA B 286 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 179 " --> pdb=" O GLY B 284 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 284 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET B 275 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN B 599 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 569 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 264 through 266 removed outlier: 6.361A pdb=" N ILE B 187 " --> pdb=" O LEU B 760 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE B 759 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AB5, first strand: chain 'B' and resid 247 through 250 removed outlier: 3.846A pdb=" N ARG B 253 " --> pdb=" O VAL B 250 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 702 through 706 removed outlier: 5.253A pdb=" N ASN B 703 " --> pdb=" O ASP B 818 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B 818 " --> pdb=" O ASN B 703 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 672 " --> pdb=" O ALA B 817 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 795 through 800 removed outlier: 6.816A pdb=" N SER C 234 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU B 717 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 751 through 752 Processing sheet with id=AB9, first strand: chain 'C' and resid 129 through 134 removed outlier: 4.169A pdb=" N ASN C 52 " --> pdb=" O GLN C 129 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N GLN C 50 " --> pdb=" O PRO C 131 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N PHE C 133 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C 48 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 90 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER C 86 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN C 92 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SER C 84 " --> pdb=" O GLN C 92 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR C 94 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE C 82 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N MET C 96 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 174 through 180 removed outlier: 4.157A pdb=" N LYS C 176 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ASP C 281 " --> pdb=" O GLY C 149 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY C 149 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 143 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N MET C 289 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N TYR C 141 " --> pdb=" O MET C 289 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N GLY C 142 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP C 324 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 144 " --> pdb=" O VAL C 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 174 through 180 removed outlier: 4.157A pdb=" N LYS C 176 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET C 275 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN C 599 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR C 603 " --> pdb=" O GLN C 626 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C 626 " --> pdb=" O TYR C 603 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 569 " --> pdb=" O ALA C 625 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 264 through 266 removed outlier: 6.258A pdb=" N ILE C 187 " --> pdb=" O LEU C 760 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 748 " --> pdb=" O ILE C 759 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU C 761 " --> pdb=" O HIS C 746 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS C 746 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AC5, first strand: chain 'C' and resid 247 through 248 removed outlier: 3.677A pdb=" N PHE C 255 " --> pdb=" O ILE C 248 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 702 through 706 removed outlier: 4.565A pdb=" N VAL C 704 " --> pdb=" O ARG C 816 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG C 816 " --> pdb=" O VAL C 704 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 712 through 717 1386 hydrogen bonds defined for protein. 4041 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: 5.28 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3876 1.32 - 1.44: 6264 1.44 - 1.57: 14022 1.57 - 1.69: 0 1.69 - 1.81: 159 Bond restraints: 24321 Sorted by residual: bond pdb=" N ILE B 819 " pdb=" CA ILE B 819 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.17e-02 7.31e+03 9.26e+00 bond pdb=" N ASP C 269 " pdb=" CA ASP C 269 " ideal model delta sigma weight residual 1.462 1.485 -0.023 7.70e-03 1.69e+04 8.93e+00 bond pdb=" CA SER C 560 " pdb=" CB SER C 560 " ideal model delta sigma weight residual 1.530 1.485 0.045 1.58e-02 4.01e+03 8.22e+00 bond pdb=" N ASN C 268 " pdb=" CA ASN C 268 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.16e-02 7.43e+03 7.76e+00 bond pdb=" N SER B 823 " pdb=" CA SER B 823 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.12e+00 ... (remaining 24316 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 32253 1.83 - 3.66: 607 3.66 - 5.48: 136 5.48 - 7.31: 21 7.31 - 9.14: 4 Bond angle restraints: 33021 Sorted by residual: angle pdb=" N VAL B 480 " pdb=" CA VAL B 480 " pdb=" C VAL B 480 " ideal model delta sigma weight residual 113.71 109.14 4.57 9.50e-01 1.11e+00 2.32e+01 angle pdb=" N PRO C 558 " pdb=" CA PRO C 558 " pdb=" C PRO C 558 " ideal model delta sigma weight residual 110.70 116.45 -5.75 1.22e+00 6.72e-01 2.22e+01 angle pdb=" N PRO B 270 " pdb=" CA PRO B 270 " pdb=" C PRO B 270 " ideal model delta sigma weight residual 110.70 105.32 5.38 1.22e+00 6.72e-01 1.94e+01 angle pdb=" N PRO A 558 " pdb=" CA PRO A 558 " pdb=" C PRO A 558 " ideal model delta sigma weight residual 110.70 115.88 -5.18 1.22e+00 6.72e-01 1.81e+01 angle pdb=" N PRO A 270 " pdb=" CA PRO A 270 " pdb=" C PRO A 270 " ideal model delta sigma weight residual 110.70 105.68 5.02 1.22e+00 6.72e-01 1.69e+01 ... (remaining 33016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13228 17.95 - 35.91: 1143 35.91 - 53.86: 174 53.86 - 71.81: 43 71.81 - 89.77: 25 Dihedral angle restraints: 14613 sinusoidal: 5802 harmonic: 8811 Sorted by residual: dihedral pdb=" CA TYR A 820 " pdb=" C TYR A 820 " pdb=" N ASP A 821 " pdb=" CA ASP A 821 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" C PHE C 556 " pdb=" N PHE C 556 " pdb=" CA PHE C 556 " pdb=" CB PHE C 556 " ideal model delta harmonic sigma weight residual -122.60 -132.71 10.11 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" CA VAL B 240 " pdb=" C VAL B 240 " pdb=" N GLU B 241 " pdb=" CA GLU B 241 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 14610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3401 0.065 - 0.130: 413 0.130 - 0.195: 13 0.195 - 0.259: 8 0.259 - 0.324: 2 Chirality restraints: 3837 Sorted by residual: chirality pdb=" CA PHE C 556 " pdb=" N PHE C 556 " pdb=" C PHE C 556 " pdb=" CB PHE C 556 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA PHE B 222 " pdb=" N PHE B 222 " pdb=" C PHE B 222 " pdb=" CB PHE B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA PRO B 270 " pdb=" N PRO B 270 " pdb=" C PRO B 270 " pdb=" CB PRO B 270 " both_signs ideal model delta sigma weight residual False 2.72 2.96 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 3834 not shown) Planarity restraints: 4227 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 559 " 0.015 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C PRO C 559 " -0.055 2.00e-02 2.50e+03 pdb=" O PRO C 559 " 0.021 2.00e-02 2.50e+03 pdb=" N SER C 560 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 557 " -0.016 2.00e-02 2.50e+03 1.67e-02 4.91e+00 pdb=" CG PHE B 557 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 557 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 557 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 557 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 557 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 557 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 266 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.38e+00 pdb=" C GLY A 266 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY A 266 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 267 " 0.012 2.00e-02 2.50e+03 ... (remaining 4224 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 477 2.69 - 3.24: 24371 3.24 - 3.80: 38083 3.80 - 4.35: 47218 4.35 - 4.90: 79700 Nonbonded interactions: 189849 Sorted by model distance: nonbonded pdb=" OD1 ASP C 821 " pdb=" N ASP C 822 " model vdw 2.138 3.120 nonbonded pdb=" OG1 THR A 781 " pdb=" OD1 ASN A 783 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG C 249 " pdb=" O ARG C 253 " model vdw 2.201 3.120 nonbonded pdb=" O SER C 718 " pdb=" OG1 THR C 794 " model vdw 2.210 3.040 nonbonded pdb=" O PRO B 775 " pdb=" OG SER B 790 " model vdw 2.213 3.040 ... (remaining 189844 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 23.340 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 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 0.045 24321 Z= 0.177 Angle : 0.630 9.138 33021 Z= 0.340 Chirality : 0.042 0.324 3837 Planarity : 0.004 0.037 4227 Dihedral : 14.024 89.769 8931 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.21 % Favored : 94.59 % Rotamer: Outliers : 0.43 % Allowed : 0.75 % Favored : 98.81 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.08 % 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: 0.17 (0.16), residues: 3051 helix: 1.39 (0.13), residues: 1668 sheet: -2.12 (0.25), residues: 381 loop : -1.07 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 725 TYR 0.009 0.001 TYR A 612 PHE 0.039 0.001 PHE B 557 TRP 0.015 0.001 TRP A 110 HIS 0.003 0.000 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.18 (24321) covalent geometry : angle 0.63046 / 0.34 (33021) hydrogen bonds : bond 0.15819 / 10.55 ( 1379) hydrogen bonds : angle 6.97865 / 5.09 ( 4041) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 362 time to evaluate : 0.888 Fit side-chains REVERT: A 42 PHE cc_start: 0.8868 (t80) cc_final: 0.8562 (t80) REVERT: A 222 PHE cc_start: 0.7846 (m-80) cc_final: 0.7594 (m-10) REVERT: A 378 MET cc_start: 0.9256 (mtm) cc_final: 0.8972 (mtm) REVERT: A 405 ILE cc_start: 0.9295 (mm) cc_final: 0.9054 (tp) REVERT: A 616 ASP cc_start: 0.7946 (p0) cc_final: 0.7645 (p0) REVERT: A 857 ASP cc_start: 0.8909 (t0) cc_final: 0.8685 (t0) REVERT: A 939 ASP cc_start: 0.8997 (t70) cc_final: 0.8537 (t0) REVERT: B 564 GLU cc_start: 0.8642 (mp0) cc_final: 0.8061 (mp0) REVERT: B 588 GLU cc_start: 0.9097 (mp0) cc_final: 0.8760 (mp0) REVERT: B 590 MET cc_start: 0.8983 (ppp) cc_final: 0.8712 (ppp) REVERT: B 603 TYR cc_start: 0.8703 (m-80) cc_final: 0.8234 (m-10) REVERT: B 822 ASP cc_start: 0.8652 (m-30) cc_final: 0.8316 (p0) REVERT: B 857 ASP cc_start: 0.8834 (t0) cc_final: 0.8581 (t0) REVERT: C 100 ASP cc_start: 0.8990 (p0) cc_final: 0.8732 (p0) REVERT: C 126 GLN cc_start: 0.8182 (pp30) cc_final: 0.7728 (pp30) REVERT: C 178 GLU cc_start: 0.8253 (tt0) cc_final: 0.8047 (tt0) REVERT: C 221 PHE cc_start: 0.7169 (p90) cc_final: 0.6831 (p90) REVERT: C 411 MET cc_start: 0.9339 (ttt) cc_final: 0.9098 (ttt) REVERT: C 626 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8321 (tp40) REVERT: C 633 ASP cc_start: 0.8492 (p0) cc_final: 0.7658 (p0) outliers start: 11 outliers final: 5 residues processed: 371 average time/residue: 0.1488 time to fit residues: 90.7356 Evaluate side-chains 277 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 271 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 267 PHE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 626 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 502 HIS A 746 HIS ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 626 GLN C 417 GLN C 502 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.063856 restraints weight = 56192.506| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.68 r_work: 0.2644 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24321 Z= 0.161 Angle : 0.602 9.851 33021 Z= 0.297 Chirality : 0.040 0.159 3837 Planarity : 0.004 0.046 4227 Dihedral : 4.457 78.107 3357 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.11 % Favored : 94.82 % Rotamer: Outliers : 1.58 % Allowed : 10.32 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.37 (0.16), residues: 3051 helix: 1.52 (0.13), residues: 1674 sheet: -1.85 (0.25), residues: 426 loop : -0.94 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 462 TYR 0.011 0.001 TYR B 141 PHE 0.026 0.001 PHE A 917 TRP 0.014 0.001 TRP C 110 HIS 0.006 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (24321) covalent geometry : angle 0.60220 / 0.30 (33021) hydrogen bonds : bond 0.04003 / 2.69 ( 1379) hydrogen bonds : angle 5.19590 / 3.77 ( 4041) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 302 time to evaluate : 1.000 Fit side-chains REVERT: A 42 PHE cc_start: 0.9007 (t80) cc_final: 0.8634 (t80) REVERT: A 249 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6842 (ttp80) REVERT: A 275 MET cc_start: 0.9100 (ttm) cc_final: 0.8889 (ttp) REVERT: A 373 MET cc_start: 0.9436 (mtm) cc_final: 0.9122 (mtp) REVERT: A 405 ILE cc_start: 0.9300 (mm) cc_final: 0.9001 (tp) REVERT: A 616 ASP cc_start: 0.8595 (p0) cc_final: 0.7937 (p0) REVERT: A 939 ASP cc_start: 0.9093 (t70) cc_final: 0.8584 (t0) REVERT: B 184 ASP cc_start: 0.8340 (p0) cc_final: 0.8129 (p0) REVERT: B 221 PHE cc_start: 0.7387 (p90) cc_final: 0.6804 (p90) REVERT: B 222 PHE cc_start: 0.8067 (m-10) cc_final: 0.7499 (t80) REVERT: B 564 GLU cc_start: 0.8971 (mp0) cc_final: 0.8248 (mp0) REVERT: B 588 GLU cc_start: 0.9052 (mp0) cc_final: 0.8785 (mp0) REVERT: B 590 MET cc_start: 0.9097 (ppp) cc_final: 0.8860 (ppp) REVERT: B 603 TYR cc_start: 0.9041 (m-80) cc_final: 0.8564 (m-10) REVERT: B 766 GLN cc_start: 0.9549 (tp40) cc_final: 0.9238 (tp-100) REVERT: B 824 LEU cc_start: 0.9356 (pp) cc_final: 0.9144 (mt) REVERT: B 831 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8886 (pm20) REVERT: B 857 ASP cc_start: 0.9212 (t0) cc_final: 0.8972 (t0) REVERT: B 924 ILE cc_start: 0.9018 (tt) cc_final: 0.8785 (tt) REVERT: C 67 GLU cc_start: 0.8954 (tp30) cc_final: 0.8742 (tp30) REVERT: C 126 GLN cc_start: 0.9173 (pp30) cc_final: 0.8855 (pp30) REVERT: C 221 PHE cc_start: 0.7287 (p90) cc_final: 0.6844 (p90) REVERT: C 411 MET cc_start: 0.9472 (ttt) cc_final: 0.9212 (ttt) REVERT: C 881 MET cc_start: 0.9447 (mmm) cc_final: 0.8956 (tpp) REVERT: C 890 MET cc_start: 0.8698 (ttp) cc_final: 0.8104 (ttp) outliers start: 40 outliers final: 23 residues processed: 317 average time/residue: 0.1410 time to fit residues: 74.9301 Evaluate side-chains 305 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 281 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 289 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 233 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 270 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 703 ASN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 940 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.061222 restraints weight = 56570.970| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.65 r_work: 0.2579 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 24321 Z= 0.232 Angle : 0.615 9.638 33021 Z= 0.303 Chirality : 0.041 0.152 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.959 41.106 3350 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.41 % Allowed : 12.77 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.39 (0.16), residues: 3051 helix: 1.62 (0.13), residues: 1641 sheet: -1.86 (0.24), residues: 450 loop : -0.95 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 912 TYR 0.019 0.001 TYR B 79 PHE 0.016 0.001 PHE B 557 TRP 0.013 0.001 TRP C 708 HIS 0.005 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (24321) covalent geometry : angle 0.61507 / 0.30 (33021) hydrogen bonds : bond 0.03771 / 2.53 ( 1379) hydrogen bonds : angle 4.92955 / 3.58 ( 4041) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.9126 (tp30) cc_final: 0.8915 (tp30) REVERT: A 221 PHE cc_start: 0.7734 (p90) cc_final: 0.7499 (p90) REVERT: A 249 ARG cc_start: 0.7318 (ttp80) cc_final: 0.6842 (ttp80) REVERT: A 275 MET cc_start: 0.9154 (ttm) cc_final: 0.8952 (ttp) REVERT: A 289 MET cc_start: 0.8472 (tmm) cc_final: 0.7576 (tmm) REVERT: A 373 MET cc_start: 0.9527 (mtm) cc_final: 0.9207 (mtp) REVERT: A 616 ASP cc_start: 0.8554 (p0) cc_final: 0.8025 (p0) REVERT: A 929 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8862 (mtm) REVERT: A 939 ASP cc_start: 0.9102 (t70) cc_final: 0.8605 (t0) REVERT: B 221 PHE cc_start: 0.7512 (p90) cc_final: 0.7202 (p90) REVERT: B 222 PHE cc_start: 0.8084 (m-10) cc_final: 0.7447 (t80) REVERT: B 590 MET cc_start: 0.9072 (ppp) cc_final: 0.8831 (ppp) REVERT: B 715 VAL cc_start: 0.8101 (OUTLIER) cc_final: 0.7879 (p) REVERT: B 766 GLN cc_start: 0.9556 (tp40) cc_final: 0.9258 (tp-100) REVERT: B 857 ASP cc_start: 0.9262 (t0) cc_final: 0.9020 (t0) REVERT: B 881 MET cc_start: 0.9262 (mmm) cc_final: 0.8614 (tpp) REVERT: C 67 GLU cc_start: 0.9078 (tp30) cc_final: 0.8840 (tp30) REVERT: C 126 GLN cc_start: 0.9227 (pp30) cc_final: 0.8879 (pp30) outliers start: 61 outliers final: 40 residues processed: 301 average time/residue: 0.1291 time to fit residues: 64.6646 Evaluate side-chains 293 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 251 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 929 MET Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 862 GLN Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 196 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 25 optimal weight: 0.0770 chunk 26 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 278 optimal weight: 40.0000 chunk 69 optimal weight: 10.0000 chunk 120 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 overall best weight: 3.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 673 GLN A 831 GLN ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.090318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.061015 restraints weight = 56304.131| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.68 r_work: 0.2574 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 24321 Z= 0.208 Angle : 0.604 15.695 33021 Z= 0.293 Chirality : 0.041 0.217 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.875 36.137 3348 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.85 % Allowed : 15.62 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.38 (0.16), residues: 3051 helix: 1.60 (0.13), residues: 1647 sheet: -1.85 (0.24), residues: 429 loop : -1.01 (0.21), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 114 TYR 0.020 0.001 TYR B 79 PHE 0.013 0.001 PHE A 95 TRP 0.013 0.001 TRP A 708 HIS 0.005 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.21 (24321) covalent geometry : angle 0.60433 / 0.29 (33021) hydrogen bonds : bond 0.03502 / 2.34 ( 1379) hydrogen bonds : angle 4.75308 / 3.46 ( 4041) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 267 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.9168 (tp30) cc_final: 0.8904 (tp30) REVERT: A 221 PHE cc_start: 0.7763 (p90) cc_final: 0.7474 (p90) REVERT: A 222 PHE cc_start: 0.7730 (m-10) cc_final: 0.7468 (m-10) REVERT: A 249 ARG cc_start: 0.7353 (ttp80) cc_final: 0.6919 (ttp80) REVERT: A 275 MET cc_start: 0.9153 (ttm) cc_final: 0.8949 (ttp) REVERT: A 289 MET cc_start: 0.8528 (tmm) cc_final: 0.7603 (tmm) REVERT: A 373 MET cc_start: 0.9535 (mtm) cc_final: 0.9219 (mtp) REVERT: A 616 ASP cc_start: 0.8610 (p0) cc_final: 0.8077 (p0) REVERT: A 715 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8130 (p) REVERT: A 881 MET cc_start: 0.9361 (tpp) cc_final: 0.9053 (mmm) REVERT: A 890 MET cc_start: 0.8759 (ttp) cc_final: 0.8558 (ttp) REVERT: A 939 ASP cc_start: 0.9086 (t70) cc_final: 0.8595 (t0) REVERT: B 221 PHE cc_start: 0.7646 (p90) cc_final: 0.7071 (p90) REVERT: B 222 PHE cc_start: 0.8086 (m-10) cc_final: 0.7406 (t80) REVERT: B 588 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8736 (mt-10) REVERT: B 715 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7908 (p) REVERT: B 831 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8676 (pm20) REVERT: B 857 ASP cc_start: 0.9277 (t0) cc_final: 0.9032 (t0) REVERT: B 881 MET cc_start: 0.9268 (mmm) cc_final: 0.8714 (tpp) REVERT: C 67 GLU cc_start: 0.9058 (tp30) cc_final: 0.8777 (tp30) REVERT: C 126 GLN cc_start: 0.9248 (pp30) cc_final: 0.8879 (pp30) REVERT: C 231 LEU cc_start: 0.9292 (tt) cc_final: 0.9051 (tt) REVERT: C 881 MET cc_start: 0.9429 (tpp) cc_final: 0.8925 (tpp) outliers start: 72 outliers final: 49 residues processed: 309 average time/residue: 0.1284 time to fit residues: 66.4534 Evaluate side-chains 308 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 255 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 892 MET Chi-restraints excluded: chain C residue 1003 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 99 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 31 optimal weight: 0.0170 chunk 133 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 151 optimal weight: 50.0000 chunk 163 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 overall best weight: 1.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 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 = 0.3372 r_free = 0.3372 target = 0.091400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.062455 restraints weight = 55994.603| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 3.66 r_work: 0.2611 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24321 Z= 0.133 Angle : 0.574 11.360 33021 Z= 0.274 Chirality : 0.040 0.187 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.782 32.644 3344 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.89 % Allowed : 16.45 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.47 (0.16), residues: 3051 helix: 1.65 (0.13), residues: 1650 sheet: -1.76 (0.24), residues: 450 loop : -0.93 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.019 0.001 TYR B 79 PHE 0.012 0.001 PHE C 750 TRP 0.011 0.001 TRP C 708 HIS 0.003 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (24321) covalent geometry : angle 0.57375 / 0.27 (33021) hydrogen bonds : bond 0.03293 / 2.21 ( 1379) hydrogen bonds : angle 4.59072 / 3.34 ( 4041) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 274 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.9139 (tp30) cc_final: 0.8868 (tp30) REVERT: A 221 PHE cc_start: 0.7759 (p90) cc_final: 0.7492 (p90) REVERT: A 222 PHE cc_start: 0.7826 (m-10) cc_final: 0.7599 (m-10) REVERT: A 275 MET cc_start: 0.9113 (ttm) cc_final: 0.8890 (ttp) REVERT: A 289 MET cc_start: 0.8526 (tmm) cc_final: 0.7638 (tmm) REVERT: A 305 GLU cc_start: 0.9319 (tp30) cc_final: 0.9055 (tp30) REVERT: A 373 MET cc_start: 0.9516 (mtm) cc_final: 0.9169 (mtp) REVERT: A 616 ASP cc_start: 0.8622 (p0) cc_final: 0.8226 (p0) REVERT: A 821 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7726 (p0) REVERT: A 939 ASP cc_start: 0.9038 (t70) cc_final: 0.8646 (t0) REVERT: B 221 PHE cc_start: 0.7771 (p90) cc_final: 0.7204 (p90) REVERT: B 222 PHE cc_start: 0.8094 (m-10) cc_final: 0.7391 (t80) REVERT: B 715 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7919 (p) REVERT: B 831 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8655 (pm20) REVERT: B 857 ASP cc_start: 0.9270 (t0) cc_final: 0.9025 (t0) REVERT: B 881 MET cc_start: 0.9297 (mmm) cc_final: 0.8678 (tpp) REVERT: C 126 GLN cc_start: 0.9258 (pp30) cc_final: 0.8885 (pp30) REVERT: C 231 LEU cc_start: 0.9297 (tt) cc_final: 0.9062 (tt) REVERT: C 588 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8605 (pt0) REVERT: C 881 MET cc_start: 0.9406 (tpp) cc_final: 0.9024 (tpp) REVERT: C 895 LEU cc_start: 0.9069 (tt) cc_final: 0.8868 (tp) outliers start: 73 outliers final: 49 residues processed: 319 average time/residue: 0.1428 time to fit residues: 77.1445 Evaluate side-chains 314 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 899 LEU Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 24 optimal weight: 5.9990 chunk 276 optimal weight: 20.0000 chunk 135 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 288 optimal weight: 2.9990 chunk 263 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 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 = 0.3369 r_free = 0.3369 target = 0.091234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.062264 restraints weight = 56555.575| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.67 r_work: 0.2609 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24321 Z= 0.145 Angle : 0.584 11.252 33021 Z= 0.278 Chirality : 0.040 0.259 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.759 29.888 3344 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.81 % Allowed : 17.24 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.50 (0.16), residues: 3051 helix: 1.67 (0.13), residues: 1650 sheet: -1.73 (0.24), residues: 450 loop : -0.93 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 932 TYR 0.018 0.001 TYR B 79 PHE 0.020 0.001 PHE B 255 TRP 0.011 0.001 TRP C 708 HIS 0.003 0.001 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (24321) covalent geometry : angle 0.58414 / 0.28 (33021) hydrogen bonds : bond 0.03254 / 2.18 ( 1379) hydrogen bonds : angle 4.53762 / 3.30 ( 4041) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 274 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.9153 (tp30) cc_final: 0.8886 (tp30) REVERT: A 221 PHE cc_start: 0.7789 (p90) cc_final: 0.7516 (p90) REVERT: A 222 PHE cc_start: 0.7864 (m-10) cc_final: 0.7619 (m-10) REVERT: A 275 MET cc_start: 0.9110 (ttm) cc_final: 0.8880 (ttp) REVERT: A 289 MET cc_start: 0.8548 (tmm) cc_final: 0.7667 (tmm) REVERT: A 305 GLU cc_start: 0.9326 (tp30) cc_final: 0.9065 (tp30) REVERT: A 616 ASP cc_start: 0.8625 (p0) cc_final: 0.8149 (p0) REVERT: A 821 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7761 (p0) REVERT: A 939 ASP cc_start: 0.9032 (t70) cc_final: 0.8640 (t0) REVERT: B 75 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8821 (tt0) REVERT: B 221 PHE cc_start: 0.7751 (p90) cc_final: 0.7248 (p90) REVERT: B 222 PHE cc_start: 0.8107 (m-10) cc_final: 0.7387 (t80) REVERT: B 588 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8688 (mt-10) REVERT: B 715 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 831 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8682 (pm20) REVERT: B 857 ASP cc_start: 0.9274 (t0) cc_final: 0.9023 (t0) REVERT: B 881 MET cc_start: 0.9403 (mmm) cc_final: 0.8834 (tpp) REVERT: C 67 GLU cc_start: 0.8921 (tp30) cc_final: 0.8631 (tp30) REVERT: C 126 GLN cc_start: 0.9268 (pp30) cc_final: 0.9021 (pp30) REVERT: C 231 LEU cc_start: 0.9315 (tt) cc_final: 0.9066 (tt) REVERT: C 415 MET cc_start: 0.9581 (tpp) cc_final: 0.9329 (mtt) REVERT: C 588 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8601 (pt0) outliers start: 71 outliers final: 57 residues processed: 318 average time/residue: 0.1431 time to fit residues: 76.9450 Evaluate side-chains 322 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 892 MET Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 136 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 749 PHE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 245 optimal weight: 0.6980 chunk 208 optimal weight: 0.9980 chunk 55 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 177 optimal weight: 30.0000 chunk 103 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.063972 restraints weight = 55753.808| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 3.70 r_work: 0.2651 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24321 Z= 0.106 Angle : 0.586 11.279 33021 Z= 0.273 Chirality : 0.040 0.221 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.713 24.931 3344 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.41 % Allowed : 18.03 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.51 (0.16), residues: 3051 helix: 1.59 (0.13), residues: 1686 sheet: -1.64 (0.24), residues: 450 loop : -0.89 (0.22), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.013 0.001 TYR B 79 PHE 0.013 0.001 PHE B 255 TRP 0.010 0.001 TRP C 708 HIS 0.002 0.000 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (24321) covalent geometry : angle 0.58567 / 0.27 (33021) hydrogen bonds : bond 0.03064 / 2.06 ( 1379) hydrogen bonds : angle 4.38843 / 3.19 ( 4041) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 294 time to evaluate : 0.954 Fit side-chains REVERT: A 38 GLU cc_start: 0.9127 (tp30) cc_final: 0.8845 (tp30) REVERT: A 221 PHE cc_start: 0.7775 (p90) cc_final: 0.7516 (p90) REVERT: A 222 PHE cc_start: 0.7842 (m-10) cc_final: 0.7590 (m-10) REVERT: A 275 MET cc_start: 0.9058 (ttm) cc_final: 0.8824 (ttp) REVERT: A 289 MET cc_start: 0.8559 (tmm) cc_final: 0.7775 (tmm) REVERT: A 305 GLU cc_start: 0.9313 (tp30) cc_final: 0.9054 (tp30) REVERT: A 616 ASP cc_start: 0.8498 (p0) cc_final: 0.8202 (p0) REVERT: A 821 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7761 (p0) REVERT: A 939 ASP cc_start: 0.8995 (t70) cc_final: 0.8580 (t0) REVERT: B 75 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8797 (tt0) REVERT: B 221 PHE cc_start: 0.7806 (p90) cc_final: 0.7203 (p90) REVERT: B 222 PHE cc_start: 0.8063 (m-10) cc_final: 0.7326 (t80) REVERT: B 564 GLU cc_start: 0.9104 (mp0) cc_final: 0.8653 (mp0) REVERT: B 588 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8628 (mt-10) REVERT: B 715 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 831 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: B 857 ASP cc_start: 0.9278 (t0) cc_final: 0.9028 (t0) REVERT: B 881 MET cc_start: 0.9353 (mmm) cc_final: 0.8557 (tpp) REVERT: B 932 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8049 (ttm-80) REVERT: C 126 GLN cc_start: 0.9260 (pp30) cc_final: 0.8713 (pp30) REVERT: C 231 LEU cc_start: 0.9304 (tt) cc_final: 0.9058 (tt) REVERT: C 415 MET cc_start: 0.9540 (tpp) cc_final: 0.9314 (mtt) REVERT: C 462 ARG cc_start: 0.8417 (ttm-80) cc_final: 0.7997 (ttm110) REVERT: C 588 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8591 (pt0) outliers start: 61 outliers final: 43 residues processed: 328 average time/residue: 0.1435 time to fit residues: 79.6894 Evaluate side-chains 325 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 277 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 749 PHE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 857 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 237 optimal weight: 10.0000 chunk 205 optimal weight: 0.9990 chunk 238 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 673 GLN ** A 940 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 = 0.3395 r_free = 0.3395 target = 0.092710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.063909 restraints weight = 56060.187| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.68 r_work: 0.2644 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24321 Z= 0.117 Angle : 0.585 10.685 33021 Z= 0.274 Chirality : 0.040 0.260 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.660 21.864 3344 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.45 % Allowed : 18.74 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.52 (0.16), residues: 3051 helix: 1.61 (0.13), residues: 1686 sheet: -1.63 (0.24), residues: 450 loop : -0.89 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.013 0.001 TYR B 79 PHE 0.014 0.001 PHE B 255 TRP 0.009 0.001 TRP C 708 HIS 0.003 0.001 HIS B 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (24321) covalent geometry : angle 0.58480 / 0.27 (33021) hydrogen bonds : bond 0.03061 / 2.06 ( 1379) hydrogen bonds : angle 4.34876 / 3.16 ( 4041) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 293 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.9133 (tp30) cc_final: 0.8862 (tp30) REVERT: A 221 PHE cc_start: 0.7775 (p90) cc_final: 0.7282 (p90) REVERT: A 222 PHE cc_start: 0.7848 (m-10) cc_final: 0.7487 (m-80) REVERT: A 275 MET cc_start: 0.9086 (ttm) cc_final: 0.8852 (ttp) REVERT: A 289 MET cc_start: 0.8571 (tmm) cc_final: 0.7768 (tmm) REVERT: A 305 GLU cc_start: 0.9324 (tp30) cc_final: 0.9059 (tp30) REVERT: A 369 LEU cc_start: 0.8927 (tp) cc_final: 0.8304 (tt) REVERT: A 373 MET cc_start: 0.8823 (mtp) cc_final: 0.8445 (mtp) REVERT: A 616 ASP cc_start: 0.8545 (p0) cc_final: 0.8326 (p0) REVERT: A 821 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7736 (p0) REVERT: A 939 ASP cc_start: 0.8998 (t70) cc_final: 0.8580 (t0) REVERT: B 422 LEU cc_start: 0.8549 (mp) cc_final: 0.8211 (tt) REVERT: B 564 GLU cc_start: 0.9115 (mp0) cc_final: 0.8646 (mp0) REVERT: B 588 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8651 (mt-10) REVERT: B 715 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7924 (p) REVERT: B 831 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8683 (pm20) REVERT: B 857 ASP cc_start: 0.9287 (t0) cc_final: 0.9039 (t0) REVERT: B 932 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7712 (ttt-90) REVERT: C 126 GLN cc_start: 0.9273 (pp30) cc_final: 0.8727 (pp30) REVERT: C 153 ASP cc_start: 0.8936 (t0) cc_final: 0.8592 (t70) REVERT: C 231 LEU cc_start: 0.9304 (tt) cc_final: 0.9055 (tt) REVERT: C 462 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7985 (ttm110) REVERT: C 588 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8631 (pt0) REVERT: C 890 MET cc_start: 0.8798 (ttp) cc_final: 0.8445 (ttp) REVERT: C 895 LEU cc_start: 0.8973 (tp) cc_final: 0.8638 (tt) outliers start: 62 outliers final: 47 residues processed: 333 average time/residue: 0.1432 time to fit residues: 80.7443 Evaluate side-chains 336 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 284 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 749 PHE Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 749 PHE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 918 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 284 optimal weight: 0.4980 chunk 228 optimal weight: 8.9990 chunk 270 optimal weight: 0.9990 chunk 220 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 112 optimal weight: 0.0670 chunk 237 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 221 optimal weight: 50.0000 chunk 204 optimal weight: 9.9990 overall best weight: 1.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 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 = 0.3390 r_free = 0.3390 target = 0.092439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.063611 restraints weight = 56070.761| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.66 r_work: 0.2638 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24321 Z= 0.128 Angle : 0.588 11.426 33021 Z= 0.276 Chirality : 0.040 0.238 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.617 19.388 3342 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.61 % Allowed : 18.86 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.54 (0.16), residues: 3051 helix: 1.63 (0.13), residues: 1686 sheet: -1.60 (0.24), residues: 450 loop : -0.91 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.014 0.001 TYR B 79 PHE 0.023 0.001 PHE C 477 TRP 0.011 0.001 TRP A 708 HIS 0.003 0.000 HIS B 700 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (24321) covalent geometry : angle 0.58812 / 0.28 (33021) hydrogen bonds : bond 0.03059 / 2.05 ( 1379) hydrogen bonds : angle 4.33149 / 3.15 ( 4041) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 286 time to evaluate : 0.923 Fit side-chains REVERT: A 38 GLU cc_start: 0.9135 (tp30) cc_final: 0.8845 (tp30) REVERT: A 221 PHE cc_start: 0.7761 (p90) cc_final: 0.7505 (p90) REVERT: A 222 PHE cc_start: 0.7859 (m-10) cc_final: 0.7600 (m-10) REVERT: A 275 MET cc_start: 0.9087 (ttm) cc_final: 0.8847 (ttp) REVERT: A 289 MET cc_start: 0.8603 (tmm) cc_final: 0.7797 (tmm) REVERT: A 305 GLU cc_start: 0.9323 (tp30) cc_final: 0.9059 (tp30) REVERT: A 369 LEU cc_start: 0.8930 (tp) cc_final: 0.8305 (tt) REVERT: A 373 MET cc_start: 0.8788 (mtp) cc_final: 0.8444 (mtp) REVERT: A 821 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7696 (p0) REVERT: A 939 ASP cc_start: 0.9001 (t70) cc_final: 0.8580 (t0) REVERT: B 422 LEU cc_start: 0.8560 (mp) cc_final: 0.8193 (tt) REVERT: B 564 GLU cc_start: 0.9118 (mp0) cc_final: 0.8640 (mp0) REVERT: B 588 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8628 (mt-10) REVERT: B 715 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7911 (p) REVERT: B 831 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8696 (pm20) REVERT: B 857 ASP cc_start: 0.9278 (t0) cc_final: 0.9027 (t0) REVERT: B 881 MET cc_start: 0.9328 (tpp) cc_final: 0.8657 (tpp) REVERT: B 932 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7742 (ttt-90) REVERT: C 67 GLU cc_start: 0.8778 (tp30) cc_final: 0.8534 (tp30) REVERT: C 126 GLN cc_start: 0.9264 (pp30) cc_final: 0.8722 (pp30) REVERT: C 153 ASP cc_start: 0.8925 (t0) cc_final: 0.8589 (t70) REVERT: C 231 LEU cc_start: 0.9311 (tt) cc_final: 0.9061 (tt) REVERT: C 353 PHE cc_start: 0.8464 (m-10) cc_final: 0.8198 (t80) REVERT: C 588 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8646 (pt0) REVERT: C 895 LEU cc_start: 0.8999 (tp) cc_final: 0.8650 (tt) outliers start: 66 outliers final: 51 residues processed: 330 average time/residue: 0.1403 time to fit residues: 78.2866 Evaluate side-chains 337 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 281 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 749 PHE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 918 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 36 optimal weight: 0.0770 chunk 40 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 292 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 281 optimal weight: 0.1980 overall best weight: 1.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 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 = 0.3397 r_free = 0.3397 target = 0.092878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.064050 restraints weight = 56100.035| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.68 r_work: 0.2649 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24321 Z= 0.117 Angle : 0.592 11.353 33021 Z= 0.278 Chirality : 0.040 0.228 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.613 19.124 3342 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.37 % Allowed : 19.18 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.53 (0.16), residues: 3051 helix: 1.61 (0.13), residues: 1686 sheet: -1.57 (0.24), residues: 450 loop : -0.91 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.017 0.001 TYR B 79 PHE 0.025 0.001 PHE B 221 TRP 0.010 0.001 TRP C 708 HIS 0.003 0.000 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (24321) covalent geometry : angle 0.59217 / 0.28 (33021) hydrogen bonds : bond 0.03050 / 2.05 ( 1379) hydrogen bonds : angle 4.31017 / 3.13 ( 4041) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6102 Ramachandran restraints generated. 3051 Oldfield, 0 Emsley, 3051 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 0.960 Fit side-chains REVERT: A 38 GLU cc_start: 0.9119 (tp30) cc_final: 0.8834 (tp30) REVERT: A 221 PHE cc_start: 0.7762 (p90) cc_final: 0.7513 (p90) REVERT: A 222 PHE cc_start: 0.7846 (m-10) cc_final: 0.7592 (m-10) REVERT: A 275 MET cc_start: 0.9073 (ttm) cc_final: 0.8834 (ttp) REVERT: A 305 GLU cc_start: 0.9308 (tp30) cc_final: 0.9047 (tp30) REVERT: A 324 ASP cc_start: 0.8529 (t0) cc_final: 0.8305 (t0) REVERT: A 369 LEU cc_start: 0.8905 (tp) cc_final: 0.8650 (tt) REVERT: A 821 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7674 (p0) REVERT: A 939 ASP cc_start: 0.9002 (t70) cc_final: 0.8586 (t0) REVERT: B 422 LEU cc_start: 0.8554 (mp) cc_final: 0.8190 (tt) REVERT: B 564 GLU cc_start: 0.9133 (mp0) cc_final: 0.8672 (mp0) REVERT: B 588 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: B 715 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7921 (p) REVERT: B 831 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8710 (pm20) REVERT: B 857 ASP cc_start: 0.9285 (t0) cc_final: 0.9038 (t0) REVERT: B 881 MET cc_start: 0.9325 (tpp) cc_final: 0.8691 (tpp) REVERT: B 932 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7648 (ttt-90) REVERT: C 126 GLN cc_start: 0.9262 (pp30) cc_final: 0.8718 (pp30) REVERT: C 153 ASP cc_start: 0.8915 (t0) cc_final: 0.8576 (t70) REVERT: C 231 LEU cc_start: 0.9308 (tt) cc_final: 0.9056 (tt) REVERT: C 353 PHE cc_start: 0.8458 (m-10) cc_final: 0.8191 (t80) REVERT: C 411 MET cc_start: 0.9514 (ttt) cc_final: 0.9053 (ttm) REVERT: C 588 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8638 (pt0) REVERT: C 895 LEU cc_start: 0.9000 (tp) cc_final: 0.8657 (tt) outliers start: 60 outliers final: 51 residues processed: 335 average time/residue: 0.1413 time to fit residues: 80.6700 Evaluate side-chains 334 residues out of total 2529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 454 GLN Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 851 VAL Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 980 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 344 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 715 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 831 GLN Chi-restraints excluded: chain B residue 851 VAL Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 888 SER Chi-restraints excluded: chain B residue 932 ARG Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 348 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 749 PHE Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain C residue 918 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 57 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 chunk 26 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 291 optimal weight: 0.5980 chunk 266 optimal weight: 1.9990 chunk 279 optimal weight: 0.7980 chunk 257 optimal weight: 0.8980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 940 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 = 0.3421 r_free = 0.3421 target = 0.094499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.065721 restraints weight = 55420.523| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.73 r_work: 0.2679 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 24321 Z= 0.107 Angle : 0.595 11.409 33021 Z= 0.278 Chirality : 0.040 0.229 3837 Planarity : 0.004 0.041 4227 Dihedral : 3.604 18.333 3342 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.10 % Allowed : 19.69 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 0.56 (0.16), residues: 3051 helix: 1.61 (0.13), residues: 1689 sheet: -1.54 (0.24), residues: 450 loop : -0.87 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 689 TYR 0.015 0.001 TYR B 79 PHE 0.023 0.001 PHE C 477 TRP 0.017 0.001 TRP B 708 HIS 0.002 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (24321) covalent geometry : angle 0.59458 / 0.28 (33021) hydrogen bonds : bond 0.02985 / 2.01 ( 1379) hydrogen bonds : angle 4.27172 / 3.11 ( 4041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4987.81 seconds wall clock time: 86 minutes 29.71 seconds (5189.71 seconds total)